Santa Fe Institute Events Wiki - User contributions [en]

"By what metric do we measure human worth?"

2013-08-02T18:55:30Z

Masad:

*[[Complex Systems Summer School 2013-QOTW|Back to QOTW!]]

{{Complex Systems Summer School 2013}}

Is a persons value based on their past or future actions?

Is it better to judge based on consequence or intention?

What qualities do you believe are most worthy of respect?

What type of person makes you happy?

What personality traits stirs your interest, your curiosity?

How do you choose your friends?

----

David: Pfft, that's easy. You just sum their marginal utility. Topic over! </economist>

Presentations 2013

2013-06-28T20:37:10Z

Masad:

{{Complex Systems Summer School 2013}}

9:00 - 9:15: "Simplicity": Mengsen Zhang (Synthesizing questions- in search of a simple analog of complexity...I'll talk a bit of alcohol and language if I have time :) )

9:15 - 9:30: "Evolving synchronous flashing in fireflies using an agent-based model of natural and sexual selection" Holly Arnold, Bryn Gaertner, John Litherland, Rebecca Mease and James Walsh

9:30 - 9:45: "Food webs" (Swati, Jian, Joana, Ren, Mauricio, Ian, Susanne, Masato)

9:45 - 10:00: NetAttack: Co-evolution of network builder and attackers (Elena, Andrea, Holly, Bruno, Johannes, David)

10:00 - 10:15: "Arbortron" (Bodnar, Driscoll)

10:15 - 10:30: BREAK

10:30 - 10:45: Cellular morphogenesis, Oskar

10:45 - 11:00: "Complexity (trans)science: Forecasting social change" (Vanessa, Alastair, Stephan, Matteo, Melinda, Hua, Nix)

11:00 - 11:15: CSSS Group Formation from a Genotype-Phenotype Perspective (Vishwa, Johannes and 许晏 XU Yan)

11:15 - 11:30: Quantifying Shakespeare: Measure for Measure (Kyle, Max, Ashkaan, Eitan, Abbie)

11:30 - 11:45: "Is the world urban system coming of age?" (Abundo, Bodnar, Driscoll, Hatton, Schweizer, Smerlak, Wright)

12:00 - 1:00: LUNCH & GROUP PHOTO

1:00 - 1:15 "Detecting Communities Using Information Flow in Social Networks" (Darmon, Omodei, Seoane, Flores, Wright, Stadler, Abundo, Nix)

1:15 - 1:30: "Linking Global Networks" (Manish, Cesar, Ren, Cheryl, Susanne)

1:30 - 1:45: "The effect of Cooperation on Resources acquisition and mortality" (Bapu, ivana, amara, pablo, maarten, agam, filipe)

2:00 - 2:15: "Robustness of interbank lending networks" (Regina, Brady, Molly, Agam, Matteo, Jim)

2:15 - 2:30: "Evolutionary Dynamics" (Bruno, Mengsen, Tom)

2:30 - 2:45: "Can hierarchical animal social structures emerge from biased cultural transmission?" a.k.a.Whales (Melinda, Lauren, Cesar, Mauricio, Ren)

2:45 - 3:00: BREAK

3:00 - 3:15: "Unfolding History" (Garland, Masad, Omodei, Seoane, Stadler, Strohecker, Xu, Zhang)

3:15 - 3:30: "Matrix Matters" (Honey, Reddy, Damerau, Strohecker)

3:30 - 3:45: "Generalizing the wealth distribution model to two countries: Effect of Tax and Trade on Inequality"

3:45-4:00: Beijing Taxis (David Masad and Hua Cai)

4:00 - 4:15 

4:15 - 4:30 

4:30 -

Presentations 2013

2013-06-26T16:01:23Z

Masad:

{{Complex Systems Summer School 2013}}

9:00 - 9:15: Mengsen Zhang (Synthesizing questions- in search of a simple analog of complexity...I'll talk a bit of alcohol and language if I have time :) )

9:15 - 9:30:

9:30 - 9:45:

9:45 - 10:00: NetAttack: Co-evolution of network builder and attackers

10:00 - 10:15:

10:15 - 10:30: BREAK

10:30 - 10:45: Cellular morphogenesis, Oskar 

10:45 - 11:00: Complexity (trans)science; Vanessa, Alastair, Stephane, Matteo, Melinda, Hua

11:00 - 11:15: CSSS Group Formation from a Genotype-phenotype Perspective (许晏 XU Yan, Vishwa, Johannes)

11:15 - 11:30: Shakespeare (Kyle, Max, Ashkaan, Eitan, Abbie)

11:30 - 11:45:

12:00 - 1:00: LUNCH & GROUP PHOTO

1:00 - 1:15 

1:15 - 1:30:

1:30 - 1:45:

2:00 - 2:15:

2:15 - 2:30:

2:30 - 2:45:

2:45 - 3:00: BREAK

3:00 - 3:15:

3:15 - 3:30: 

3:30 - 3:45: 

3:45-4:00: 

4:00 - 4:15 

4:15 - 4:30 

4:30 - 4:45 

5:00: Final Remarks & Farewell Dinner

Complex Systems Summer School 2013-After Hours

2013-06-22T07:27:54Z

Masad: /* Museum Hill - Saturday 22nd (or Sunday 23rd) */

{{Complex Systems Summer School 2013}}

==Moon solstice picnic - Saturday 22nd==

Friends of mine from Santa Fe have invited me for a hike & picnic Saturday evening, to watch the year's biggest moon rise on the hill behind st john's. They're very generous people, and when I told them about the school they insisted that I bring friends along. Since they'll cook and bring the food, I think I cannot reasonably invite more than 4 people though. Write your name and join us! (Meeting at 6:30pm at the fish pond) --Matteo

1. 
2. 
3. 
4. 

==Museum Hill - Saturday 22nd (or Sunday 23rd)==
Would anyone be interested in checking out some of the museums on "Museum Hill" near St. John's? The day is flexible, if people going to Tent Rocks are also interested.
I propose Saturday 10AM departure - it's within walking distance so anyone can come later as well.
Possible museums include:
Museum of International Folk Art, 
Museum of Indian Arts & Culture, 
Wheelwright Museum of the American Indian 
Here is some [http://www.santafenm.info/museums.htm more info about the museums].
Anyone interested? --Molly

I'm in. --David

==Tent Rocks National Monument on Saturday 22nd==
I would like to propose a field trip next Saturday (the 22nd), to visit the [http://www.blm.gov/nm/st/en/prog/recreation/rio_puerco/kasha_katuwe_tent_rocks.html Tent Rocks National Monument], which should be a very beautiful place.

Please write your name here if you are interested, so that we can see how many cars we have to rent.

===JP's Ferrari (5 seats)===
This car will go to the Farmer's Market in the morning, followed by Tent Rocks. 
1. JP 
2. Kevin 
3. Masato 
4. Melinda 
5. Bruno 

===Tom's Lamborghini (5 seats)===
This car will depart from the benches at 10 AM Saturday, and go directly to Tent Rocks. 
1. Tom 
2. Elisa 
3. Jim 
4. Bapu 
5. Luiño 

===Rental Stretch Limo (n seats)===
Degree of stretch depends on n of riders... 
1. 
2. 
3. 
4. 
... 

==June 14 Danger Zone==
Text/Call me at 850.545.0034 if you're interested in heading downtown tonight.

We need some partying tonight. Some people are meeting at 7pm to have dinner downtown. Another group is meeting at 8pm -directly to the drinks. Let's coordinate to meet all there. I'm in the 8pm group -Regina (202.412.4555)

--[[Ashkaan_Fahimipour | Ashkaan]]

==June 17 Karaoke==

Some of us are heading down to do some [http://www.cowgirlsantafe.com/events/783 Karaoke at the Cowgirl] on Monday, let's meet in the parking lot at 8pm-ish and head down together? Swati's gonna sing us some Whitney Houston!

==June 19 Rodeo de Santa Fe==

We are planning to head to the [http://rodeodesantafe.org/ Rodeo] on Wednesday June 19 at 6:00p.m. please meet drivers in the parking circle and post your car if you can drive. Note you can also split a cab there:

'''Juniper's Car''' 
1. Juniper 
2. Bapu 
3. Johannes 
4. Ashkaan 
5.Filipe 

'''JP's Car''' 
1.JP 
2.Amara 
3.Elisa 
4.Kevin 
5.Cheryl 

'''Brady's Car''' 
1. Brady 
2. Jian 
3. Oskar 
4. Swati 
5. Hua 

'''Lauren's Car''' 
1. Lauren 
2. Reniel 
3. David 
4. Ivana 
5. Stephan 

'''Still needs a Ride''' 
1. 
2. Agam 
3. 
4. Jody 
5. Melinda 
6. Luíño 
7. Molly 
8. Andrea 
9. Jim 
10. Masato 

==June 21 Madrid to see Juniper's Brother's band and to dance with hippies==

My brother's band [http://www.reverbnation.com/toddandthefox Todd and the Fox] is playing at the Mine Shaft in Madrid on June 21. Madrid is a ridiculous hippy town and has some of the best people watching there is. To boot, my brother's band is awesome and we can dance and have a great time http://www.reverbnation.com/show/10280700 --Juniper

Thumbs up!! -- [[Luís_Seoane | Luíño]]

Sounds great to me!! -- [[Jody_Wright | Jody]]

Sounds fun! I'd love to go. -Molly

I'm in too! -- Kevin

Sounds good! -- Melinda

I'm in too! -- Elisa

I'm in too! -- Johannes

I guess we have to rent cars in order to get there. Anybody wants to organize this? -- Kerstin

I'm in too! -- Filipe

Sorry this is kind of far and my car is already full, so you all will need to self organize for this one. I'll probably get there around 8:30 or so and maybe eat at the [http://www.thehollarrestaurant.com/ Holler] before hand, it's really yummy fancy southern food --Juniper

Is anyone with a car planning to go to this concert tonight? If yes, would you be willing to volunteer spaces in your car here and people can sign up? [[Jody_Wright | Jody]]

==More Games!==

So... I was thinking it might be fun to have a second games night some time this week- either to catch up on the Mafia/werewolf game that we didn't have on Sunday, or perhaps some other game. Some of you may have encountered [[That Game]]... which is as always being updated and altered. If you missed out on the first round, or want to play again (or simply want a chance to watch JP dissolving in laughter) then come along.
As for Time/Place... Ummm... I feel like Thursday evening might be good, perhaps upstairs lower common room... but if other times/day/place suggested then that's good too.

==Bandelier Field Trip==

We're taking a trip to [http://www.nps.gov/band/index.htm Bandelier National Monument] on Saturday June 8th. Please visit the [[Bandelier 2013 | Bandelier Field Trip]] Page to sign up!

==More Hiking!==

Check the [[Complex Systems Summer School 2013-Hiking]] page to see current plans!

Didn't get enough hiking at Bandelier? Come hiking/camping with me! I plan on going on a long hike (all day, preferably 10+ miles) one of the next two weekends. I brought things for camping and would love to do that if there is interest and it is possible to rent tents/sleeping bags in town (or if people want to just sleep outside, also fun). If that is not really possible or people would rather just go for a single day that is great as well. I am open to a lot of different things, there is so much great hiking around Santa Fe!

Some suggestions:
* [http://www.backpacker.com/april_1999_destinations_new_mexico_pecos_wilderness/destinations/696 Pecos Wilderness] - just outside of Santa Fe, lots of trails!
* [http://www.summitpost.org/wheeler-peak-nm/150429 Wheeler Peak] - tallest mountain in New Mexico, outside of Taos (would require either camping at the base or waking up very early to do it the day of)
** Near Taos we can find these [https://www.google.com/maps/preview#!data=!4m18!3m17!1m1!1sSanta+Fe+Institute%2C+1399+Hyde+Park+Road%2C+Santa+Fe%2C+New+Mexico!1m5!1sManby+Hot+Springs!2s0x87177428acfba0e5%3A0x69769a1d19abcbff!3m2!3d36.5083168!4d-105.7242545!3m8!1m3!1d10957!2d-105.7242545!3d36.5083162!3m2!1i1366!2i656!4f13.1&fid=0 hotsprings]!!!!!!!
* [http://www.fodors.com/world/north-america/usa/new-mexico/taos/review-465844.html Carson National Forest] - North of Santa Fe, another beautiful forest, lots of different entrance locations

I am up for any other suggestions if people have heard of trails they want to go on. Depending on how the fires progress we may or may not be limited, but should be able to do something! Send me an email if you are interested and we can talk logistics (bstoll1234@gmail.com) [[Brady_Stoll|Brady]]

I would love to go! I had a hike in mind too--Tesuque Peak, which is just by the ski area and is 12 miles, but I am up for any of them! -Lauren (lash1937@gmail.com)

I'm interested! -Hua (caih@umich.edu)

I'm defintley interested - Wheeler Peak sounds very interesting (I have to get camping stuff though)! - johannes (johannes dot schmidt at boku dot ac dot at)

If we did Wheeler Peak, I am highly in favor of the longer class 1 route. The shorter class 2 route has a scree slope at the end, and I really dislike scree (it scares me). If we camped at the trailhead, I have a 3 person tent that we could use. --Lauren

If you'd like a similar experience to Wheeler Peak, but a lot closer, I recommend Santa Fe Baldy (12600'). Well above treeline, with fantastic vistas in all directions. The trailhead is only about 20 minutes away at the Santa Fe Ski Basin. The roundtrip hike is about 14 miles, making it a reasonable day hike. As always with any mountain around here, you need to be off the exposed sections by about 2PM because of the danger from thunderstorms! --John L

More hiking would rock!(Although I'm not sure about optimal length...) --Todd

==Music on the Hill==

St. John's hosts [http://www.stjohnscollege.edu/events/SF/music.shtml live music] on the soccer field this Wednesday (June 12) as well as next Wednesday (June 19) and the Wednesday after (June 26). Performances start around 6:00 PM. It looks like all of the performers will be doing jazz. I really hope to make the June 19 performance, as this will be big band, which is (usually) great for dancing. Any other swing dancers in our group? --[[Vanessa_Schweizer | Vanessa]]

* sounds fun to me! -- Hua
* I'm definitely interested! --Molly
* Sounds fun to me as welll! --Brady
* Sounds fun! --Jody

==Mafia/Werewolf==
[[JP]] LOVES to Play [http://en.wikipedia.org/wiki/Mafia_(party_game) Mafia/Werewolf]. Let's set up a time one of these evenings in the lower commons...

This sounds pretty cool. [[todd_bodnar | Todd]]

I like Mafia a lot, and I also brought a card game called [http://en.wikipedia.org/wiki/Fluxx Fluxx], and also know a few other games you can play with just paper and pencil (like [http://natsdistractions.wordpress.com/2009/12/13/great-party-game/ Bucket of Nouns]). I think a game night would be fun! --Molly

I would love to play Go if anyone is interested. --John D -- Count me in!! -- [[Luís_Seoane | Luíño]]

We should probably set a time/day/place if we actually want this to happen... I suggest 7:00am on sunday, with the lower common room thing, unless something else is happening then.

I like the game! Count me in! -- Hua

==Dance party==

Would anyone be interested in some sort of clubbing/dance party some time this month? And to be clear I don't mean going down to a bar to sit round drinking beers- that can be fun too, but I'm meaning something more music/dance focused.
If so,

What bars/clubs do people know of the might work? what music do they provide?

What music are people interested in? Remember, music that is good to listen to is not always good for dancing (and to be fair, there's plenty of music which is fun to dance to, but might not actually be "good")

Also, didn't someone mention some degree of DJing or music abilities? I can't remember, but if so, we could try to get our hands on the light rigs in the lecture hall and just make our own dance part from scratch...

*Our own dance party from scratch sounds fun to me. --[[Vanessa_Schweizer | Vanessa]]

So, some investigation indicates that hosting a large scale party at St Johns could be fairly impossible. She suggested hiring a venue in town... but I figure if that's the case we might as well just head down there and take it over by force of numbers.

*There is a CSSS "Dance with Breadloaf workshop" scheduled for June 22 starting at 8:00 PM. Is this an actual dance, or is this a complexity science thing??? --[[Vanessa_Schweizer | Vanessa]]

==Mountain Biking==

I would like to go mountain biking on sunday (9th of June). Anybody interested in joining me? We can rent a bike in the city for either 30$ (hard tail) or 60$(fully), helmets are 4$ extra. For those who are interested: please put your name and your height (needed for bike reservation) here until Thursday evening, I'm going to reserve the bikes then. [[Johannes_Schmidt]]

==Athletic Things==

I've heard lots of people talking about running/walking etc, and at dinner last night we mentioned that it would be fun to have a running group. Anyone interested in having a running/walking group either in the mornings or evenings? Post interest here!

I'm interested in a (quick) '''walking group''' in the mornings. It's great to exercise a bit in this nice weather and be able to talk at the same time. [[Regina_Martinez |Regina]]
*I would also be up for quick walking - whether we mean walking briskly or walking for 20-30 min. --[[Vanessa_Schweizer | Vanessa]]

Also, I love ultimate frisbee! Anyone interested in either learning or playing a game perhaps sunday or after dinner one day next week? Let me know! [[Brady_Stoll|Brady]]
*Ultimate would be fun, although I had a pretty bad knee injury years ago and haven't done that much running since then. I could see how long I would last. --[[Vanessa_Schweizer | Vanessa]]
*That's fine, anything would be fun, even just throwing/teaching people to throw! -Brady
* Down to play. Anything planned for today? - Bapu
* I don't have any specific plans today, but would love to either throw or teach if you're interested before the sun goes down. Play for sure tomorrow? Lets say tomorrow after dinner for those interested
*'''Lets play frisbee today! (Wed) Meet after dinner and we'll walk over to the fields, or meet us there!'''

Or basketball? Anybody want to play a pickup game?
-I would play a pick up game -Brady

==Yoga==

Anyone interested in '''yoga tomorrow (Sunday 9th) at 7pm?''' Some of us are going to [[http://www.santafecommunityyoga.org/index.php/classes2/schedule]]. We are meeting at 6:30pm. There is only one more space in Lauren's car. But, if there are more people interested, we can try to find a solution for the commute. [[Regina_Martinez | Regina]]

Hi Regina - I would be interested in joining you for yoga if there is still space. Please email me at [[jjwright49@me.com]] and let me know. Thanks! - [[Jody_Wright | Jody]]

Anyone want to go to yoga tomorrow (Tuesday the 11th) evening? We were thinking of going to Hatha yoga at 5:30, so leaving campus at 5:00. We'll go to dinner afterwards too. Send me an email (lash1937@gmail.com) if interested. [[Lauren_Shoemaker | Lauren]]

==Sightseeing Weekend==

Anyone interested in going on a weekend road trip? This could be more of an 'easy going' option to the hiking trip proposed above. I was thinking of maybe driving up to Taos and doing some whitewater rafting and general sightseeing. Let me know if you are interested or have any other ideas. I don't have a car but am able to drive...

- [[Ivana_Stankov | Ivana]]

==THERE IS A FOURTH WEEKEND!!==

If you, like me, believe that CSSS lives on after Saturday 29...

If you, like me, are hanging around because you can't leave this sacred piece of ground anymore...

If you, like me, believe this month is only the beginning of a life that wasn't before...

Then you believe on the forth weekend!! I know many of you will stay a few days after CSSS is over and it would be nice to organize ourselves soon. So, if we choose to go somewhere, say taking a flight, we could get cheaper prices, etc! Also we will be needing shelter after the 29th. This might be an urgent thing ;) Let's use this to organize ourselves! I post some ideas below that I've heard around these days. -- [[Luís_Seoane | Luíño]]

*Trip to the Gran Canyon?
*Camping in some national park?
*Trip to San Francisco?
*Trip to Las Vegas where we make up random couples and get married :?

I vote for Grand Canyon + San Francisco. I have my plane back home from Albuquerque on the 7th of July, so I am totally in for post school plans! -- Elisa

If you come to San Francisco, I can probably show you some cool places. --[[Nix_Barnett | Nix]]

==Indoor climbing/bouldering on saturday (22)==

Me (Oskar), Jian and Swahi are visiting the local climbing gym tomorrow. If you wanna try bouldering and maybe some rope climbing, we are leaving from the cafeteria at 10.00 after breakfast. If you feel like coming, you can email me at oskarxvi at gmail dot com (or just show up). We will visit the market and grap some lunch in town afterwards. See you!

http://climbsantafe.com/

Complex Systems Summer School 2013-Hiking

2013-06-16T01:00:39Z

Masad: /* Long one-day trippers */

Renting Gear:
REI has plenty of gear, but to be sure that we have what we need we should reserve it tonight or tomorrow morning. Here are the prices (going from memory so may be off but is close) 
* 4 person tents: $23 1st day, I think $5 the second (they also have 2 and 3 person tents, so if we just have 7 going maybe get 1 4- and 1 3- person tent) 
* Sleeping Bags: $15 1st day, $5 additional days 
* Sleeping Pads: $12 1st day, $3 additional days 

I put the additional day prices just so yall know if you want to plan longer trips later. I'll place reservation based on what is listed below, so make sure that is correct!

We decided to go this weekend to the Pecos Wilderness and climb Santa Fe Baldy. One group with ~10 people is going to go Saturday mid-morning ish, do a day hike and camp that night. The other group is going to (likely) leave Sunday and meet the first group out there, and we'll climb Baldy together.

We have to be below tree line by 2-ish (sooner if it looks like a storm is brewing), so should get back by dinner time, or can decide to go to dinner somewhere else in town.

We need to rent probably 1 car (I will drive 5 people to camp, Lauren will drive 4-5 people to day hike, +1 car for camping), and rent tents and sleeping bags, plus one stove for cooking.

In order to finalise numbers and know how much equipment to rent, please sign up here in whatever category applies and indicate whether you need a sleeping bag/mat!

== Overnight campers ==

# Brady
# Kevin (needs mat)
# Johannes (needs bag+mat)
# Jian (needs bag+mat)
# Swati (needs bag, mat)
#
#
#

== Long one-day trippers ==

# Lauren
# Hua
# Regina
# Elena
# Melinda

* Hi all: we've booked two cars for the Sunday hiking (pick up Sat 15 8h30pm; drop off Sun 16 8h30 at the airport) at the cost of US$46 each car (plus gas to be shared). We just need to figure out how to get at the airport, but this will happen:)

The original hiking trail is closed because of the fires, so Lauren has found us another one, near Bandolier. Unfortunately, we won't be able to meet up with the other group. Fortunately, it means we can leave St. John's at 8AM. So if you're coming, meet Sunday morning at 7:50AM.

Please ADD or CONFIRM your name!

# Mauricio (confirmed)
# Ren (confirmed)
# Cheryl (confirmed)
# Bapu
# Oskar (confirmed)
# Andrea (confirmed)
# David (confirmed)
# Masato (confirmed)
# Joana (confirmed)
# Yan (confirmed)

== Planning stuff ==

Here's some info on the state of the wildfires and what we're allowed to do fire-wise, for those who know what that means: [http://firerestrictions.us/nm/]

And here's a general weather forecast which isn't looking too bad! [http://www.weather.com/weather/weekend/Santa+Fe+NM+USNM0292:1:US]

Some info on Santa Fe Baldy [http://www.summitpost.org/santa-fe-baldy/151395]

Complex Systems Summer School 2013-Hiking

2013-06-15T07:54:29Z

Masad: /* Long one-day trippers */

Renting Gear:
REI has plenty of gear, but to be sure that we have what we need we should reserve it tonight or tomorrow morning. Here are the prices (going from memory so may be off but is close) 
* 4 person tents: $23 1st day, I think $5 the second (they also have 2 and 3 person tents, so if we just have 7 going maybe get 1 4- and 1 3- person tent) 
* Sleeping Bags: $15 1st day, $5 additional days 
* Sleeping Pads: $12 1st day, $3 additional days 

I put the additional day prices just so yall know if you want to plan longer trips later. I'll place reservation based on what is listed below, so make sure that is correct!

We decided to go this weekend to the Pecos Wilderness and climb Santa Fe Baldy. One group with ~10 people is going to go Saturday mid-morning ish, do a day hike and camp that night. The other group is going to (likely) leave Sunday and meet the first group out there, and we'll climb Baldy together.

We have to be below tree line by 2-ish (sooner if it looks like a storm is brewing), so should get back by dinner time, or can decide to go to dinner somewhere else in town.

We need to rent probably 1 car (I will drive 5 people to camp, Lauren will drive 4-5 people to day hike, +1 car for camping), and rent tents and sleeping bags, plus one stove for cooking.

In order to finalise numbers and know how much equipment to rent, please sign up here in whatever category applies and indicate whether you need a sleeping bag/mat!

== Overnight campers ==

# Brady
# Kevin (needs mat)
# Johannes (needs bag+mat)
# Jian (needs bag+mat)
# Swati (needs bag, mat)
#
#
#

== Long one-day trippers ==

# Lauren
# Hua
# Regina
# Elena
# Melinda
# Mauricio (I guess only if 4 more people want to rent a car..)
# Ren
# Cheryl
# Bapu
# Oskar (if its not too late)
# Andrea (if late entries are accepted!!)
# David (if there's even more room)

Hey long one-day trippers! Let's get together at the lunch break and make some final plans for this weekend? -Lauren

== Planning stuff ==

Here's some info on the state of the wildfires and what we're allowed to do fire-wise, for those who know what that means: [http://firerestrictions.us/nm/]

And here's a general weather forecast which isn't looking too bad! [http://www.weather.com/weather/weekend/Santa+Fe+NM+USNM0292:1:US]

Some info on Santa Fe Baldy [http://www.summitpost.org/santa-fe-baldy/151395]

Unfolding History

2013-06-12T17:39:11Z

Masad: /* Literature */

Trying to give new impulse to this project: let us use this site to share info and tools!

==Brainstorming==

Some of the ideas that have been buzzing around:
*Make an agent based model.
*Take empirical data from the wikipedia.
*Agents biasing History.
**Do conflicts in a country reflect on their account of History?
*External vs. internal history: the cost of inner encoding vs. relying on the environment to encode important traits.

Please, post those missing!!

==Scripts==

It is very easy and fast to parse files with python. [https://www.dropbox.com/sh/my8s4yhh7rqyobc/GcdhVSRiUk This] links to a dropbox folder containing a few sample data manually cropped from the wikipedia and three python scripts to parse the data.

[[File:EditsChipre.png|661px]]

==Tools==

The wikipedia has got a [https://en.wikipedia.org/wiki/Wikipedia:Statistics large collection of tools] to extract statistics from the site. After a loose search, nothing was found that resembles what I (Luíño) had in mind. There are very interesting models and fits to data, though, of how an article grows in time or how much this or that user affects a wiki. If we wanted to do something with the wikipedia eventually, we should check out that what we need is has not already been invented. Someone up to navigate through these tools and tells us about them?

==Literature==

The following more or less related papers have been posted to the project by different colleagues:
*[http://www.amazon.com/The-Evolution-of-God-ebook/dp/B002AKPEHW/ref=sr_1_1?ie=UTF8&qid=1370537236&sr=8-1&keywords=the+evolution+of+god The Evolution of God] -- by [[Pablo_Galindo]].
*A model on [http://www.sciencedirect.com/science/article/pii/S0022519310004790 religion diversification] that can be very handy if we decided to make a model -- by [[Cesar_Flores_Garcia|Cesar]].
*[http://link.springer.com/chapter/10.1007/978-3-642-36844-8_10#page-1 Network approach to history] -- by [[Giuliano_Andrea_Pagani|Andrea]].
*A nice work on [http://www.merl.com/papers/docs/TR99-16.pdf Unfolding Narrative] -- by [[Carol_Strohecker Carol Strohecker]].
* Brian Keegan wrote [http://www.brianckeegan.com/dissertation/ his dissertation] on something pretty similar, and has done some other work on Wikipedia edits of current events. --David

Surely more people has approached the problem of History formation from a Complex Systems approach. It would be interesting to go over the literature and maybe find some insight. Someone would like to do that?

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-12T17:22:38Z

Masad: /* How big can a city be? */

[[Link title]]{{Complex Systems Summer School 2013}}

==Project Proposals==

=='''Modeling self-organization of "arbortron" by cost-driven growth in spatial networks'''==

References:

Formation and structure of ramified charge transportation networks in an electromechanical system
http://www.pnas.org/content/102/3/536.short

Emergence of hierarchy in cost-driven growth of spatial networks
http://www.pnas.org/content/110/22/8824.abstract

-许晏（XU Yan）

I'm in!
-张萌森 Mengsen

I am in (listening silently). However, I would love to see a game theoretic explanation for the race condition. -Vishwa

=='''Emergence of cooperation in social networks, e.g., CSSS 2013'''==
Current group members: Vishwa, Yan

Genotype vs. Phenotype (to be added...)

Each player (e.g., CSSS participant) has a background knowledge & skill set, which is characterized as a "gene" sequence (genotype): if Bob knows nonlinear dynamics but is not familiar with Netlogo, then the genotype of him is (1 0 ...). (To be finished...)

-许晏（XU Yan）

=='''MOOCs'''==
I have had an interest in MOOCs and their potential role in the future of education/ as a means of providing education to non-traditional students. This has been in the back of my mind for some time, but I have no experience dealing with real social data (including how to access it) and was hoping other people might be interested. I did a brief search and found that it may be possible to use twitter data. The questions I am interested in are where MOOCs are popular (globally), how it spread, what kind of topics, etc. Anyone else interested?

-Swati

An automated cluster analysis of the content of Coursera catalogs would be quite straightforward. It could help get a sense of meaningful clusters of content regarding how courses present themselves, and also what categories are salient for MOOC's. [[Manish_Nag | --Manish]]

=='''Food webs'''==
It seems like there is A LOT of interest in food webs amongst this group. Since there are so many people, maybe it would be worth coming together and dividing into smaller groups based on the questions (there are many!) people are interested in addressing and skills. I think it would good be to have some coordinated effort, for efficiency and productivity. We could divide questions, or parts of bigger questions, or approach the same questions, using different methods and then compare results and try to understand the similarities and differences. Maybe we could meet at 3 pm today (Wed) or at dinner.

-Swati

=='''A Midsummer Night's Project: Comedy and Tragedy in Shakespeare'''==

Max Kleiman-Weiner and I have a corpus of all the Shakespeare plays and have been talking (with many of you, too!) about building a system to automatically classify Shakespeare plays as either comedy or tragedy. A simple approach would be to just use a bag of words to see if the plays can be classified based on lexical content alone. We have also been discussing building social networks for each play based on which characters interact (i.e., who speaks before and after whom). We suspect that the social network structure of a comedy and tragedy should look different from each other. Do characters in comedies have more connections? Do tragedies and comedies start off the same and then have networks that evolve differently over the course of the play? Or are they different from Act I? This may be an opportunity to look at how social networks change over time in a specific domain. We could also look at the different roles of men and women in the social networks of the plays.

-Kyle M

This sounds interesting and doable. I've done a work on author attribution of opinion articles before using only syntactic (function words like prepositions and articles, punctuations), structural (sentence length, paragraph length) and lexical (other non-specific words) features. It'd be nice to see if the same thing will work for this. I think it will be more fascinating to explore the social network approach and we should definitely give it a shot if there's still time.

-Cheryl

Stories are always good. Incidentally, are you familiar with Kurt Vonnegut's commentary on the shapes of stories? If not, it's not hard to find. If so, there may be something to be said for attempting to determine whether a story conforms to more specific tropes (e.g. Cinderella stories and "The Chosen One"). Moreover, if enough distinct patterns do emerge out Shakespeare's plays, it may prove interesting to compare these to other stories (e.g. novels available on Project Gutenberg).

-Eitan

There is now a DropBox with the corpus and some preliminary Python scripts - so come find me if you're interested in getting linked in.

-Max

See project page for this here: [http://tuvalu.santafe.edu/events/workshops/index.php/Comedy_and_Tragedy_in_Shakespeare].

=='''Recursive Agents'''==

A common theme that I've seen in complexity is that you can represent many different systems (cells, agents, civilizations, for example) with more or less the same rules. I'm wondering if anyone would be interested in modeling this? Essentially we develop a recursive rule set: agents' behavior are based on a set of their 'inner agents,' which also follow similar rules.

-Todd

=='''Global Emergent Risk'''==

In the current phase of globalization, networks in logistics, travel, finance, disease, energy, and ecology are growingly increasingly interconnected on a global scale. Hence, situations arise where mortgage defaults in the US bring down the Icelandic pension system, and a volcano in Iceland disrupts global air traffic. Given the scale of interconnectedness, can complexity science help develop a sense of how small perturbations in one global network might cascade into large unforeseen failures in another network? I'm wondering if we can help build a more generic grammar for describing interconnected networks and the risks posed by such systems. Would it be possible to mitigate risk at smaller local levels of scale, or do small corrections of local risk inevitably cascade into larger risks that we lack the ability to respond to (think wildfires in the Southwest where more frequent small fires would help reduce the chance of large scale fires that cannot be controlled.) I'd love to talk with anyone interested in ecology, globalization, risk, and network modelling.

My advisor at Princeton is already funded for a three year interdisciplinary symposium on Global Emergent Risk, so if people are interested, we have resources to carry on a larger research engagement.

--[[Manish_Nag | Manish]]

- I don't know if large risk cascades are inevitable, but these are timely questions. I have colleagues at the [http://gcrinstitute.org/ Global Catastrophic Risk Institute] who are also interested in this topic. I'm not sure what building a "more generic grammar" means, but the cross-impact balance method is pretty generic. Hopefully you can make our [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]]! Our group is kicking around methods for a project at the moment and have not decided on research questions, so perhaps we can join forces. --[[Vanessa_Schweizer | Vanessa]]

- To clarify, what I meant by "generic grammar" is some way to describe a set of networks and cross network dependencies that can be decoupled from the content of the network. We could use this language to describe interconnections between hypothetical logistics, travel, financial networks for example, and then use simulations to understand the conditions where risks might be amplified and/or jump across from one network to another. --[[Manish_Nag | Manish]]

- I'd love to join discussions on this as I agree that there's a need to start thinking about network of networks and not just networks in isolation. The [http://arxiv.org/abs/1010.5829 paper by Gao, Stanley et al.] on the robustness of a network of networks might be useful. --[[Cheryl_Abundo | Cheryl]]

- I'm in .[[Reniel_Cabral | Ren]]

- I'm thinking if we can possibly use a self-organized criticality (SOC) type of model to trigger a cascade of failures in a network of networks. Not sure though if it has been done. [[Cheryl_Abundo | Cheryl]]

- Thought this paper may be useful for your work [http://69.164.193.67/site_media/publication_pdfs/Guimera-2004-Eur.Phys.J.B-38-381.pdf] - Vishwa

=='''Alcohol Consumption and Language Fluency'''==

There's a interesting thing about me and some of my friends who speak a foreign language. There seems to be a kind of non-linear curve that depicts my blood alcohol concentration and the fluency of my speaking English (Chinese is my native language). For example, usually after one beer, I start to talk faster, and semantically relevant words pop up in my mind more fluently or spontaneously. Or say, I express the same idea with less stuttering and in shorter time. But after some point, i.e. 32 oz of beer, even it might still sound fluent, regarding the physical property of the speech, the grammatical structure of the sentences start to break down. Ultimately, i.e. half bottle of rum, I only repeat 2-3 very short sentences/phrases independent of the presence or the identity of my audience(s) (i.e. murmuring in English for hours to a group of Chinese friends). 
We know that alcohol can influence our behavior by, among other things, binding to certain neural receptors (like GABAa?). I just thought it might be interesting to model how alcohol intake influences the dynamics of language production via regulating neuron signaling. I'm also wondering about what it might imply about our brain dynamics when we're silent. 
Here's a short survey [http://www.surveymonkey.com/s/QYT7LYV] if you like to let me know your experience on this topic.
Welcome to talk to me if you find this interesting, or silly, or you simply want to correct my grammar. Thanks! 
-Mengsen Zhang

@Mengsen I'd be very interested in doing some empirical work on this topic.
-Max Kleiman-Weiner

I've experienced this same thing with Spanish, Bahasa Indonesia, and playing billiards/pool. Sadly, my math skills do not improve with drinking, and math could arguably be considered a language. This is a creative topic with solid scientific underpinnings that nicely lend themselves to complex systems modeling, I suspect. Fun! – [[Kristen_Honey | Kristen Honey]]

On a related note:
http://xkcd.com/323/

-Eitan

=='''How the ocean can help us heal complex chronic disease'''==

The human body is its own ecosystem -- much like the ocean -- with resilience, hysteresis, synergistic properties, and multi-system dynamics that depend on matrix conditions. Can we use our understanding of the ocean and ecosystems to help us heal? Can we model different scales -- an ocean, a human body, and a microbial community -- to explore ecosystem/human/microbial health in a holistic context that depends on shared key elements like flow & trace minerals as building blocks for function? As one example to think about, chronic illnesses like HIV/AIDS or Lyme disease disrupt the immune system and human body functions (e.g., methylation pathways, detox pathways), preventing optimal function that weakens the human body and makes it vulnerable to other infections. It’s a downward spiral of negative feedbacks, analogous to a backed-up, atrophying ocean or estuary that causes fish kills, destroys coral reefs, etc... analogous to microbial communities that shift when environmental/matrix condition change. I suspect our knowledge of the ocean & large ecosystems, which we can see and visualize, can inform new thinking about system dynamics for health & recovery at the scale of a human body and at the scale of individual microbes & microbial communities...

Anyone else interested? – [[Kristen_Honey | Kristen Honey]]

- This sounds like a really nice idea. It would be interesting to understand how the disease-mediated degradation of immune/metabolic networks (the loss or alteration of edges and nodes?) affects the response of these networks to further perturbations (e.g. asymptotic stability and resilience, [http://www.jstor.org/stable/2266047 transient reactivity], cascading effects of node loss, etc.). I have little knowledge of the medical literature, but I am experienced in ecological network analysis including information theoretic analyses of weighted food webs. -- [[Ashkaan_Fahimipour | Ashkaan]]

- I liked the idea very much. In fact I am looking at similar issues related to management of ecosystems which display hysteresis and [http://arno.uvt.nl/show.cgi?fid=121389 regime shifts]. Here is some pertinet information related to [http://www.esajournals.org/doi/abs/10.1890/1051-0761%281999%29009%5B0751%3AMOEFLS%5D2.0.CO%3B2 shallow lakes] and its [http://ideas.repec.org/p/att/wimass/200026.html complex dynamics]. Your idea of scaling down to human level is interesting -- [[Puduru Reddy | Vishwa]]

- Sounds interesting. I have experience in microbial oceanography, but not so much with infectious disease. I'll be there for the dinner meeting. - [[Jody_Wright | Jody Wright]]

FRIDAY 6/7 BEER & WINE BRAINSTORMING ACCOMPLISHED!: Let's convene tonight after SFI, 8:30ish or 9:00ish, Friday June 7th, downtown for some DOWN TIME! We've already put our brains together & focused project scope. Now it's beer & wine & fun in Santa Fe with everyone! :)

Here is the new project page [http://tuvalu.santafe.edu/events/workshops/index.php/Ocean_Biology]

==
Join us for project discussion & brainstorming ideas, Wednesday June 5th dinner at 5:00. Everyone welcome! ==

=='''GDELT'''==

[[David_Masad | I'd]] love to play around with the new [http://gdelt.utdallas.edu/ Global Data on Events, Location and Tone (GDELT)] dataset, which has 200+ million timestamped and geocoded political events. Here's a [http://ideas.foreignpolicy.com/posts/2013/04/10/what_can_we_learn_from_the_last_200_million_things_that_happened_in_the_world writeup of it in Foreign Policy] -- David

=='''Research Network Formation'''==

I'd be interested in collecting some data from CSSS attendants. Some kind of way to study social network formation. -- [[Todd_Bodnar | Todd]]

Perhaps we could collect survey questions people might be interested in looking at in a [https://docs.google.com/document/d/1h_8TUyuDNT1DhPIyZuGwuvrqSExLgwoocsKZl4jFSk8/edit?usp=sharing Google Doc]? --[[Molly_King | Molly]]

My new crazy idea, inspired by [http://blog.premise.is/blog/2013/5/5/mapping-the-produce-manifold these guys], is doing something with computer vision. Maybe there's a way to photograph sitting arrangements and extract data from that? -- David

Project meeting after the lab Wednesday 6/5 for all those interested.

=='''Self-consistent networks for socio-economic institutions (CIB analysis and Markov chains)'''==

Project update: Some core members of the group are starting to assign tasks for the project. If some folks are still shopping for projects and want to check out what we're up to, please visit our [[Complex_Systems_Summer_School_2013-CIB_Markov | project page]]. --[[User:Vanessas|Vanessas]] 02:12, 6 June 2013 (UTC)

[[Pablo_Galindo | Pablo]] and [[Vanessa_Schweizer | I]] started to discuss a project where we could use [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] to investigate the implications of alternative hypotheses for interrelationships between various socio-economic/political factors. We began discussing this from the perspective of testing competing political economic theories to see what types of institutions (e.g. styles and stability of governance) would be self-consistent according to the theories. However, I would be open to other topics, including research questions inspired by GDELT. If there is interest to learn more about the CIB technique, I could put together a tutorial. --[[Vanessa_Schweizer | Vanessa]]

- There's a paper written by Brian Arthur here at the SFI that might help us frame our topic. Its called Complexity Economics. Basically sets the "rules" for thinking about economics in a whole different way.
It is a very good starting point so we don't go any further wasting time taking into account economic models that are vague, non-accurate and out of date. [[Pablo_Galindo | Pablo]] [?]

Elaborating more on the idea. If we focus on human action as the essence of culture. Understanding human action as the use of beliefs, attitudes and resources (which are scarce) pursuing a state of higher satisfaction. And culture as the sum of all beliefs, attitudes and unintentional consequences of the human action. We can state that the emergence of socio-econmic/political factors are the unintentional consequence of intentional individual actions that at the same time affect the way people act, in what they believe and what attitude they'll have toward the satisfaction of their needs. (Theres a loop between human action and culture - culture affects human action and human action affects culture and so forth)
Some "institutions" will emerge as a consequence of human action but not human design. That is one of the characteristics of a "good" type of institution. (e.g. Money, language, private property, contracts, a certain type of government) and it would be interesting to test the robustness of that spontaneously emerged institution against human designed institution who's robustness is just that is law enforced.
I dunno If you get my point? Compare the qualities of spontaneously emerged institutions against human designed institutions. Its more or less comparing spontaneously emerged institutions (no leader needed to coordinate like the birds flocking) vs. human designed institutions (leader needed to coordinate al human actions).

==
A [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]] on cross-impact balances and Markov chains is scheduled for Wed. June 5 at ~4:15. Everyone is welcome, even if your project interests lie elsewhere. ==

=='''Genetic algorithms to evaluate network formation or real-world data'''==
I have an ill-defined, wacky idea to possibly use genetic algorithms to evaluate the formation of networks as either following preferential attachment or homophily (aka similarity) rules. This [http://www.nature.com/doifinder/10.1038/nature11459 short Nature paper] looks at the debate between preferential attachment and similarity/homophily dynamics. I don't have a clear idea of what this would look like, but I think it might be fun to think about ways to use genetic algorithms to solve network problems. Talk to me if you think this remotely interesting and we can evolve an idea together? --[[Molly_King | Molly]]

Another possibility would be using genetic algorithms or attachment algorithms to compare to models of real-world data to understand how these networks likely formed and predict future edges.

Molly, I would like to investigate using GA to create an organizational network structure (think org chart or military chain of command or even project groups at the CSSS) and then compare it to existing structures. Let's talk! -John L

Some people were also talking about co-evolution of a network and an attacker that disconnects nodes or edges. -- David

Everyone interested in this and related meet Wed 6/5 at 4pm in main lecture hall - group of folks interested in studying network evolution/fitness/information/energy spread meeting. --Molly

Seem to be two branches of this: 
1) network evolution toward a predefined fitness function (energy, information efficiency, etc.) via genetic algorithms - what structures evolve? 
2) co-evolution of a network and attacks of different forms - what structural changes take place? which structures are robust to attacks?

===1) network evolution toward a predefined fitness function===

=== 2) co-evolution of a network and attacker ===

Interested members: Elena, Andrea, Stephan, Bruno, Johannes, David M., Holly, Mauricio

We're thinking about co-evolving a network and an attacker agent. The network's fitness is robustness (to be defined later) to attack, and the attacker's fitness is disruption of the network. Both also need to be subject to some sort of resource constraint -- otherwise the optimal network is fully-connected, and the attacker's optimal strategy is just disconnecting all of the nodes.

Some background reading:
http://www.talkorigins.org/faqs/tierra.html

http://www.researchgate.net/publication/220841044_Formal_Methods_for_Modeling_Socio-technical_Innovation_between_Adversaries?ev=prf_pub

Tools:
Probably Java or Python. We need something that has network metrics already, so we don't need to code them ourselves. Possibly use a GA package / library as well.

I created a page for the project and started to discuss some of the issues: [[NetAttac]]

=='''Caribou Management Dynamics'''==

This project would model caribou management dynamics in a prototype NW Alaska community during a caribou shortage. Agents in the model would be informed by data from household subsistence surveys and from management history. The goal would be to evaluate the abilities of different management strategies to achieve biological harvest goals while maximizing economic efficiencies in the community. This is a real-world problem with near-term applications. Caribou cycle on 30-to-50 year periods. The Western Arctic Caribou Herd is currently in decline. During the last caribou “crash” in this region, the state management system attempted to reorganize caribou production, which generated considerable political and social disruption, precipitated widespread passive resistance among Native peoples, and left a legacy of contempt for both management (among some Inuit) and for Inuit hunters (among some sport users). The hope is to reduce conflicts during the expected nadir of the population. Comments and cooperators welcome! [[James Magdanz | Jim]]

Neat topic with data, I assume! I'm interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Evolving synchronized flashes in fireflies, and other polymorphic traits'''==

[[Bryn_Gaertner | I ]] was thinking about how some, but not all, species of fireflies can synchronize their flashes, as was mentioned in both lectures today (June 4). The mechanism is fairly simple, it seems, so we should be able to evolve it using a simple genetic algorithm, right? This is only half-baked at the moment, and I haven't checked to see if it has been done already, but I thought it would be neat to explore the space around these biological phenomena. More of a fun project than a serious "lets publish this!" type of project. Bonus points if we can work some neural network stuff into it. [[Bryn_Gaertner]]. -- EDIT -- Upon further discussion with [[Rebecca_Mease | Rebecca]] and [[Holly_Arnold | Holly]], we would like to extend this. Still using genetic algorithms, under what conditions can we evolve a stable polymorphic trait in a population, and under what conditions does a monomorphic trait evolve? This is applicable for traits in a population, but we would like to use the same model to evolve (for example) multiple or novel sensory modalities in a species, number of members in a food web, predation strategies, etc. Interested? Find us at lunch!

=='''How do historic facts collapse into written history?'''==

Let's begin with a nice example: [http://en.wikipedia.org/wiki/Gilgamesh Gilgamesh], the fifth king of Uruk, decided to gather together some stories that local tribes and surrounding cultures had been telling for years, along with things that previous kings had done. This became the [http://en.wikipedia.org/wiki/Epic_of_Gilgamesh Epic of Gilgamesh]. Someone later does a cover of the original book with some new contributions and turns it into what nowadays is the bible and the torah. Another remake of the tale turns these books into the quran, and until today... you know the rest of the story already. Peer reviewed quality, just like Nature or PNAS.

It might be interesting to study how history goes from facts to a written, definitive form which is not (and maybe cannot be) completely faithfully to the actual events. There is huge room to use, for example, models of agents that contribute to form a History with pieces of information that sums up, sometimes with contradicting versions, sometimes with hidden interests, etc etc. Furthermore, we have a great tool in the wikipedia!! We can track, for example, how many changes are made on different entries over time. We can check whether there are some generalities, how the number of edits depends on the time gone after the historic event, maybe we can quantify how successive stories differ from each other and whether there are turning points that dramatically change the whole thing...

So this is the general framework. I think this is a very exciting topic and I'd be glad to talk about this with anyone!! Just contact me! -- [[Luís_Seoane | Luíño]]

So this is the book I told you about: http://www.amazon.com/The-Evolution-of-God-ebook/dp/B002AKPEHW/ref=sr_1_1?ie=UTF8&qid=1370537236&sr=8-1&keywords=the+evolution+of+god [[Pablo_Galindo]]

You may be interested in related idea about diversification of religion: http://www.sciencedirect.com/science/article/pii/S0022519310004790 -- [[Cesar_Flores_Garcia|Cesar]]

You might be interested in this network approach to history [http://link.springer.com/chapter/10.1007/978-3-642-36844-8_10#page-1] -- [[Giuliano_Andrea_Pagani|Andrea]]

Wiki site [http://tuvalu.santafe.edu/events/workshops/index.php/Unfolding_History here]!

=='''Meta Food Webs'''==

I'd like to throw out an idea I've had for a while: Most animals use space in very important ways -- predators encounter and consume prey in both 2D and 3D environments, birds and fish migrate across continents in search of resources and mates, and plant pollinators fly or walk from flower to flower, in turn providing an indispensable economic service to humans. The study of food webs attempts to understand how networks of species that eat each other persist in the face of (sometimes constant) external perturbations. Yet, network-level food web studies seldom address the dynamics of animal movement, and I see this as a fundamental shortcoming in our understanding of nature. Recently, scientists in fields like computer science, physics and neurobiology have begun to model and explore [http://www.nature.com/srep/2012/120831/srep00620/full/srep00620.html?WT.ec_id=SREP-20120904 multi-level or multiplex networks] -- networks of nested networks. This seems like a reasonable candidate for the theoretical study of multiple food webs that are linked by spatial networks of animal movement. One preliminary question that comes to mind: How do the number of "mobile" species and the "speed of movement" alter important dynamical properties of complex food webs at larger spatial scales (i.e. at the meta-food web scale)? I am not dead set on answering this question, and I look forward to gaining insight from scientists who study other types of networks. I'm also not set on the multiplex network framework. Potential alternatives that come to mind are IBMs, PDEs on graphs or integrodifference equations. I look forward to any suggestions or bright ideas! --[[Ashkaan_Fahimipour | Ashkaan]]

Very cool topic. Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''(Evolution of) Aging'''==
Sorry that this one is a bit long. I'd like to brainstorm with anybody interested to see if there could be a viable project in the following direction.

Let me first define aging: deterioration that happens as an organism, e.g. a human being, gets physiologically older, eventually leading to increased mortality and/or decreased fecundity.

Some background into the 'classic' theory: Evolution is about getting to be there in the future, that is, you and/or related organisms, for instance offspring. Increased mortality and decreased fecundity as such are clearly unfavorable to getting to be there in the future. Then why could it evolve? Well, evolution tends to become less sensitive to anything happening to an organism as time progresses, because events that take place at some point in time can affect only events that are future to that event. All offspring that an organism already has at some point cannot be affected anymore, and this is a non-decreasing function of time. This can be formalized, and I'd be happy to write down the math if anybody wonders.

It has, however, limited value to theorize too much about age-specific events, while in fact events at different ages are tied together in pathways of causality, dynamic change and so on; age per se is not a cause of anything, and changes at some age do not happen independent of changes at other ages. There are a number of sufficient arguments why the 'age-specific' picture does not capture this reality. I'm skipping these arguments for now, but ask if you are interested.

We have two things that matter for the evolution of aging. 1. The declining sensitivity of fitness to age-specific changes (of some standardized magnitude). 2. The fact that there are constraints that make that what happens at age x is not independent from what happens at the ages in its neighborhood. Thus, the trick is to figure out what the constraints are - this is where complexity may come in - and to combine these with the effect on fitness that age-related change has. The effect on fitness may be solved analytically, but there are various reasons why computation may be preferable, specifically the not always realistic assumptions that are necessary to allow for analytical solutions.

Mechanistically, people tend to think about aging in two ways. The first is that aging is caused by the accumulation of damage. If this damage were all repaired, aging would not occur. People then try to think of reasons why repair would be imperfect. The second way to think about it is as a gradual loss of robustness/control, sometimes in the context of reliability engineering (is anybody familiar with that?). Beautiful medical example: old people need more insulin to process a standardized dose of sugar, and their regulation shows more peaks, especially upward peaks, than that of young people, who tend to need less insulin to process the standardized dose of sugar. Of course, if you consider loss of control as a type of damage, the two are the same, but the distinction is perhaps helpful because the way people tend to think about damage is not in a dynamical way, but just as protein aggregates sitting in the brain, inhibiting the function, cartilage that looses its suspension, etcetera. Again of course, both may influence each other.

Now toward a project proposal. If I think about how complexity may (in part) determine physiological constraints, I think of the following. Usually people tend to think of repair being limited by available energy. But to repair something, the body needs to have available somewhere the information necessary to restore the initial state, and use that information at the place where the damage has occurred to be able to repair. This is where I hypothesize complexity comes in. The necessity of different components of the body to interact may put constraints on repair other than just energetic, it is also a question of whether the energy can actually be used for the repair (flow through the system in the necessary way). That may require space, a certain chemical environment, hormonal setting etcetera that may be incompatible with the proper function of an organism. (Can you repair a car when it is driving?) Also in the 'control/robustness thinking', you have to get back to the original situation to avoid aging. Is that compatible with the best evolutionary outcome?

These are just some ideas I'm throwing at you, as you see it's not perfectly fleshed out yet, which is good, because it should benefit from your perspective. So anybody interested, please let me know!

Cheers,
Maarten

Neat ideas & I welcome more discussion around these topics. Aging is cool from the academic science side, if not from the personal experience side, lol. It seems to me that these same models/concepts for aging also apply to loss of functionality from chronic illness... illness expedites aging? – [[Kristen_Honey | Kristen Honey]]

==Quantifying Synchrony in Dynamics Occuring on Networks==

[http://arxiv.org/pdf/1110.2724v1.pdf Recent work] has focused on developing information theoretic measures for quantifying directed information transfer, with particular applications to social media. These metrics are motivated by the work being done in theoretical / computational neuroscience on the analysis of spike trains. To do this analysis, the behavior of users on a social media platform like Twitter are treated as point processes, where we only keep track of when a tweet occurs, and ignore its content. That is, we treat a user's behavior over time as 'spikes.' Despite the simplicity of the approach, it was found to be successful in identifying key actors within real social networks.

I am interested in applying a similar methodology, but using a [http://arxiv.org/abs/q-bio/0609008 different measure] of synchrony motivated by computational mechanics. This method seeks to learn the hidden states that generate a user's behavior (very much in the flavor of a Hidden Markov Model, but with a few key twists), and then considers the mutual information between the state sequences of the two users.

A first step for this project would be implementing the methodology proposed by Shalizi, et al., on the toy model proposed by Steeg, et al.

If that is successful (and completed quickly), I have a data set (network connections and behavior) of fifteen thousand Twitter users collected over a three month period. We are interested in using this approach to identify dynamical communities (not only users who are connected, but users who behave in synchrony) within the social network. This takes us beyond typical structural community detection that has had great success in the past decade.

These approaches should work with any sort of dynamics occurring on top of a network-type structure, so if you have a different system you would like to use as a test case, I would be very interested to hear about it!

[[David_Darmon | Dave Darmon]]

===A spin off?===

Sorry for editing in your proposal, Dave, but I wanted to comment an idea I have been interested in for a time now. There is this great technique used in neuroscience to pin down the most effective time-course excitation that a neuron can get so that it fires. It basically averages the input a neuron had been getting before each of its spikes. You can find a thorough description in the very popular [http://www.amazon.com/Theoretical-Neuroscience-Computational-Mathematical-Modeling/dp/0262541858 Dayan & Abbott] book on neuroscience. Since you mention the abstraction from tweets to spikes, I would be very interesting in applying such neuro-inspired analysis to this social interactions. Neuroscience has got many more techniques, so I do not pose it as a closed matter. Just open for discussion, but seems like everybody is sleeping by now ;) -- [[Luís_Seoane | Luíño]]

You're referring to the spike-triggered average? I hadn't thought of that!

All of the work I've done has only considered a single user's time series for prediction. I would certainly be interested in looking at how including the 'inputs' to the user (or at least the inputs that occur on Twitter) impact this process. The spike-triggered average seems like a great first start. Computational mechanics also has some tricks in its toolbox that could be used for this sort of input-output problem. -- [[David_Darmon | Dave D]]

===comment on spin off===
Hi, I used spike-triggered averaging (and higher-dimensional extensions, which might be useful in your case) during my thesis, so I would be interested in talking about the application to other systems. [[Rebecca_Mease| Rebecca]]

Great! The folks interested in this project will be meeting during the 3pm time slot today. We don't have a formal meeting place planned: the best I can say is to look for me!

[[David_Darmon | Dave D]]

Hi there!! Is this group still meeting? I remain interested in many aspects of the project. Would you like to talk maybe tomorrow at SFI or afterwards? -- [[Luís_Seoane | Luíño]]

Yes, we are still meeting! I'm hoping to put together a project page soon. We should definitely meet at during the project block at SFI. [[David_Darmon | Dave D]]

===Project Page===

The project page may be found here: [http://tuvalu.santafe.edu/events/workshops/index.php/Synchrony_on_Networks].

=='''Energy resources supply patterns from biological systems to humans'''==

My idea is to start a brainstorming, it is nothing more than some disjoints thoughts!!! And many questions without an answer so far!! :-)

I would like to investigate how biological systems obtain their energy requirements. Are there patterns or network structure that evolution has developed and that are efficient for animals/plants?
Can we replicate these structures/networks/patterns in the way we (humans) obtain our energy? Can we learn something from the evolution of the energy provisioning of other species? Is that feasible?
My primary idea (given my research bias) is to then apply the findings to the structure of the electrical system. Is the current centralized generation and long distance distribution something that appears in nature? Is there a more efficient way that emerged from evolution in biological context that we can use for future provisioning?

We can apply this not only to electrical systems but more in general to the way we use our resources.

Anyone interested with ideas, feedbacks, thoughts? – [[Giuliano_Andrea_Pagani | Andrea]]

Ecological networks are, indeed, finely structured both topologically and energetically. I'd very much like to talk to you about this idea in more detail. --[[Ashkaan_Fahimipour | Ashkaan]]

Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Cellular morphogenesis - The evolution of organisms' shape'''==

I am interested in genetic design, not as much the modifications of already existing plants and animals but rather the capabilities of from-the-ground-up design of completely new organisms. One of the most basic question when it comes to multicellular organisms is how they end up with their particular shape and how it is a product of cell growth, membrane adhesion, chemical signalling etc. I suggest a project where we explore what types of shapes can emerge in simple cell growth models and how the shape can be controlled by tuning the organisms genes, the interactions. When we have something running, one interesting continuation would be to apply genetic algorithms on the growth parameters and se what happens with the emerging shape if we for example assign high fitness to high surface area but low volume, high moment of inertia or maybe concentric shells of different cell types. We can also compare our results with simple, real organisms and se if nature found similar solutions (shapes).

There are different cellular models we could use, most reasonable would be a cellular potts model (B) or a vertex dynamic model (D) [http://ars.els-cdn.com/content/image/1-s2.0-S0070215309890042-gr4.jpg], depending on what type of details we want to include. I suggest we start out with 2D simulations.

I also believe this project can steer into many different directions, so if you like parts of the premise and have ideas on other directions we could take this, say hi.

Max Planck instutute with a group on this subject: [http://www.mpipz.mpg.de/smith]

A vertex dynamics model investigating how a specific cell morphogenesis could occur: [http://dev.biologists.org/content/113/4/1231.full.pdf+html]

[[Oskar_Lindgren | Oskar]] email me at oskarxvi at gmail dot com

=='''How big can a city be?'''==

West et al. have discovered striking—and universal—patterns in the way cities scale with size (see [http://www.ted.com/talks/geoffrey_west_the_surprising_math_of_cities_and_corporations.html West's Ted talk], [http://www.nature.com/nature/journal/v467/n7318/abs/467912a.html short Nature paper], [http://www.pnas.org/content/104/17/7301.short longer PNAS paper]). Do these scaling laws allow us to predict how big a city can be?

Here's a motivating analogy. The mass of an animal grows scales the cube of its size L, but the cross-sectional area of its leg bones scales only like the square of L. This implies that bigger animals must have bulkier leg bones in order to sustain their own weight. (Think of the legs of a mouse versus the legs of an elephant.) Since the bones can never get bigger than the animal itself, this immediately tells you that land animals cannot be arbitrarily large: they must have a maximum size. If you plug in the numbers and estimate this maximum size, you find a value consistent with the largest known dinosaurs. In fact, with similar reasonings—which were discovered by Galileo, by the way—you can easily find how tall trees can be, how high animals can jump, etc [http://galileo.phys.virginia.edu/classes/304/scaling.pdf].

Now, to run a similar argument for cities, we should understand what constraints would limit their size (the equivalent of "the legs of an animal can never be larger than the animal itself"). These constraints may be technical, social—I'm not sure. (Crimes are perhaps an example. West et al. show that the number of crimes committed in a city grows faster than the number of inhabitants. Clearly then, at some point the likelihood to get shot the next day will get too high, and people will start leaving the city.) I wonder if the social scientists among us have any insight about such constraints, and whether we can actually come up with a prediction for the maximal size of a city based on them. – [[Matteo_Smerlak | Matteo]]

- Scaling patterns for cities are fascinating, but a potential data limitation to the PNAS paper is that the study was applied to cities in the US, EU and China. It can be argued that these economies have particular similarities that may not be transferable to cities in developing countries that are not China (e.g. Jakarta, Delhi, Manila). To complicate matters a bit more, there is little consensus on what a city is -- is it defined by the political boundary? What about the economic boundary determined by bedroom communities (suburbs)? If one takes the latter view of a metropolitan area, the population densities of some "cities" in developing countries is truly astounding. The New York metropolitan area can be interpreted as spanning 4500 sq. miles with 20 million people (a density of ~4600 people/sq. mile). Under the same interpretation, Jakarta spans only 1075 sq. miles with 25 million people (a density of ~25,000 people/sq. mile!!!). The point of my comment is that I wonder how well the scaling findings of West et al. hold up for cities in developing countries (that do not include China). It seems possible that there are scaling patterns there as well, but they might be different. By the way, I got my numbers for population densities from [http://www.newgeography.com/content/002808-world-urban-areas-population-and-density-a-2012-update Demographia]. --[[Vanessa_Schweizer | Vanessa]]

- Because of national differences, there's certainly no consensus yet on how to define the boundaries of a city. Even [http://unstats.un.org/unsd/demographic/sconcerns/densurb/densurbmethods.htm UN] recognizes this and suggests following the boundaries established by individual countries. On the point of whether scaling patterns will be the same for developed and developing countries, the scaling patterns might still be the same (wealth creation leads to superlinear scaling while economies of scale results to sublinear scaling) but the actual value of the scaling exponents might vary. It would be interesting to see whether such two sets of exponents exist as it might explain why the experience of living in two cities of the same density can be different (case in point Manila with a pop'n density of 21.9 M vs Shanghai or NY with 20.9 M). To quantify the living conditions/living experience of cities, we can use the [http://www.businessweek.com/news/2012-08-15/melbourne-remains-most-liveable-city-in-the-world Economist Intelligence Unit’s 2012 Global Liveability Survey]. If data is now available for developing countries, it wouldn't be hard to check this. But having lived in Manila and seeing how inefficient collection of census data in such cities can be, I doubt if we can have a substantial sample of developing countries with complete data. We can probably check [http://www.quandl.com/ here].

As for setting the thresholds in computing for the maximal city size, we can use the parameter values for Melbourne as according to the EIU survey, it is the most livable city in the world. If somehow we decide that using this is not a good way of defining the thresholds and there's no other way of setting them, jumping off from Vanessa's point, what we can also do is have several sets of parameter constraints and say that if city A falls under category A with parameter constraints {A}, then this is the maximal size it can have. We can do some clustering analysis of the parameter space to determine the city categories. I think it would be worthwhile to talk to someone from the cities group here in SFI as they've already mentioned before how population growth behaves with the different scaling patterns.--[[Cheryl Abundo | Cheryl]]

— Maximal city size is an interesting question and hard to answer with the boundary problem mentioned by Vennesa and Cheryl— Michael Batty also talks about this problem in 'Cities and Complexity' http://www.amazon.com/Cities-Complexity-Understanding-Cellular-Agent-Based/dp/0262524791. In biological organisms the upper limit is bounded not only by the cross sectional area of bones but also by the metabolic rate which slows down as an organism increases in size to a 3/4 power law (Klieber, West et al.) Metabolism in organisms is basically how ''efficient'' an organism is. What would be the corresponding metabolism of a city? Here is an idea: What if 'urban metabolism' were to be measured as wealth distribution (correlating with the distribution of blood in an organism)? Functional organisms distribute blood to all service volumes and limit non-essential ones when in pathological states. Crime, as you mention Matteo, increases super-linearly and one might very well imagine a large city becoming too dangerous to function— such as the LA riots or something. Perhaps this is like pathology in organisms where crime is, in essence, the system attacking itself, i.e. cancer, immune disorders etc.

West et al. have also found that infrastructure increases sub-linearly with population size making a city, at least physically, more efficient the larger it becomes. Here is a quote from the paper 'A Unified Theory of Urban Living':

“Cities manifest remarkably universal, quantifiable features. This is shown by new analyses of large urban data sets, spanning several decades and hundreds of urban centres in regions and countries around the world from the United States and Europe to China and Brazil. Surprisingly, size is the major determinant of most characteristics of a city; history, geography and design have secondary roles. Three main characteristics vary systematically with population. One, the space required per capita shrinks, thanks to denser settlement and a more intense use of infrastructure. Two, the pace of all socio- economic activity accelerates, leading to higher productivity. And three, economic and social activities diversify and become more interdependent, resulting in new forms of economic specialization and cultural expression. We have recently shown that these general trends can be expressed as simple mathematical ‘laws’. For example, doubling the population of any city requires only about an 85% increase in infrastructure, whether that be total road surface, length of electrical cables, water pipes or number of petrol stations. This systematic 15% savings happens because, in general, creating and operating the same infrastructure at higher densities is more efficient, more economically viable, and often leads to higher-quality services and solutions that are impossible in smaller places. Interestingly, there are similar savings in carbon footprints7,8 — most large, developed cities are ‘greener’ than their national average in terms of per capita carbon emissions. It is as yet unclear whether this is also true for cities undergoing extremely rapid development, as in China or India, where data are poor or lacking.
Similar economies of scale are found in organisms and communities like anthills and beehives, where the savings are closer to 20%. Such regularities originate in the mathematical properties of the multiplenetworks that sustain life, from the cardiovascular to the intracellular. This suggests that similar network dynamics underlie economies of scale in cities” (West, Bettencourt, A Unified Theory of Urban Living 2010).

I have been developing a tool in NetLogo to measure the fractal dimension of cities which, together with other metrics such as density, could afford an appropriate means to gauge the efficiency of various cities with the assumption that higher fractal dimension = more efficient distribution networks. I am interested in simulating cities with genetic algorithms and dimensioning the results— this technique could possibly support an endogenous limit to growth hypothesis using some fitness criteria such as the EIU parameters. Ecological services certainly decrease with city size and has prompted West to suggest that innovation must increase at an ever faster rate to offset the negatives imposed by growth. Here is another quote from West et al.:

“Open-ended growth is the primary assumption upon which modern cities and economies are based. Sustaining that growth with limited resources requires that major innovations — such as those historically associated with iron, coal and digital technology — be made at a continuously accelerating rate. The time between the ‘Computer Age’ and the ‘Information and Digital Age’ was some 20 years, compared to thousands of years between the Stone, Bronze and Iron Ages.Making major technological paradigm shifts systematically faster is clearly not sustainable, potentially leading to collapse of the entire urbanized socio-economic fabric. Avoiding this requires understanding whether we can continue to innovate and create wealth without continuous growth and its compounded negative social and environmental impacts” (West, Bettencourt 2010).

Fractal dimension applied to cities is still in its infancy and I wonder if this metric itself is necessary to refine relative to the questions this project presents. Multi-fractals for instance are a more nuanced metric and have not been applied to cities to my knowledge. [[John Driscoll | John Driscoll]]

'''To those still interested in discussing this further, I suggest we meet at lunch time later (6 June, 12pm)''' -Cheryl

Somewhat relevant data viz of [http://bostonography.com/2013/live-mbta-bus-speeds/ bus speeds in Boston]. Probably replicable for many other cities too, and tells us something about city topology. --David

=='''PRISM / NSA'''==

New media accounts are talking about the scale of the US National Security Agency's surveillance program (Hey, NSA folks!). It looks like they're running some network analysis with >70 trillion (not a typo) edges. We've got a good group of network people here. Anyone want to do something topical and try to put together a discussion / estimation of what can and can't be done with data that big? -- David

Any website with info about this? Someone interested to meet over this topic? -- [[Luís_Seoane | Luíño]]

Interesting topic, let me know when/if you wanna discuss about it -- [[Giuliano_Andrea_Pagani | Andrea]]

Maybe an old and not so scientific [http://www.slate.com/articles/news_and_politics/explainer/2006/05/how_the_nsa_does_social_network_analysis.html article]

=='''Evolutionary Dynamics and Fitness Landscapes'''==

After some extra investigation of the model presented by Tom in his talk this afternoon, we actually found some very interesting structure in the population that survived in the end - there are always pure solutions with exactly four genotypes. We have the impression that it could lead to a more formal treatment of this solution.

For those who haven't attended the lecture, the idea is the following: we start with a uniformly distributed population of genotypes (a string of 0s and 1s) and every organism always chooses to mate (cross-over + random point mutations) with the '''most different''' (according to a Hamming distance) organism nearby (there is a spatial structure). The fitness is not explicit, which makes the model somewhat more interesting!

Due to the symmetry, the corresponding landscape has several peaks with the same height, and according to the mutation rate there are some attractors which we think may be related to eigenvectors. We believe we could derive an [http://en.wikipedia.org/wiki/Error_threshold_(evolution) error threshold] for that model.

If anybody is interested in discussing with us informally and/or joining this group, it would definitely contribute a lot!

Bruno

''This sounds fun but I'm not exactly sure what you have in mind. Hope to discuss at meals!! -Mengsen.''

Count me in, yes! :) – [[Kristen_Honey | Kristen Honey]]

Complex Systems Summer School 2013-Blog

2013-06-12T15:38:07Z

Masad:

{{Complex Systems Summer School 2013}}

Use this page as an informal forum to share your opinion and discuss anything at CSSS'13.

Students are encouraged to share their observations, insights, and opinions about daily lecture content as well as extracurricular activities.

Post your own links to notes, interesting articles, and anything else you think might contribute to the program.
----

The origins of Robby the Robot: the 1956 sci-fi classic Forbidden Planet. For you Shakespeare fans, it's a retelling of The Tempest. --Manish

[[File:Poster - Forbidden Planet 03.jpg|400px]]

----

For those of you interested in modeling cities, here [[http://www.economist.com/blogs/babbage/2013/06/urbanisation]] is a nice article in the Economist from today (June 6th)- Swati
----

[http://badhessian.org/ Bad Hessian], a computational sociology blog.

I think I may have mentioned it to several people, but Google Earth Engine is basically the last 20 years of Landsat imagery on a Google Earth / Google Maps interface. It very compellingly demonstrates the explosive growth over the past 20 years. http://earthengine.google.org/#intro -- [[JP]]

''Click on Las Vegas or Dubai or something like that to go to the applet''

----

As requested, here is "I Have No Mouth, and I Must Scream." A possible "worst case" unfriendly AI scenario (far worse than Skynet). Warning: You might find it disturbing. I added a bit of color, and included the punchcode images from the original work: [http://complextropy.com/nomouth/ I Have No Mouth, and I Must Scream] --[[Nix_Barnett | Nix]]

----

Since Dr. Hubler is illustrating video feedback, you might like to see this video that Jim Crutchfield made in 1984 on the nonlinear dynamics of video feedback: [https://www.youtube.com/watch?v=B4Kn3djJMCE video] --[[Nix_Barnett | Nix]]

----

For anyone who was wondering: the [http://www.amazon.com/Accoutrements-11761-Yodelling-Pickle/dp/B0010VS078/ref=sr_1_1?ie=UTF8&qid=1370537203&sr=8-1&keywords=yodeling+pickle yodelling pickle]

* Yodeling Pickle had something to say about free will. Unfortunately, no-one takes her seriously due to the language barrier. :( I wonder if someone has tried tossing her into an FMRI... --[[Nix_Barnett | Nix]]

----

Like the rule 110 elementary cellular automaton, Conway's Game of Life is Turing complete. This means you can 'build a computer' in the 'universe' that is Conway's Game of Life that can compute 'anything.' This person built a computer that implements Conway's Game of life... *in* Conway's Game of Life: [https://www.youtube.com/watch?v=xP5-iIeKXE8 Life in Life] --[[Nix_Barnett | Nix]]

----

Here is the trailer for the movie that came out in 2012 about when a group of four men prove that P=NP. [[http://www.youtube.com/watch?v=6ybd5rbQ5rU]]

----

A proof of the halting state problem, written in the style of Dr. Seuss. [http://ebiquity.umbc.edu/blogger/2008/01/19/how-dr-suess-would-prove-the-halting-problem-undecidable/ Scooping the loop snooper]

Complex Systems Summer School 2013-Schedule

2013-06-11T06:06:03Z

Masad:

{{Complex Systems Summer School 2013}}

To access a mobile app of the schedule, logistics, and faculty list please use your mobile device to visit: http://my.yapp.us/Z53CQX

Please plan to arrive June 2 and depart on June 29, 2013

The program lectures will be held from June 3 to June 28, 2013

Please note that dormitories will only be available from June 2 to June 29, 2013

'''For a list of local happenings in Santa Fe visit: http://www.santafe.com/'''



{| border="1" cellpadding="2"
! scope="col"width="100" align="center | Time
! scope="col"width="700" align="center | Activity

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 2
|-
|
|All events at St. John's College Unless Otherwise Noted
|-
|width="15%" | 11:00 p.m. - 5:00 p.m.
|Registration and check-in at [http://conferenceservices.sjcsf.edu/map.htm St. John's College in the Peterson Student Center.]
|-
|5:30 p.m. - 8:30 p.m.
|Welcome Reception & Dinner in [http://conferenceservices.sjcsf.edu/map.htm Peterson Student Center (upstairs) in Junior Commons Room]

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 3

|-
|width="15%" |9:00 a.m. - 9:30 a.m.
|Welcome and Introduction by CSSS Director [http://santafe.edu/about/people/profile/Sander%20(F.A.)%20Bais Sander Bais]

|-
|9:30 a.m. - 10:45 a.m.
|[http://santafe.edu/about/people/profile/Melanie%20Mitchell Melanie Mitchell] - Introduction to Complexity
|-
|10:45 a.m. - 11:00 a.m.
|Break
|-
| 11:00 a.m. - 12:15 p.m.
|Melanie Mitchell - Introduction to Complexity
|-
|12:15 p.m. - 1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Alfred%20H%C3%BCbler Alfred Hubler] - Physics Lab Introduction
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Student Introductions
|-
|4:15 p.m. - 5:00 p.m.
|Navigating the Complex Systems Summer School
|-
|5:00 - 6:30 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 4
|-
|9:00 a.m - 10:15 a.m.
|Melanie Mitchell - Introduction to Complexity
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Elizabeth%20Bradley Liz Bradley] - Dynamics I
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://csel.cs.colorado.edu/~garlanjt/ Joshua Garland], Computer Lab I: Maps & Flows
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://www.santafe.com/blogs/andrew-lovato Andrew Lovato], Introduction to Santa Fe
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|-
|6:45 p.m.
|Shuttle leaves for David Eagleman Public Lecture at James A. Little Theater
|-
|7:30 p.m. - 8:30 p.m.
|[http://www.eagleman.com/ David Eagleman], Public Lecture - The Brain and the Law
|-
|9:00 p.m.
|Shuttle departs to St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 5
|-
|9:00 a.m - 10:15 a.m.
|Liz Bradley, Dynamics II
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Alfred Hubler, Physics Lab Introduction
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Liz Bradley - Dynamics III
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - p.m.
|Brainstorming on Projects
|-
|4:00 p.m. - 5:00ish p.m.
|Optional Meeting for groups interested in network evolution / genetic algorithms / information transfer / attacker robustness - large lecture hall
|-
|4:00 p.m. - 5:00 (?) p.m.
|Optional [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]] on [http://arxiv.org/abs/0912.5352 cross-impact balances] and Markov chains - large lecture hall

|-
|5:00 p.m. - 6:00 p.m.
|Dinner / Discussion for people with an interested in global risk at dining hall
|-
|5:30 p.m. - 7:30 p.m.
|[[ Physics Lab 2013 | Lab Section I ]]

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 6
|-
|9:00 a.m - 10:15 a.m.
|Joshua Garland - Data Analysis Lab
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Liz Bradley - Dynamics IV: Applications
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Andreas%20Wagner Andreas Wagner], Evolution
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Introduction to Student Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|5:30 p.m. - 7:30 p.m.
|[[Physics Lab 2013 | Lab Section II ]]

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 7 at '''Santa Fe Institute'''
|-
|8:30 a.m
|Shuttle leaves St. John's to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|Andreas Wagner, Evolution
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Andreas Wagner, Evolution
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Time to work on Projects
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 3:30 p.m.
|Tea with SFI Community
|-
|3:30 p.m. - 4:45 p.m.
|Sander Bais - Symmetry Breaking as a Road to Diversity
|-
|5:00 p.m. - 7:30 p.m.
|BBQ at SFI
|-
|8:00 p.m.
|Shuttle leaves SFI and goes back to St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 8

|-
|9:00 a.m - 5:00 p.m.
|Unofficial trip to Bandelier National Monument
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 9
|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 10

|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Mercedes%20Pascual Mercedes Pascual], Emergence: case studies on pathogen diversity from an ecological perspective
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Mercedes Pascual, Anticipating critical transitions: model-free approaches and spatial considerations in ecological and epidemiological systems.

|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Jessica%20Flack Jessica Flack] - Robustness and Resilience
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Jessica Flack - Robustness and Resilience
|-
|5:30 p.m. - 7:30 p.m.
|[[Physics Lab 2013 | Lab Section III]]
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|6:30 p.m. - 7:30 p.m.
|[[Complex_Systems_Summer_School_2013-Tutorials#Python | Intro to Python workshop]]
|-
|-
|7:45 p.m.
|NetLogo workshop with tom
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 11

|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Cristopher%20Moore Cris Moore] - Algorithms and Landscapes
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| Cris Moore - NP-Completeness and the P vs. NP Question
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/John%20German John German], Science Writing Seminar
|-
|2:45 p.m. - 3:00 p.m.
|Vote on CSSS 2013 T-Shirt
|-
|3:00 p.m. - 4:15 p.m.
|Time to Work on Projects -- Tutorial on Genetic Algorithms & Multi-Objective Optimization.
|-
|5:30 p.m. - 7:30 p.m.
| [[Physics Lab 2013| Lab Section IV ]]
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 12

|-
|9:00 a.m - 10:15 a.m.
|Cris Moore - Monte Carlo Algorithms and Phase Transitions
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| Cris Moore - The Power of Randomness
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Time to work on projects
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/Clio%20Andris Clio Andris], Introduction to Networks
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Evening Lecture - [http://santafe.edu/about/people/profile/John%20Harte John Harte] - Theoretical Ecology
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 13

|-
|9:00 a.m - 10:15 a.m.
|Cris Moore, Quantum Computation
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Jennifer%20A.%20Dunne Jennifer Dunne] - Ecological Networks
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Jennifer Dunne - Ecological Networks
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/James%20P.%20Crutchfield Jim Crutchfield] - Complexity
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|6:30 p.m. - 8:00 p.m.
|[Jim Crutchfield and [http://complextropy.com/cv.html Nix Barnett] - Complexity Lab
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 14 at '''Santa Fe Institute'''

|-
|8:30 a.m
|Shuttle leaves St. John's to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|Jim Crutchfield - Complexity
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| Jim Crutchfield - Complexity
|-
|12:00 p.m. - 1:45 p.m.
|Lunch
|-
|1:45 p.m. - 3:00 p.m.
|Time to work on projects
|-
|3:00 p.m. - 3:30 p.m.
|Tea w. SFI community
|-
|3:30 p.m. - 4:30 p.m.
|Panel Discussion on General Questions on Complexity
|-
|5:00 p.m.
|Shuttle back to St. John's College
|-
|5:30 p.m. - 6:00 p.m.
|Dinner at St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 15

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 16
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 17
|-
|9:00 a.m - 10:15 a.m.
|Clio Andris - Cities Project
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| [http://santafe.edu/about/people/profile/Marcus%20J%20Hamilton Marcus Hamilton] - Cities Project
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Elhanan Borenstein - Modeling Microbial Metabolism
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/Elhanan%20Borenstein Elhanan Borenstein] - Modeling Microbial Metabolism
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 18
|-
|9:00 a.m - 10:00 a.m.
|Time to Work on Projects
|-
|10:00 a.m. - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Ginger%20Richardson Ginger Richardson] - Omidyar Fellowship Presentation
|-
|10:45 am - 12:00 p.m.
|Time to work on projects
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://tuvalu.santafe.edu/~simon/ Simon DeDeo] and [http://santafe.edu/about/people/profile/James%20O'Dwyer James O'Dwyer]
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
| Simon DeDeo and James O'Dwyer
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 19
|-
|9:00 a.m - 10:45 a.m.
|Time to work on Projects
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Laura%20Fortunato Laura Fortunato] - Cultural Evolution
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Simon DeDeo and James O'Dwyer
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to Work on Projects or (optional) Simon DeDeo-Reductionism, Naturalism, and Undecidability- in the Junior Commons Room
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 20
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Cosma%20Shalizi Cosma Shalizi]
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Cosma Shalizi - Statistics and Machine Learning
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Time to work on projects
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to work on projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Evening Lecture: [http://santafe.edu/about/people/profile/Tanmoy%20Bhattacharya Tanmoy Bhattacharya] -Infectious Disease
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 21 at '''Santa Fe Institute'''

|-
|8:30 a.m
|Shuttles leave St. John's College to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|Cosma Shalizi - Statistics and Machine Learning
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Cosma Shalizi - Statistics and Machine Learning
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 3:00 p.m.
|Time to work on projects
|-
|3:00 p.m. - 3:30 p.m.
|Break
|-
|3:30 p.m. - 4:30 p.m.
|Glue Session with Sander Bais
|-
|5:00 p.m.
|Shuttle back to St. John's
|-
|5:30 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 22
|-
|8:00 p.m - 12:00 a.m.
|2013 CSSS Dance with Breadloaf workshop in St. John's College Coffee Shop
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 23
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 24
|-
|9:00 a.m - 10:15 a.m.
|[http://tuvalu.santafe.edu/~aaronc/ Aaron Clauset], Networks I
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Aaron Clauset, Networks II
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Scott%20Ortman Scott Ortman] - Evolution of Social Complexity
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Evening Lecture - [http://santafe.edu/about/people/profile/Geoffrey%20West Geoffrey West], Cities
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 25
|-
|9:00 a.m - 10:15 a.m.
|Aaron Clauset - Networks III
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://tuvalu.santafe.edu/~ole/ Ole Peters] - Non-Ergodic Economics
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Aaron Clauset - Networks IV
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Ole Peters - Non-Ergodic Economics
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 26
|-
|9:00 a.m - 10:15 a.m.
|[http://www.css.gmu.edu/?q=node/27 Rob Axtell] - Modeling Financial Markets
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Rob Axtell - Modeling Financial Markets
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Aaron Clauset, Human Social Dynamics and Online Competition
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|6:45 p.m.
|Shuttle leaves for Leonard Susskind Public Lecture at James A. Little Theater
|-
|7:30 p.m. - 8:30 p.m.
|[https://physics.stanford.edu/people/faculty/leonard-susskind Leonard Susskind] Public Lecture - The Cosmic Landscape
|-
|9:00 p.m.
|Shuttle departs to St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 27
|-
|9:00 a.m - 4:15 a.m.
|Day to work on presentations
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 28 at '''Santa Fe Institute'''
|-
|8:30 a.m
|Shuttle leaves St. John's College for SFI
|-
|9:00 a.m - 10:15 a.m.
|Presentations
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Presentations
|-
|12:00 p.m. - 1:00 p.m.
|Lunch
|-
|1:00 p.m. - 1:15 p.m.
|Group Photo
|-
|1:30 p.m. - 3:00 p.m.
|Presentations
|-
|3:00 p.m. - 3:30 p.m.
|Break
|-
|3:30 p.m. - 5:00 p.m.
|Presentations and Closing Remarks
|-
|5:00 p.m. - 7:00 p.m.
|Farewell BBQ at SFI
|-
|7:30 p.m.
|Shuttles go back to St. John's
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 29
|-
|10:00 a.m.
|Check-out and departure (don't forget to return your keys!)
|-

Complex Systems Summer School 2013-Tutorials

2013-06-11T02:46:55Z

Masad:

{{Complex Systems Summer School 2013}}

CSSS participants come from a wide range of disciplines. Participants are encouraged to share their knowledge by organizing their own tutorials.

Also, please post requests for tutorials here.

This is not a Tutorial! I [[Pablo_Galindo]] had nowhere else to post it! Its an article pointing out 15 mistakes that could sink your academic careers!
http://chronicle.com/article/Self-Sabotage-in-the-Academic/138875/

'''Network Visualization Using Gelphi'''
I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai | Hua]]
I'm in -- Mauricio

* Hua, thanks!. I'm in! [[Regina_Martinez | Regina]]

'''Bayesian Modeling'''
I'd love to attend tutorials on Bayesian Modeling. I will be happy if someone can give a series of tutorials on this topic. [[Reniel_Cabral | Ren]]

I would also be interested in this! -Brady
same here! [[Ivana_Stankov | Ivana]]
* I'm in -- Mauricio

* I might be able to help with this, though likely in more of a discussion format, perhaps with some slides stolen from a colleague :) [[Nix_Barnett | Nix]]

* Thanks [[Nix_Barnett | Nix]]! [[Reniel_Cabral | Ren]]

* I'm in! Thanks. [[Regina_Martinez | Regina]]

'''Dynamics in Networks'''

I am very interested in learning about network dynamics. Anyone else interested in having a tutorial on that? [[Regina_Martinez | Regina]]

* I'm very experienced with hidden Markov models, which are a generalization of Markov chains. These are networks with a (potentially stochastic) dynamic. Maybe this would help! [[Nix_Barnett | Nix]]

* [[Nix_Barnett | Nix]], that's great! Many thanks. I'm in for this one and the Bayesian-- Regina
* I'm in -- Mauricio

'''Cross impact balances and Markov chains'''

For anyone who could not make the tutorial, [https://docs.google.com/file/d/0B_w3ogGtuejzVG1Ma2tKenN2QjQ/edit?usp=sharing here is a copy of the slides], which provide another way of interpreting [http://www.cross-impact.de/english/CIB_e_Alg.htm web pages explaining the CIB algorithm]. Note that from the cross-impact balance analysis web site, you can download the free software to play with CIB analysis yourself. I am also happy to talk more one-on-one if needed! --[[User:Vanessas|Vanessas]] 02:24, 6 June 2013 (UTC)

As part of brainstorming for a possible project, three of us have decided to do a tutorial on [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] (delivered by [[Vanessa_Schweizer | Vanessa]]) and Markov chains (delivered by [[Alastair_Jamieson-lane | Alastair]] and [[Matteo_Smerlak | Matteo]]). We think these methods could be leveraged to research some interesting questions. All are invited to this tutorial regardless of their interest in contributing to a project using these methods. This tutorial will be Wed. June 5th at 4:00 PM in the large lecture hall. --[[Vanessa_Schweizer | Vanessa]] 
PS -- For those interested in examples of studies that have used CIB analysis, see this one on [http://iopscience.iop.org/1748-9326/7/4/044011/article century-long socioeconomic scenarios] or this abstract on a [http://link.springer.com/article/10.1007%2Fs10389-011-0473-8 qualitative model regarding obesity development and prevention].

'''Genetic Algorithms and Multi-Objective Optimization'''

I have seen many people interested in implementing GAs to evolve networks, which is something I have done for some of my research. I also worked with Multi-Objective Optimization (MOO), which is perfectly possible with GAs and has been around for a while; but it has not become so mainstream. I propose to make a brief tutorial of classic Genetic Algorithm vs. Multi-Objective Genetic Algorithm. Enough people interested? If we are a few of us, we could just meet up and I'll tell you the basics! -- [[Luís_Seoane | Luíño]]

I would be very interested! --[[Molly_King | Molly]]

Me too --[[Mauricio_Cantor]]

Me too --[[Elena_Stepanova | Elena]]

Me too! --[[Matteo_Smerlak | Matteo]]

Me too --[[Cheryl_Abundo | Cheryl]]

I'm in! [[Regina_Martinez | Regina]]

Yes! [[James_Magdanz | Jim]]

We scheduled this tutorial for Tuesday at 3:00 pm, just before the time to work on projects. Hope that you find it interesting! -- [[Luís_Seoane | Luíño]]

'''Nix's Bag O' Mathematical Tools'''

I'm planning on giving a number of tutorials to supplement Jim Crutchfield and I's lectures. The purpose of these should be to help you with your projects ( and encourage usage of our methods ;) ). I think it'd be cool for people to use this area to suggest topics to focus on. I started an empty bulleted list below. This will become more clear after we've given our lectures, but feel free to throw ideas out there when they come up. General topics might be: Information theory, time series analysis/modeling/prediction, symbolic dynamics (coarse-graining dynamical systems, i.e. what Liz Bradley discussed briefly), hidden Markov models, signal processing, bayesian inference, complexity measures, etc. [[Nix_Barnett | Nix]]
*Intro to information theory. There seems to be some interest in this. I'd be happy to give a tutorial, but I should note that it will be covered (at a rapid pace) in Jim Crutchfield's lecture. [[Nix_Barnett | Nix]]
* I really want to learn how to fit hidden Markov models to data. --David
* I'm very interested, Nix. Many thanks! [[Regina_Martinez | Regina]]
* i'm in!! [[AmaraAl_Sayegh|amara]]
* i'm in also! [[Ivana_Stankov | Ivana]]
* I'm in -- Mauricio

== '''Python''' ==

Downloads:

[http://www.example.com Python] Python (get version 2.*, not 3.*)

[http://ipython.org/install.html IPython]

You can find links to the key scientific packages for Python [http://www.scipy.org/ here]

If you're new to coding, one good resource is [http://www.codecademy.com/tracks/python Codecademy]. [http://learnpythonthehardway.org/ Learn Python the Hard Way] is exactly what it sounds like, and is also good. Finally, Google is your friend, and there's plenty of help online for pretty much anything Python-related.

To launch Python, just open a terminal / command line window and type ''python''. If you've installed IPython, you can open an IPython command line with ''ipython''.

To launch the IPython Notebook, run ''ipython notebook'' -- This will launch a notebook window in your browser. If you close it out, it's probably running at 127.0.0.1:8888 (but check the terminal window). Be sure to save your work, and when you're done shut down the server with command/control-C in the terminal.

If you've installed Matplotlib, you can embed plots in the notebook by launching it as ''ipython notebook --pylab inline''

Notes from the CSSS tutorial are up online [http://nbviewer.ipython.org/urls/raw.github.com/dmasad/CSSS_PythonInto/master/QuickNotes.ipynb here]. I've also put up a quick and dirty [http://nbviewer.ipython.org/urls/raw.github.com/dmasad/CSSS_PythonInto/master/QuickNotes.ipynb implementation of a very basic genetic algorithm in Python].

Complex Systems Summer School 2013-Tutorials

2013-06-11T02:45:47Z

Masad:

{{Complex Systems Summer School 2013}}

CSSS participants come from a wide range of disciplines. Participants are encouraged to share their knowledge by organizing their own tutorials.

Also, please post requests for tutorials here.

This is not a Tutorial! I [[Pablo_Galindo]] had nowhere else to post it! Its an article pointing out 15 mistakes that could sink your academic careers!
http://chronicle.com/article/Self-Sabotage-in-the-Academic/138875/

'''Network Visualization Using Gelphi'''
I will be showing people some basic features of using Gelphi to visualize networks this week. If there are other people who are also interested, we could turn it into a tutorial. -- [[Hua_Cai | Hua]]
I'm in -- Mauricio

* Hua, thanks!. I'm in! [[Regina_Martinez | Regina]]

'''Bayesian Modeling'''
I'd love to attend tutorials on Bayesian Modeling. I will be happy if someone can give a series of tutorials on this topic. [[Reniel_Cabral | Ren]]

I would also be interested in this! -Brady
same here! [[Ivana_Stankov | Ivana]]
* I'm in -- Mauricio

* I might be able to help with this, though likely in more of a discussion format, perhaps with some slides stolen from a colleague :) [[Nix_Barnett | Nix]]

* Thanks [[Nix_Barnett | Nix]]! [[Reniel_Cabral | Ren]]

* I'm in! Thanks. [[Regina_Martinez | Regina]]

'''Dynamics in Networks'''

I am very interested in learning about network dynamics. Anyone else interested in having a tutorial on that? [[Regina_Martinez | Regina]]

* I'm very experienced with hidden Markov models, which are a generalization of Markov chains. These are networks with a (potentially stochastic) dynamic. Maybe this would help! [[Nix_Barnett | Nix]]

* [[Nix_Barnett | Nix]], that's great! Many thanks. I'm in for this one and the Bayesian-- Regina
* I'm in -- Mauricio

'''Cross impact balances and Markov chains'''

For anyone who could not make the tutorial, [https://docs.google.com/file/d/0B_w3ogGtuejzVG1Ma2tKenN2QjQ/edit?usp=sharing here is a copy of the slides], which provide another way of interpreting [http://www.cross-impact.de/english/CIB_e_Alg.htm web pages explaining the CIB algorithm]. Note that from the cross-impact balance analysis web site, you can download the free software to play with CIB analysis yourself. I am also happy to talk more one-on-one if needed! --[[User:Vanessas|Vanessas]] 02:24, 6 June 2013 (UTC)

As part of brainstorming for a possible project, three of us have decided to do a tutorial on [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] (delivered by [[Vanessa_Schweizer | Vanessa]]) and Markov chains (delivered by [[Alastair_Jamieson-lane | Alastair]] and [[Matteo_Smerlak | Matteo]]). We think these methods could be leveraged to research some interesting questions. All are invited to this tutorial regardless of their interest in contributing to a project using these methods. This tutorial will be Wed. June 5th at 4:00 PM in the large lecture hall. --[[Vanessa_Schweizer | Vanessa]] 
PS -- For those interested in examples of studies that have used CIB analysis, see this one on [http://iopscience.iop.org/1748-9326/7/4/044011/article century-long socioeconomic scenarios] or this abstract on a [http://link.springer.com/article/10.1007%2Fs10389-011-0473-8 qualitative model regarding obesity development and prevention].

'''Python'''

Downloads:

[http://www.example.com Python] Python (get version 2.*, not 3.*)

[http://ipython.org/install.html IPython]

You can find links to the key scientific packages for Python [http://www.scipy.org/ here]

If you're new to coding, one good resource is [http://www.codecademy.com/tracks/python Codecademy]. [http://learnpythonthehardway.org/ Learn Python the Hard Way] is exactly what it sounds like, and is also good. Finally, Google is your friend, and there's plenty of help online for pretty much anything Python-related.

To launch Python, just open a terminal / command line window and type ''python''. If you've installed IPython, you can open an IPython command line with ''ipython''.

To launch the IPython Notebook, run ''ipython notebook'' -- This will launch a notebook window in your browser. If you close it out, it's probably running at 127.0.0.1:8888 (but check the terminal window). Be sure to save your work, and when you're done shut down the server with command/control-C in the terminal.

If you've installed Matplotlib, you can embed plots in the notebook by launching it as ''ipython notebook --pylab inline''

Notes from the CSSS tutorial are up online [http://nbviewer.ipython.org/urls/raw.github.com/dmasad/CSSS_PythonInto/master/QuickNotes.ipynb here]. I've also put up a quick and dirty [http://nbviewer.ipython.org/urls/raw.github.com/dmasad/CSSS_PythonInto/master/QuickNotes.ipynb implementation of a very basic genetic algorithm in Python].

'''Genetic Algorithms and Multi-Objective Optimization'''

I have seen many people interested in implementing GAs to evolve networks, which is something I have done for some of my research. I also worked with Multi-Objective Optimization (MOO), which is perfectly possible with GAs and has been around for a while; but it has not become so mainstream. I propose to make a brief tutorial of classic Genetic Algorithm vs. Multi-Objective Genetic Algorithm. Enough people interested? If we are a few of us, we could just meet up and I'll tell you the basics! -- [[Luís_Seoane | Luíño]]

I would be very interested! --[[Molly_King | Molly]]

Me too --[[Mauricio_Cantor]]

Me too --[[Elena_Stepanova | Elena]]

Me too! --[[Matteo_Smerlak | Matteo]]

Me too --[[Cheryl_Abundo | Cheryl]]

I'm in! [[Regina_Martinez | Regina]]

Yes! [[James_Magdanz | Jim]]

We scheduled this tutorial for Tuesday at 3:00 pm, just before the time to work on projects. Hope that you find it interesting! -- [[Luís_Seoane | Luíño]]

'''Nix's Bag O' Mathematical Tools'''

I'm planning on giving a number of tutorials to supplement Jim Crutchfield and I's lectures. The purpose of these should be to help you with your projects ( and encourage usage of our methods ;) ). I think it'd be cool for people to use this area to suggest topics to focus on. I started an empty bulleted list below. This will become more clear after we've given our lectures, but feel free to throw ideas out there when they come up. General topics might be: Information theory, time series analysis/modeling/prediction, symbolic dynamics (coarse-graining dynamical systems, i.e. what Liz Bradley discussed briefly), hidden Markov models, signal processing, bayesian inference, complexity measures, etc. [[Nix_Barnett | Nix]]
*Intro to information theory. There seems to be some interest in this. I'd be happy to give a tutorial, but I should note that it will be covered (at a rapid pace) in Jim Crutchfield's lecture. [[Nix_Barnett | Nix]]
* I really want to learn how to fit hidden Markov models to data. --David
* I'm very interested, Nix. Many thanks! [[Regina_Martinez | Regina]]
* i'm in!! [[AmaraAl_Sayegh|amara]]
* i'm in also! [[Ivana_Stankov | Ivana]]
* I'm in -- Mauricio

Complex Systems Summer School 2013-Schedule

2013-06-10T16:34:47Z

Masad:

{{Complex Systems Summer School 2013}}

To access a mobile app of the schedule, logistics, and faculty list please use your mobile device to visit: http://my.yapp.us/Z53CQX

Please plan to arrive June 2 and depart on June 29, 2013

The program lectures will be held from June 3 to June 28, 2013

Please note that dormitories will only be available from June 2 to June 29, 2013

'''For a list of local happenings in Santa Fe visit: http://www.santafe.com/'''



{| border="1" cellpadding="2"
! scope="col"width="100" align="center | Time
! scope="col"width="700" align="center | Activity

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 2
|-
|
|All events at St. John's College Unless Otherwise Noted
|-
|width="15%" | 11:00 p.m. - 5:00 p.m.
|Registration and check-in at [http://conferenceservices.sjcsf.edu/map.htm St. John's College in the Peterson Student Center.]
|-
|5:30 p.m. - 8:30 p.m.
|Welcome Reception & Dinner in [http://conferenceservices.sjcsf.edu/map.htm Peterson Student Center (upstairs) in Junior Commons Room]

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 3

|-
|width="15%" |9:00 a.m. - 9:30 a.m.
|Welcome and Introduction by CSSS Director [http://santafe.edu/about/people/profile/Sander%20(F.A.)%20Bais Sander Bais]

|-
|9:30 a.m. - 10:45 a.m.
|[http://santafe.edu/about/people/profile/Melanie%20Mitchell Melanie Mitchell] - Introduction to Complexity
|-
|10:45 a.m. - 11:00 a.m.
|Break
|-
| 11:00 a.m. - 12:15 p.m.
|Melanie Mitchell - Introduction to Complexity
|-
|12:15 p.m. - 1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Alfred%20H%C3%BCbler Alfred Hubler] - Physics Lab Introduction
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Student Introductions
|-
|4:15 p.m. - 5:00 p.m.
|Navigating the Complex Systems Summer School
|-
|5:00 - 6:30 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 4
|-
|9:00 a.m - 10:15 a.m.
|Melanie Mitchell - Introduction to Complexity
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Elizabeth%20Bradley Liz Bradley] - Dynamics I
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://csel.cs.colorado.edu/~garlanjt/ Joshua Garland], Computer Lab I: Maps & Flows
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://www.santafe.com/blogs/andrew-lovato Andrew Lovato], Introduction to Santa Fe
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|-
|6:45 p.m.
|Shuttle leaves for David Eagleman Public Lecture at James A. Little Theater
|-
|7:30 p.m. - 8:30 p.m.
|[http://www.eagleman.com/ David Eagleman], Public Lecture - The Brain and the Law
|-
|9:00 p.m.
|Shuttle departs to St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 5
|-
|9:00 a.m - 10:15 a.m.
|Liz Bradley, Dynamics II
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Alfred Hubler, Physics Lab Introduction
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Liz Bradley - Dynamics III
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - p.m.
|Brainstorming on Projects
|-
|4:00 p.m. - 5:00ish p.m.
|Optional Meeting for groups interested in network evolution / genetic algorithms / information transfer / attacker robustness - large lecture hall
|-
|4:00 p.m. - 5:00 (?) p.m.
|Optional [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]] on [http://arxiv.org/abs/0912.5352 cross-impact balances] and Markov chains - large lecture hall

|-
|5:00 p.m. - 6:00 p.m.
|Dinner / Discussion for people with an interested in global risk at dining hall
|-
|5:30 p.m. - 7:30 p.m.
|[[ Physics Lab 2013 | Lab Section I ]]

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 6
|-
|9:00 a.m - 10:15 a.m.
|Joshua Garland - Data Analysis Lab
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Liz Bradley - Dynamics IV: Applications
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Andreas%20Wagner Andreas Wagner], Evolution
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Introduction to Student Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|5:30 p.m. - 7:30 p.m.
|[[Physics Lab 2013 | Lab Section II ]]

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 7 at '''Santa Fe Institute'''
|-
|8:30 a.m
|Shuttle leaves St. John's to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|Andreas Wagner, Evolution
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Andreas Wagner, Evolution
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Time to work on Projects
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 3:30 p.m.
|Tea with SFI Community
|-
|3:30 p.m. - 4:45 p.m.
|Sander Bais - Symmetry Breaking as a Road to Diversity
|-
|5:00 p.m. - 7:30 p.m.
|BBQ at SFI
|-
|8:00 p.m.
|Shuttle leaves SFI and goes back to St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 8

|-
|9:00 a.m - 5:00 p.m.
|Unofficial trip to Bandelier National Monument
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 9
|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 10

|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Mercedes%20Pascual Mercedes Pascual], Emergence: case studies on pathogen diversity from an ecological perspective
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Mercedes Pascual, Anticipating critical transitions: model-free approaches and spatial considerations in ecological and epidemiological systems.

|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Jessica%20Flack Jessica Flack] - Robustness and Resilience
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Jessica Flack - Robustness and Resilience
|-
|5:30 p.m. - 7:30 p.m.
|[[Physics Lab 2013 | Lab Section III]]
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|6:30 p.m. - 7:30 p.m.
|Intro to Python workshop
|-
|-
|7:45 p.m.
|NetLogo workshop with tom
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 11

|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Cristopher%20Moore Cris Moore] - Algorithms and Landscapes
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| Cris Moore - NP-Completeness and the P vs. NP Question
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/John%20German John German], Science Writing Seminar
|-
|2:45 p.m. - 3:00 p.m.
|Vote on CSSS 2013 T-Shirt
|-
|3:00 p.m. - 4:15 p.m.
|Time to Work on Projects -- Tutorial on Genetic Algorithms & Multi-Objective Optimization.
|-
|5:30 p.m. - 7:30 p.m.
| [[Physics Lab 2013| Lab Section IV ]]
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 12

|-
|9:00 a.m - 10:15 a.m.
|Cris Moore - Monte Carlo Algorithms and Phase Transitions
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| Cris Moore - The Power of Randomness
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Time to work on projects
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/Clio%20Andris Clio Andris], Introduction to Networks
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Evening Lecture - [http://santafe.edu/about/people/profile/John%20Harte John Harte] - Theoretical Ecology
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 13

|-
|9:00 a.m - 10:15 a.m.
|Cris Moore, Quantum Computation
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Jennifer%20A.%20Dunne Jennifer Dunne] - Ecological Networks
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Jennifer Dunne - Ecological Networks
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/James%20P.%20Crutchfield Jim Crutchfield] - Complexity
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|6:30 p.m. - 8:00 p.m.
|[Jim Crutchfield and [http://complextropy.com/cv.html Nix Barnett] - Complexity Lab
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 14 at '''Santa Fe Institute'''

|-
|8:30 a.m
|Shuttle leaves St. John's to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|Jim Crutchfield - Complexity
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| Jim Crutchfield - Complexity
|-
|12:00 p.m. - 1:45 p.m.
|Lunch
|-
|1:45 p.m. - 3:00 p.m.
|Time to work on projects
|-
|3:00 p.m. - 3:30 p.m.
|Tea w. SFI community
|-
|3:30 p.m. - 4:30 p.m.
|Panel Discussion on General Questions on Complexity
|-
|5:00 p.m.
|Shuttle back to St. John's College
|-
|5:30 p.m. - 6:00 p.m.
|Dinner at St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 15

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 16
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 17
|-
|9:00 a.m - 10:15 a.m.
|Clio Andris - Cities Project
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
| [http://santafe.edu/about/people/profile/Marcus%20J%20Hamilton Marcus Hamilton] - Cities Project
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Elhanan Borenstein - Modeling Microbial Metabolism
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|[http://santafe.edu/about/people/profile/Elhanan%20Borenstein Elhanan Borenstein] - Modeling Microbial Metabolism
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 18
|-
|9:00 a.m - 10:00 a.m.
|Time to Work on Projects
|-
|10:00 a.m. - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Ginger%20Richardson Ginger Richardson] - Omidyar Fellowship Presentation
|-
|10:45 am - 12:00 p.m.
|Time to work on projects
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://tuvalu.santafe.edu/~simon/ Simon DeDeo] and [http://santafe.edu/about/people/profile/James%20O'Dwyer James O'Dwyer]
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
| Simon DeDeo and James O'Dwyer
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 19
|-
|9:00 a.m - 10:45 a.m.
|Time to work on Projects
|-
|10:45 am - 12:00 p.m.
|[http://santafe.edu/about/people/profile/Laura%20Fortunato Laura Fortunato] - Cultural Evolution
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Simon DeDeo and James O'Dwyer
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to Work on Projects or (optional) Simon DeDeo-Reductionism, Naturalism, and Undecidability- in the Junior Commons Room
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 20
|-
|9:00 a.m - 10:15 a.m.
|[http://santafe.edu/about/people/profile/Cosma%20Shalizi Cosma Shalizi]
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Cosma Shalizi - Statistics and Machine Learning
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Time to work on projects
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to work on projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Evening Lecture: [http://santafe.edu/about/people/profile/Tanmoy%20Bhattacharya Tanmoy Bhattacharya] -Infectious Disease
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 21 at '''Santa Fe Institute'''

|-
|8:30 a.m
|Shuttles leave St. John's College to go to SFI
|-
|9:00 a.m - 10:15 a.m.
|Cosma Shalizi - Statistics and Machine Learning
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Cosma Shalizi - Statistics and Machine Learning
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 3:00 p.m.
|Time to work on projects
|-
|3:00 p.m. - 3:30 p.m.
|Break
|-
|3:30 p.m. - 4:30 p.m.
|Glue Session with Sander Bais
|-
|5:00 p.m.
|Shuttle back to St. John's
|-
|5:30 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 22
|-
|8:00 p.m - 12:00 a.m.
|2013 CSSS Dance with Breadloaf workshop in St. John's College Coffee Shop
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 23
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 24
|-
|9:00 a.m - 10:15 a.m.
|[http://tuvalu.santafe.edu/~aaronc/ Aaron Clauset], Networks I
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Aaron Clauset, Networks II
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|[http://santafe.edu/about/people/profile/Scott%20Ortman Scott Ortman] - Evolution of Social Complexity
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|7:00 p.m. - 8:30 p.m.
|Evening Lecture - [http://santafe.edu/about/people/profile/Geoffrey%20West Geoffrey West], Cities
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 25
|-
|9:00 a.m - 10:15 a.m.
|Aaron Clauset - Networks III
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|[http://tuvalu.santafe.edu/~ole/ Ole Peters] - Non-Ergodic Economics
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Aaron Clauset - Networks IV
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Ole Peters - Non-Ergodic Economics
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 26
|-
|9:00 a.m - 10:15 a.m.
|[http://www.css.gmu.edu/?q=node/27 Rob Axtell] - Modeling Financial Markets
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Rob Axtell - Modeling Financial Markets
|-
|12:00 p.m. - 1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Aaron Clauset, Human Social Dynamics and Online Competition
|-
|2:45 p.m. - 3:00 p.m.
|Break
|-
|3:00 p.m. - 4:15 p.m.
|Time to work on Projects
|-
|5:00 p.m. - 6:00 p.m.
|Dinner
|-
|6:45 p.m.
|Shuttle leaves for Leonard Susskind Public Lecture at James A. Little Theater
|-
|7:30 p.m. - 8:30 p.m.
|[https://physics.stanford.edu/people/faculty/leonard-susskind Leonard Susskind] Public Lecture - The Cosmic Landscape
|-
|9:00 p.m.
|Shuttle departs to St. John's College
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 27
|-
|9:00 a.m - 4:15 a.m.
|Day to work on presentations
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 28 at '''Santa Fe Institute'''
|-
|8:30 a.m
|Shuttle leaves St. John's College for SFI
|-
|9:00 a.m - 10:15 a.m.
|Presentations
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 am - 12:00 p.m.
|Presentations
|-
|12:00 p.m. - 1:00 p.m.
|Lunch
|-
|1:00 p.m. - 1:15 p.m.
|Group Photo
|-
|1:30 p.m. - 3:00 p.m.
|Presentations
|-
|3:00 p.m. - 3:30 p.m.
|Break
|-
|3:30 p.m. - 5:00 p.m.
|Presentations and Closing Remarks
|-
|5:00 p.m. - 7:00 p.m.
|Farewell BBQ at SFI
|-
|7:30 p.m.
|Shuttles go back to St. John's
|-

|- bgcolor="#aaaaaa" align="center"
| 
| Saturday, June 29
|-
|10:00 a.m.
|Check-out and departure (don't forget to return your keys!)
|-

NetAttac

2013-06-10T15:16:08Z

Masad: /* Possible Tools */

We're thinking about co-evolving a network and an attacker agent to see which topologies emerge in the network and which strategies may be used by agents within the network to create that topology. The starting point of our idea was the question if networks containing nodes that are "too big too fail" may reduce the resilience if directed attacks against important nodes are performed against the network - or if the networks can in fact reorganize rapidly in case of the failure of a central node.

== Open Issues to be discussed ==

* Define a proper set of research questions: we should probably come up with some guiding research questions.
* Who is evolving? Agents or the Network? We have to decide if our basic building blocks that evolve are the nodes that apply different linking strategies (i.e. every agent has a genome representing linking strategies) or if the network itself evolves (i.e. the network configuration is the genome). The same applies to the attacker: is there one central attacker or do we have a group of attackers (which may cooperate)
* Fitness of Network components and attackers: we have to find a good fitness measure, which very much is connected with the definition of our evolving entities. If we decide that single nodes evolve, fitness of a single node in the network could be simply survival - and to survive, links to neighbours are necessary, e.g. to harvest energy from the network.
* Network aim: what is the main aim of the network? What is transported through the network and how is this related to the fitness of the network (or the nodes in the network)?
* Resource constraints: we could introduce a single resource, e.g. energy, that may be used either for consumption, for building links, or for transporting over these links.
* Genome: how does the genome of attackers and network (or network nodes) look like?
* Strategies for network components and attackers: which strategies may be implemented by the different agents?
* Real world examples: are there any real world examples we can relate to?

Some further questions on the table:

* Do we consider addition of new nodes? (it depends on the idea of network we have and if we consider it a closed or open system)
* Related to the question above, do we consider a fair process, I mean attacker destroys n links, the net replicates creating n new links? Or attacker can blow up nodes? How do we react? Creating as many links as the node degree?
* When does our evolution/attack finish? Do we set n moves that net and attacker can perform?
* Should we put game theory concepts into the picture? (It is a 2/multi player game) Is there a game theory expert in the group?

== Minutes of meeting 7th June ==

We have decided the following in today's meeting:

* Reference real-life example is terrorist vs CIA or mafia vs police situations.
* The attacker tries to fragment the network, the attacked tries to recostruct it.
* The network we are dealing with is at least in the first place to keep things simple:
- undirected

- unweighted

- no self links

- no duplicate links

* We start with a network already in place.
* The attacker has the whole info about the network.
* The attacked has local information (I guess we didn't finally agreed on it, isn't it?).
* Attack is on nodes, one node per iteration can be removed.
* Attacker has the goal to minimize hierarchy.
* Fitness metric: global reach (proxy for hierarchy).
* The network react to the attack on the node (that has a degree d) by: attaching a new node with degree 1 and creating (d-1) new links between existing nodes.
* The "game" finishes when the network is no more connected.

'''TODO: define the genetic algorithm, the strategy of the attacked since it has local information (or not?)'''

'''If I skipped something please add.'''

Sorry, I missed previous meeting. Thank you for the notes. I want to clarify last point for myself:
“Game finishes when network is no more connected”. Does it mean that to finish a game I need only one node that is fully isolated? (CIA willn’t agree that they should stop their fight with terrorists on this).
I was thinking of more realistic game: CIA goal is to destroy all nodes (especially if they know all network). And node is destroyed if it is attacked directly or if it got isolated. Game finishes when no nodes remain. All the rest of procedure – adding new node and re-linking nodes is the same

Elena

The answer as I think it right now is yes. Then the CIA could start two different "new games" on the two network partitions and try to destroy those as well. We can talk about it in the next meeting. -- Andrea

Another question: how many rounds does the game go? My suggestion is that the number should be random. -- David

== Possible Tools ==

Java with [http://jung.sourceforge.net/ jung library]
Python with [http://networkx.github.io/ networkX]

Comment: I (Andrea) looked into networkX (we were mentioning it yesterday) a bit and all the metrics to analyze and the generation of graphs seems to be there.

Viualization with [https://gephi.org/ gephi] ?

Version control / coordination via [http://www.github.com GitHub]?

== Meetings ==
June 7th, 1h30pm

Next meeting is: Tuesday @ 15.00 (?) other suggestions?

== Background reading ==

[http://www.talkorigins.org/faqs/tierra.html]

[http://www.researchgate.net/publication/220841044_Formal_Methods_for_Modeling_Socio-technical_Innovation_between_Adversaries?ev=prf_pub]

== Dropbox material ==

I have created a simple initial file in python/networkX disrupting a random network using betweenness centrality as the metric to find the most important node. If you write down your mail associated to your dropbox account we can start sharing material (David you can share your code for the hierarchy measure), I'll send you an invitation to the share. -- [[Giuliano_Andrea_Pagani | Andrea]]

NetAttac

2013-06-10T15:10:55Z

Masad: /* Minutes of meeting 7th June */

We're thinking about co-evolving a network and an attacker agent to see which topologies emerge in the network and which strategies may be used by agents within the network to create that topology. The starting point of our idea was the question if networks containing nodes that are "too big too fail" may reduce the resilience if directed attacks against important nodes are performed against the network - or if the networks can in fact reorganize rapidly in case of the failure of a central node.

== Open Issues to be discussed ==

* Define a proper set of research questions: we should probably come up with some guiding research questions.
* Who is evolving? Agents or the Network? We have to decide if our basic building blocks that evolve are the nodes that apply different linking strategies (i.e. every agent has a genome representing linking strategies) or if the network itself evolves (i.e. the network configuration is the genome). The same applies to the attacker: is there one central attacker or do we have a group of attackers (which may cooperate)
* Fitness of Network components and attackers: we have to find a good fitness measure, which very much is connected with the definition of our evolving entities. If we decide that single nodes evolve, fitness of a single node in the network could be simply survival - and to survive, links to neighbours are necessary, e.g. to harvest energy from the network.
* Network aim: what is the main aim of the network? What is transported through the network and how is this related to the fitness of the network (or the nodes in the network)?
* Resource constraints: we could introduce a single resource, e.g. energy, that may be used either for consumption, for building links, or for transporting over these links.
* Genome: how does the genome of attackers and network (or network nodes) look like?
* Strategies for network components and attackers: which strategies may be implemented by the different agents?
* Real world examples: are there any real world examples we can relate to?

Some further questions on the table:

* Do we consider addition of new nodes? (it depends on the idea of network we have and if we consider it a closed or open system)
* Related to the question above, do we consider a fair process, I mean attacker destroys n links, the net replicates creating n new links? Or attacker can blow up nodes? How do we react? Creating as many links as the node degree?
* When does our evolution/attack finish? Do we set n moves that net and attacker can perform?
* Should we put game theory concepts into the picture? (It is a 2/multi player game) Is there a game theory expert in the group?

== Minutes of meeting 7th June ==

We have decided the following in today's meeting:

* Reference real-life example is terrorist vs CIA or mafia vs police situations.
* The attacker tries to fragment the network, the attacked tries to recostruct it.
* The network we are dealing with is at least in the first place to keep things simple:
- undirected

- unweighted

- no self links

- no duplicate links

* We start with a network already in place.
* The attacker has the whole info about the network.
* The attacked has local information (I guess we didn't finally agreed on it, isn't it?).
* Attack is on nodes, one node per iteration can be removed.
* Attacker has the goal to minimize hierarchy.
* Fitness metric: global reach (proxy for hierarchy).
* The network react to the attack on the node (that has a degree d) by: attaching a new node with degree 1 and creating (d-1) new links between existing nodes.
* The "game" finishes when the network is no more connected.

'''TODO: define the genetic algorithm, the strategy of the attacked since it has local information (or not?)'''

'''If I skipped something please add.'''

Sorry, I missed previous meeting. Thank you for the notes. I want to clarify last point for myself:
“Game finishes when network is no more connected”. Does it mean that to finish a game I need only one node that is fully isolated? (CIA willn’t agree that they should stop their fight with terrorists on this).
I was thinking of more realistic game: CIA goal is to destroy all nodes (especially if they know all network). And node is destroyed if it is attacked directly or if it got isolated. Game finishes when no nodes remain. All the rest of procedure – adding new node and re-linking nodes is the same

Elena

The answer as I think it right now is yes. Then the CIA could start two different "new games" on the two network partitions and try to destroy those as well. We can talk about it in the next meeting. -- Andrea

Another question: how many rounds does the game go? My suggestion is that the number should be random. -- David

== Possible Tools ==

Java with [http://jung.sourceforge.net/ jung library]
Python with [http://networkx.github.io/ networkX]

Comment: I (Andrea) looked into networkX (we were mentioning it yesterday) a bit and all the metrics to analyze and the generation of graphs seems to be there.

Viualization with [https://gephi.org/ gephi] ?

== Meetings ==
June 7th, 1h30pm

Next meeting is: Tuesday @ 15.00 (?) other suggestions?

== Background reading ==

[http://www.talkorigins.org/faqs/tierra.html]

[http://www.researchgate.net/publication/220841044_Formal_Methods_for_Modeling_Socio-technical_Innovation_between_Adversaries?ev=prf_pub]

== Dropbox material ==

I have created a simple initial file in python/networkX disrupting a random network using betweenness centrality as the metric to find the most important node. If you write down your mail associated to your dropbox account we can start sharing material (David you can share your code for the hierarchy measure), I'll send you an invitation to the share. -- [[Giuliano_Andrea_Pagani | Andrea]]

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-06T22:51:59Z

Masad:

[[Link title]]{{Complex Systems Summer School 2013}}

==Project Proposals==

=='''MOOCs'''==
I have had an interest in MOOCs and their potential role in the future of education/ as a means of providing education to non-traditional students. This has been in the back of my mind for some time, but I have no experience dealing with real social data (including how to access it) and was hoping other people might be interested. I did a brief search and found that it may be possible to use twitter data. The questions I am interested in are where MOOCs are popular (globally), how it spread, what kind of topics, etc. Anyone else interested?

-Swati

An automated cluster analysis of the content of Coursera catalogs would be quite straightforward. It could help get a sense of meaningful clusters of content regarding how courses present themselves, and also what categories are salient for MOOC's. [[Manish_Nag | --Manish]]

=='''Food webs'''==
It seems like there is A LOT of interest in food webs amongst this group. Since there are so many people, maybe it would be worth coming together and dividing into smaller groups based on the questions (there are many!) people are interested in addressing and skills. I think it would good be to have some coordinated effort, for efficiency and productivity. We could divide questions, or parts of bigger questions, or approach the same questions, using different methods and then compare results and try to understand the similarities and differences. Maybe we could meet at 3 pm today (Wed) or at dinner.

-Swati

=='''A Midsummer Night's Project: Comedy and Tragedy in Shakespeare'''==

Max Kleiman-Weiner and I have a corpus of all the Shakespeare plays and have been talking (with many of you, too!) about building a system to automatically classify Shakespeare plays as either comedy or tragedy. A simple approach would be to just use a bag of words to see if the plays can be classified based on lexical content alone. We have also been discussing building social networks for each play based on which characters interact (i.e., who speaks before and after whom). We suspect that the social network structure of a comedy and tragedy should look different from each other. Do characters in comedies have more connections? Do tragedies and comedies start off the same and then have networks that evolve differently over the course of the play? Or are they different from Act I? This may be an opportunity to look at how social networks change over time in a specific domain. We could also look at the different roles of men and women in the social networks of the plays.

-Kyle M

This sounds interesting and doable. I've done a work on author attribution of opinion articles before using only syntactic (function words like prepositions and articles, punctuations), structural (sentence length, paragraph length) and lexical (other non-specific words) features. It'd be nice to see if the same thing will work for this. I think it will be more fascinating to explore the social network approach and we should definitely give it a shot if there's still time.

-Cheryl

Stories are always good. Incidentally, are you familiar with Kurt Vonnegut's commentary on the shapes of stories? If not, it's not hard to find. If so, there may be something to be said for attempting to determine whether a story conforms to more specific tropes (e.g. Cinderella stories and "The Chosen One"). Moreover, if enough distinct patterns do emerge out Shakespeare's plays, it may prove interesting to compare these to other stories (e.g. novels available on Project Gutenberg).

-Eitan

There is now a DropBox with the corpus and some preliminary Python scripts - so come find me if you're interested in getting linked in.

-Max

See project page for this here: [http://tuvalu.santafe.edu/events/workshops/index.php/Comedy_and_Tragedy_in_Shakespeare].

=='''Recursive Agents'''==

A common theme that I've seen in complexity is that you can represent many different systems (cells, agents, civilizations, for example) with more or less the same rules. I'm wondering if anyone would be interested in modeling this? Essentially we develop a recursive rule set: agents' behavior are based on a set of their 'inner agents,' which also follow similar rules.

-Todd

=='''Global Emergent Risk'''==

In the current phase of globalization, networks in logistics, travel, finance, disease, energy, and ecology are growingly increasingly interconnected on a global scale. Hence, situations arise where mortgage defaults in the US bring down the Icelandic pension system, and a volcano in Iceland disrupts global air traffic. Given the scale of interconnectedness, can complexity science help develop a sense of how small perturbations in one global network might cascade into large unforeseen failures in another network? I'm wondering if we can help build a more generic grammar for describing interconnected networks and the risks posed by such systems. Would it be possible to mitigate risk at smaller local levels of scale, or do small corrections of local risk inevitably cascade into larger risks that we lack the ability to respond to (think wildfires in the Southwest where more frequent small fires would help reduce the chance of large scale fires that cannot be controlled.) I'd love to talk with anyone interested in ecology, globalization, risk, and network modelling.

My advisor at Princeton is already funded for a three year interdisciplinary symposium on Global Emergent Risk, so if people are interested, we have resources to carry on a larger research engagement.

--[[Manish_Nag | Manish]]

- I don't know if large risk cascades are inevitable, but these are timely questions. I have colleagues at the [http://gcrinstitute.org/ Global Catastrophic Risk Institute] who are also interested in this topic. I'm not sure what building a "more generic grammar" means, but the cross-impact balance method is pretty generic. Hopefully you can make our [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]]! Our group is kicking around methods for a project at the moment and have not decided on research questions, so perhaps we can join forces. --[[Vanessa_Schweizer | Vanessa]]

- To clarify, what I meant by "generic grammar" is some way to describe a set of networks and cross network dependencies that can be decoupled from the content of the network. We could use this language to describe interconnections between hypothetical logistics, travel, financial networks for example, and then use simulations to understand the conditions where risks might be amplified and/or jump across from one network to another. --[[Manish_Nag | Manish]]

- I'd love to join discussions on this as I agree that there's a need to start thinking about network of networks and not just networks in isolation. The [http://arxiv.org/abs/1010.5829 paper by Gao, Stanley et al.] on the robustness of a network of networks might be useful. --[[Cheryl_Abundo | Cheryl]]

- I'm in .[[Reniel_Cabral | Ren]]

- I'm thinking if we can possibly use a self-organized criticality (SOC) type of model to trigger a cascade of failures in a network of networks. Not sure though if it has been done. [[Cheryl_Abundo | Cheryl]]

=='''Alcohol Consumption and Language Fluency'''==
 
''(This is just one of my random thoughts, don't take it too seriously. I'm bringing it up in case it would actually add interesting noises to anyone's thought process)'' 
There's a interesting thing about me and some of my friends who speak a foreign language. There seems to be a kind of non-linear curve that depicts my blood alcohol concentration and the fluency of my speaking English (Chinese is my native language). For example, usually after one beer, I start to talk faster, and semantically relevant words pop up in my mind more fluently or spontaneously. Or say, I express the same idea with less stuttering and in shorter time. But after some point, i.e. 32 oz of beer, even it might still sound fluent, regarding the physical property of the speech, the grammatical structure of the sentences start to break down. Ultimately, i.e. half bottle of rum, I only repeat 2-3 very short sentences/phrases independent of the presence or the identity of my audience(s) (i.e. murmuring in English for hours to a group of Chinese friends). 
We know that alcohol can influence our behavior by, among other things, binding to certain neural receptors (like GABAa?). I just thought it might be interesting to model how alcohol intake influences the dynamics of language production via regulating neuron signaling. I'm also wondering about what it might imply about our brain dynamics when we're silent. 
Welcome to talk to me if you find this interesting, or silly, or you simply want to correct my grammar. Thanks! 
-Mengsen Zhang

@Mengsen I'd be very interested in doing some empirical work on this topic.
-Max Kleiman-Weiner

I've experienced this same thing with Spanish, Bahasa Indonesia, and playing billiards/pool. Sadly, my math skills do not improve with drinking, and math could arguably be considered a language. This is a creative topic with solid scientific underpinnings that nicely lend themselves to complex systems modeling, I suspect. Fun! – [[Kristen_Honey | Kristen Honey]]

On a related note:
http://xkcd.com/323/

-Eitan

=='''How the ocean can help us heal complex chronic disease'''==

The human body is its own ecosystem -- much like the ocean -- with resilience, hysteresis, synergistic properties, and multi-system dynamics that depend on matrix conditions. Can we use our understanding of the ocean and ecosystems to help us heal? Can we model different scales -- an ocean, a human body, and a microbial community -- to explore ecosystem/human/microbial health in a holistic context that depends on shared key elements like flow & trace minerals as building blocks for function? As one example to think about, chronic illnesses like HIV/AIDS or Lyme disease disrupt the immune system and human body functions (e.g., methylation pathways, detox pathways), preventing optimal function that weakens the human body and makes it vulnerable to other infections. It’s a downward spiral of negative feedbacks, analogous to a backed-up, atrophying ocean or estuary that causes fish kills, destroys coral reefs, etc... analogous to microbial communities that shift when environmental/matrix condition change. I suspect our knowledge of the ocean & large ecosystems, which we can see and visualize, can inform new thinking about system dynamics for health & recovery at the scale of a human body and at the scale of individual microbes & microbial communities...

Anyone else interested? – [[Kristen_Honey | Kristen Honey]]

- This sounds like a really nice idea. It would be interesting to understand how the disease-mediated degradation of immune/metabolic networks (the loss or alteration of edges and nodes?) affects the response of these networks to further perturbations (e.g. asymptotic stability and resilience, [http://www.jstor.org/stable/2266047 transient reactivity], cascading effects of node loss, etc.). I have little knowledge of the medical literature, but I am experienced in ecological network analysis including information theoretic analyses of weighted food webs. -- [[Ashkaan_Fahimipour | Ashkaan]]

- I liked the idea very much. In fact I am looking at similar issues related to management of ecosystems which display hysteresis and [http://arno.uvt.nl/show.cgi?fid=121389 regime shifts]. Here is some pertinet information related to [http://www.esajournals.org/doi/abs/10.1890/1051-0761%281999%29009%5B0751%3AMOEFLS%5D2.0.CO%3B2 shallow lakes] and its [http://ideas.repec.org/p/att/wimass/200026.html complex dynamics]. Your idea of scaling down to human level is interesting -- [[Puduru Reddy | Vishwa]]

- Sounds interesting. I have experience in microbial oceanography, but not so much with infectious disease. I'll be there for the dinner meeting. - [[Jody_Wright | Jody Wright]]

==
Join us for project discussion & brainstorming ideas, Wednesday June 5th dinner at 5:00. Everyone welcome! ==

=='''GDELT'''==

[[David_Masad | I'd]] love to play around with the new [http://gdelt.utdallas.edu/ Global Data on Events, Location and Tone (GDELT)] dataset, which has 200+ million timestamped and geocoded political events. Here's a [http://ideas.foreignpolicy.com/posts/2013/04/10/what_can_we_learn_from_the_last_200_million_things_that_happened_in_the_world writeup of it in Foreign Policy] -- David

=='''Research Network Formation'''==

I'd be interested in collecting some data from CSSS attendants. Some kind of way to study social network formation. -- [[Todd_Bodnar | Todd]]

Perhaps we could collect survey questions people might be interested in looking at in a [https://docs.google.com/document/d/1h_8TUyuDNT1DhPIyZuGwuvrqSExLgwoocsKZl4jFSk8/edit?usp=sharing Google Doc]? --[[Molly_King | Molly]]

My new crazy idea, inspired by [http://blog.premise.is/blog/2013/5/5/mapping-the-produce-manifold these guys], is doing something with computer vision. Maybe there's a way to photograph sitting arrangements and extract data from that? -- David

Project meeting after the lab Wednesday 6/5 for all those interested.

=='''Self-consistent networks for socio-economic institutions (CIB analysis and Markov chains)'''==

Project update: Some core members of the group are starting to assign tasks for the project. If some folks are still shopping for projects and want to check out what we're up to, please visit our [[Complex_Systems_Summer_School_2013-CIB_Markov | project page]]. --[[User:Vanessas|Vanessas]] 02:12, 6 June 2013 (UTC)

[[Pablo_Galindo | Pablo]] and [[Vanessa_Schweizer | I]] started to discuss a project where we could use [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] to investigate the implications of alternative hypotheses for interrelationships between various socio-economic/political factors. We began discussing this from the perspective of testing competing political economic theories to see what types of institutions (e.g. styles and stability of governance) would be self-consistent according to the theories. However, I would be open to other topics, including research questions inspired by GDELT. If there is interest to learn more about the CIB technique, I could put together a tutorial. --[[Vanessa_Schweizer | Vanessa]]

- There's a paper written by Brian Arthur here at the SFI that might help us frame our topic. Its called Complexity Economics. Basically sets the "rules" for thinking about economics in a whole different way.
It is a very good starting point so we don't go any further wasting time taking into account economic models that are vague, non-accurate and out of date. [[Pablo_Galindo | Pablo]] [?]

Elaborating more on the idea. If we focus on human action as the essence of culture. Understanding human action as the use of beliefs, attitudes and resources (which are scarce) pursuing a state of higher satisfaction. And culture as the sum of all beliefs, attitudes and unintentional consequences of the human action. We can state that the emergence of socio-econmic/political factors are the unintentional consequence of intentional individual actions that at the same time affect the way people act, in what they believe and what attitude they'll have toward the satisfaction of their needs. (Theres a loop between human action and culture - culture affects human action and human action affects culture and so forth)
Some "institutions" will emerge as a consequence of human action but not human design. That is one of the characteristics of a "good" type of institution. (e.g. Money, language, private property, contracts, a certain type of government) and it would be interesting to test the robustness of that spontaneously emerged institution against human designed institution who's robustness is just that is law enforced.
I dunno If you get my point? Compare the qualities of spontaneously emerged institutions against human designed institutions. Its more or less comparing spontaneously emerged institutions (no leader needed to coordinate like the birds flocking) vs. human designed institutions (leader needed to coordinate al human actions).

==
A [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]] on cross-impact balances and Markov chains is scheduled for Wed. June 5 at ~4:15. Everyone is welcome, even if your project interests lie elsewhere. ==

=='''Genetic algorithms to evaluate network formation or real-world data'''==
I have an ill-defined, wacky idea to possibly use genetic algorithms to evaluate the formation of networks as either following preferential attachment or homophily (aka similarity) rules. This [http://www.nature.com/doifinder/10.1038/nature11459 short Nature paper] looks at the debate between preferential attachment and similarity/homophily dynamics. I don't have a clear idea of what this would look like, but I think it might be fun to think about ways to use genetic algorithms to solve network problems. Talk to me if you think this remotely interesting and we can evolve an idea together? --[[Molly_King | Molly]]

Another possibility would be using genetic algorithms or attachment algorithms to compare to models of real-world data to understand how these networks likely formed and predict future edges.

Molly, I would like to investigate using GA to create an organizational network structure (think org chart or military chain of command or even project groups at the CSSS) and then compare it to existing structures. Let's talk! -John L

Some people were also talking about co-evolution of a network and an attacker that disconnects nodes or edges. -- David

Everyone interested in this and related meet Wed 6/5 at 4pm in main lecture hall - group of folks interested in studying network evolution/fitness/information/energy spread meeting. --Molly

Seem to be two branches of this: 
1) network evolution toward a predefined fitness function (energy, information efficiency, etc.) via genetic algorithms - what structures evolve? 
2) co-evolution of a network and attacks of different forms - what structural changes take place? which structures are robust to attacks?

===1) network evolution toward a predefined fitness function===

=== 2) co-evolution of a network and attacker ===

Interested members: Elena, Andrea, Stephan, Bruno, Johannes, David M., Holly

We're thinking about co-evolving a network and an attacker agent. The network's fitness is robustness (to be defined later) to attack, and the attacker's fitness is disruption of the network. Both also need to be subject to some sort of resource constraint -- otherwise the optimal network is fully-connected, and the attacker's optimal strategy is just disconnecting all of the nodes.

Some background reading:
http://www.talkorigins.org/faqs/tierra.html

http://www.researchgate.net/publication/220841044_Formal_Methods_for_Modeling_Socio-technical_Innovation_between_Adversaries?ev=prf_pub

Tools:
Probably Java or Python. We need something that has network metrics already, so we don't need to code them ourselves. Possibly use a GA package / library as well.

I created a page for the project and started to discuss some of the issues: [[NetAttac]]

=='''Caribou Management Dynamics'''==

This project would model caribou management dynamics in a prototype NW Alaska community during a caribou shortage. Agents in the model would be informed by data from household subsistence surveys and from management history. The goal would be to evaluate the abilities of different management strategies to achieve biological harvest goals while maximizing economic efficiencies in the community. This is a real-world problem with near-term applications. Caribou cycle on 30-to-50 year periods. The Western Arctic Caribou Herd is currently in decline. During the last caribou “crash” in this region, the state management system attempted to reorganize caribou production, which generated considerable political and social disruption, precipitated widespread passive resistance among Native peoples, and left a legacy of contempt for both management (among some Inuit) and for Inuit hunters (among some sport users). The hope is to reduce conflicts during the expected nadir of the population. Comments and cooperators welcome! [[James Magdanz | Jim]]

Neat topic with data, I assume! I'm interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Evolving synchronized flashes in fireflies, and other polymorphic traits'''==

[[Bryn_Gaertner | I ]] was thinking about how some, but not all, species of fireflies can synchronize their flashes, as was mentioned in both lectures today (June 4). The mechanism is fairly simple, it seems, so we should be able to evolve it using a simple genetic algorithm, right? This is only half-baked at the moment, and I haven't checked to see if it has been done already, but I thought it would be neat to explore the space around these biological phenomena. More of a fun project than a serious "lets publish this!" type of project. Bonus points if we can work some neural network stuff into it. [[Bryn_Gaertner]]. -- EDIT -- Upon further discussion with [[Rebecca_Mease | Rebecca]] and [[Holly_Arnold | Holly]], we would like to extend this. Still using genetic algorithms, under what conditions can we evolve a stable polymorphic trait in a population, and under what conditions does a monomorphic trait evolve? This is applicable for traits in a population, but we would like to use the same model to evolve (for example) multiple or novel sensory modalities in a species, number of members in a food web, predation strategies, etc. Interested? Find us at lunch!

=='''How do historic facts collapse into written history?'''==

Let's begin with a nice example: [http://en.wikipedia.org/wiki/Gilgamesh Gilgamesh], the fifth king of Uruk, decided to gather together some stories that local tribes and surrounding cultures had been telling for years, along with things that previous kings had done. This became the [http://en.wikipedia.org/wiki/Epic_of_Gilgamesh Epic of Gilgamesh]. Someone later does a cover of the original book with some new contributions and turns it into what nowadays is the bible and the torah. Another remake of the tale turns these books into the quran, and until today... you know the rest of the story already. Peer reviewed quality, just like Nature or PNAS.

It might be interesting to study how history goes from facts to a written, definitive form which is not (and maybe cannot be) completely faithfully to the actual events. There is huge room to use, for example, models of agents that contribute to form a History with pieces of information that sums up, sometimes with contradicting versions, sometimes with hidden interests, etc etc. Furthermore, we have a great tool in the wikipedia!! We can track, for example, how many changes are made on different entries over time. We can check whether there are some generalities, how the number of edits depends on the time gone after the historic event, maybe we can quantify how successive stories differ from each other and whether there are turning points that dramatically change the whole thing...

So this is the general framework. I think this is a very exciting topic and I'd be glad to talk about this with anyone!! Just contact me! -- [[Luís_Seoane | Luíño]]

So this is the book I told you about: http://www.amazon.com/The-Evolution-of-God-ebook/dp/B002AKPEHW/ref=sr_1_1?ie=UTF8&qid=1370537236&sr=8-1&keywords=the+evolution+of+god [[Pablo_Galindo]]

You may be interested in related idea about diversification of religion: http://www.sciencedirect.com/science/article/pii/S0022519310004790 -- [[Cesar_Flores_Garcia|Cesar]]

=='''Meta Food Webs'''==

I'd like to throw out an idea I've had for a while: Most animals use space in very important ways -- predators encounter and consume prey in both 2D and 3D environments, birds and fish migrate across continents in search of resources and mates, and plant pollinators fly or walk from flower to flower, in turn providing an indispensable economic service to humans. The study of food webs attempts to understand how networks of species that eat each other persist in the face of (sometimes constant) external perturbations. Yet, network-level food web studies seldom address the dynamics of animal movement, and I see this as a fundamental shortcoming in our understanding of nature. Recently, scientists in fields like computer science, physics and neurobiology have begun to model and explore [http://www.nature.com/srep/2012/120831/srep00620/full/srep00620.html?WT.ec_id=SREP-20120904 multi-level or multiplex networks] -- networks of nested networks. This seems like a reasonable candidate for the theoretical study of multiple food webs that are linked by spatial networks of animal movement. One preliminary question that comes to mind: How do the number of "mobile" species and the "speed of movement" alter important dynamical properties of complex food webs at larger spatial scales (i.e. at the meta-food web scale)? I am not dead set on answering this question, and I look forward to gaining insight from scientists who study other types of networks. I'm also not set on the multiplex network framework. Potential alternatives that come to mind are IBMs, PDEs on graphs or integrodifference equations. I look forward to any suggestions or bright ideas! --[[Ashkaan_Fahimipour | Ashkaan]]

Very cool topic. Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''(Evolution of) Aging'''==
Sorry that this one is a bit long. I'd like to brainstorm with anybody interested to see if there could be a viable project in the following direction.

Let me first define aging: deterioration that happens as an organism, e.g. a human being, gets physiologically older, eventually leading to increased mortality and/or decreased fecundity.

Some background into the 'classic' theory: Evolution is about getting to be there in the future, that is, you and/or related organisms, for instance offspring. Increased mortality and decreased fecundity as such are clearly unfavorable to getting to be there in the future. Then why could it evolve? Well, evolution tends to become less sensitive to anything happening to an organism as time progresses, because events that take place at some point in time can affect only events that are future to that event. All offspring that an organism already has at some point cannot be affected anymore, and this is a non-decreasing function of time. This can be formalized, and I'd be happy to write down the math if anybody wonders.

It has, however, limited value to theorize too much about age-specific events, while in fact events at different ages are tied together in pathways of causality, dynamic change and so on; age per se is not a cause of anything, and changes at some age do not happen independent of changes at other ages. There are a number of sufficient arguments why the 'age-specific' picture does not capture this reality. I'm skipping these arguments for now, but ask if you are interested.

We have two things that matter for the evolution of aging. 1. The declining sensitivity of fitness to age-specific changes (of some standardized magnitude). 2. The fact that there are constraints that make that what happens at age x is not independent from what happens at the ages in its neighborhood. Thus, the trick is to figure out what the constraints are - this is where complexity may come in - and to combine these with the effect on fitness that age-related change has. The effect on fitness may be solved analytically, but there are various reasons why computation may be preferable, specifically the not always realistic assumptions that are necessary to allow for analytical solutions.

Mechanistically, people tend to think about aging in two ways. The first is that aging is caused by the accumulation of damage. If this damage were all repaired, aging would not occur. People then try to think of reasons why repair would be imperfect. The second way to think about it is as a gradual loss of robustness/control, sometimes in the context of reliability engineering (is anybody familiar with that?). Beautiful medical example: old people need more insulin to process a standardized dose of sugar, and their regulation shows more peaks, especially upward peaks, than that of young people, who tend to need less insulin to process the standardized dose of sugar. Of course, if you consider loss of control as a type of damage, the two are the same, but the distinction is perhaps helpful because the way people tend to think about damage is not in a dynamical way, but just as protein aggregates sitting in the brain, inhibiting the function, cartilage that looses its suspension, etcetera. Again of course, both may influence each other.

Now toward a project proposal. If I think about how complexity may (in part) determine physiological constraints, I think of the following. Usually people tend to think of repair being limited by available energy. But to repair something, the body needs to have available somewhere the information necessary to restore the initial state, and use that information at the place where the damage has occurred to be able to repair. This is where I hypothesize complexity comes in. The necessity of different components of the body to interact may put constraints on repair other than just energetic, it is also a question of whether the energy can actually be used for the repair (flow through the system in the necessary way). That may require space, a certain chemical environment, hormonal setting etcetera that may be incompatible with the proper function of an organism. (Can you repair a car when it is driving?) Also in the 'control/robustness thinking', you have to get back to the original situation to avoid aging. Is that compatible with the best evolutionary outcome?

These are just some ideas I'm throwing at you, as you see it's not perfectly fleshed out yet, which is good, because it should benefit from your perspective. So anybody interested, please let me know!

Cheers,
Maarten

Neat ideas & I welcome more discussion around these topics. Aging is cool from the academic science side, if not from the personal experience side, lol. It seems to me that these same models/concepts for aging also apply to loss of functionality from chronic illness... illness expedites aging? – [[Kristen_Honey | Kristen Honey]]

==Quantifying Synchrony in Dynamics Occuring on Networks==

[http://arxiv.org/pdf/1110.2724v1.pdf Recent work] has focused on developing information theoretic measures for quantifying directed information transfer, with particular applications to social media. These metrics are motivated by the work being done in theoretical / computational neuroscience on the analysis of spike trains. To do this analysis, the behavior of users on a social media platform like Twitter are treated as point processes, where we only keep track of when a tweet occurs, and ignore its content. That is, we treat a user's behavior over time as 'spikes.' Despite the simplicity of the approach, it was found to be successful in identifying key actors within real social networks.

I am interested in applying a similar methodology, but using a [http://arxiv.org/abs/q-bio/0609008 different measure] of synchrony motivated by computational mechanics. This method seeks to learn the hidden states that generate a user's behavior (very much in the flavor of a Hidden Markov Model, but with a few key twists), and then considers the mutual information between the state sequences of the two users.

A first step for this project would be implementing the methodology proposed by Shalizi, et al., on the toy model proposed by Steeg, et al.

If that is successful (and completed quickly), I have a data set (network connections and behavior) of fifteen thousand Twitter users collected over a three month period. We are interested in using this approach to identify dynamical communities (not only users who are connected, but users who behave in synchrony) within the social network. This takes us beyond typical structural community detection that has had great success in the past decade.

These approaches should work with any sort of dynamics occurring on top of a network-type structure, so if you have a different system you would like to use as a test case, I would be very interested to hear about it!

[[David_Darmon | Dave Darmon]]

===A spin off?===

Sorry for editing in your proposal, Dave, but I wanted to comment an idea I have been interested in for a time now. There is this great technique used in neuroscience to pin down the most effective time-course excitation that a neuron can get so that it fires. It basically averages the input a neuron had been getting before each of its spikes. You can find a thorough description in the very popular [http://www.amazon.com/Theoretical-Neuroscience-Computational-Mathematical-Modeling/dp/0262541858 Dayan & Abbott] book on neuroscience. Since you mention the abstraction from tweets to spikes, I would be very interesting in applying such neuro-inspired analysis to this social interactions. Neuroscience has got many more techniques, so I do not pose it as a closed matter. Just open for discussion, but seems like everybody is sleeping by now ;) -- [[Luís_Seoane | Luíño]]

You're referring to the spike-triggered average? I hadn't thought of that!

All of the work I've done has only considered a single user's time series for prediction. I would certainly be interested in looking at how including the 'inputs' to the user (or at least the inputs that occur on Twitter) impact this process. The spike-triggered average seems like a great first start. Computational mechanics also has some tricks in its toolbox that could be used for this sort of input-output problem. -- [[David_Darmon | Dave D]]

===comment on spin off===
Hi, I used spike-triggered averaging (and higher-dimensional extensions, which might be useful in your case) during my thesis, so I would be interested in talking about the application to other systems. [[Rebecca_Mease| Rebecca]]

Great! The folks interested in this project will be meeting during the 3pm time slot today. We don't have a formal meeting place planned: the best I can say is to look for me!

[[David_Darmon | Dave D]]

=='''Energy resources supply patterns from biological systems to humans'''==

My idea is to start a brainstorming, it is nothing more than some disjoints thoughts!!! And many questions without an answer so far!! :-)

I would like to investigate how biological systems obtain their energy requirements. Are there patterns or network structure that evolution has developed and that are efficient for animals/plants?
Can we replicate these structures/networks/patterns in the way we (humans) obtain our energy? Can we learn something from the evolution of the energy provisioning of other species? Is that feasible?
My primary idea (given my research bias) is to then apply the findings to the structure of the electrical system. Is the current centralized generation and long distance distribution something that appears in nature? Is there a more efficient way that emerged from evolution in biological context that we can use for future provisioning?

We can apply this not only to electrical systems but more in general to the way we use our resources.

Anyone interested with ideas, feedbacks, thoughts? – [[Giuliano_Andrea_Pagani | Andrea]]

Ecological networks are, indeed, finely structured both topologically and energetically. I'd very much like to talk to you about this idea in more detail. --[[Ashkaan_Fahimipour | Ashkaan]]

Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Cellular morphogenesis - The evolution of organisms' shape'''==

I am interested in genetic design, not as much the modifications of already existing plants and animals but rather the capabilities of from-the-ground-up design of completely new organisms. One of the most basic question when it comes to multicellular organisms is how they end up with their particular shape and how it is a product of cell growth, membrane adhesion, chemical signalling etc. I suggest a project where we explore what types of shapes can emerge in simple cell growth models and how the shape can be controlled by tuning the organisms genes, the interactions. When we have something running, one interesting continuation would be to apply genetic algorithms on the growth parameters and se what happens with the emerging shape if we for example assign high fitness to high surface area but low volume, high moment of inertia or maybe concentric shells of different cell types. We can also compare our results with simple, real organisms and se if nature found similar solutions (shapes).

There are different cellular models we could use, most reasonable would be a cellular potts model (B) or a vertex dynamic model (D) [http://ars.els-cdn.com/content/image/1-s2.0-S0070215309890042-gr4.jpg], depending on what type of details we want to include. I suggest we start out with 2D simulations.

I also believe this project can steer into many different directions, so if you like parts of the premise and have ideas on other directions we could take this, say hi.

Max Planck instutute with a group on this subject: [http://www.mpipz.mpg.de/smith]

A vertex dynamics model investigating how a specific cell morphogenesis could occur: [http://dev.biologists.org/content/113/4/1231.full.pdf+html]

[[Oskar_Lindgren | Oskar]] email me at oskarxvi at gmail dot com

=='''How big can a city be?'''==

West et al. have discovered striking—and universal—patterns in the way cities scale with size (see [http://www.ted.com/talks/geoffrey_west_the_surprising_math_of_cities_and_corporations.html West's Ted talk], [http://www.nature.com/nature/journal/v467/n7318/abs/467912a.html short Nature paper], [http://www.pnas.org/content/104/17/7301.short longer PNAS paper]). Do these scaling laws allow us to predict how big a city can be?

Here's a motivating analogy. The mass of an animal grows scales the cube of its size L, but the cross-sectional area of its leg bones scales only like the square of L. This implies that bigger animals must have bulkier leg bones in order to sustain their own weight. (Think of the legs of a mouse versus the legs of an elephant.) Since the bones can never get bigger than the animal itself, this immediately tells you that land animals cannot be arbitrarily large: they must have a maximum size. If you plug in the numbers and estimate this maximum size, you find a value consistent with the largest known dinosaurs. In fact, with similar reasonings—which were discovered by Galileo, by the way—you can easily find how tall trees can be, how high animals can jump, etc [http://galileo.phys.virginia.edu/classes/304/scaling.pdf].

Now, to run a similar argument for cities, we should understand what constraints would limit their size (the equivalent of "the legs of an animal can never be larger than the animal itself"). These constraints may be technical, social—I'm not sure. (Crimes are perhaps an example. West et al. show that the number of crimes committed in a city grows faster than the number of inhabitants. Clearly then, at some point the likelihood to get shot the next day will get too high, and people will start leaving the city.) I wonder if the social scientists among us have any insight about such constraints, and whether we can actually come up with a prediction for the maximal size of a city based on them. – [[Matteo_Smerlak | Matteo]]

- Scaling patterns for cities are fascinating, but a potential data limitation to the PNAS paper is that the study was applied to cities in the US, EU and China. It can be argued that these economies have particular similarities that may not be transferable to cities in developing countries that are not China (e.g. Jakarta, Delhi, Manila). To complicate matters a bit more, there is little consensus on what a city is -- is it defined by the political boundary? What about the economic boundary determined by bedroom communities (suburbs)? If one takes the latter view of a metropolitan area, the population densities of some "cities" in developing countries is truly astounding. The New York metropolitan area can be interpreted as spanning 4500 sq. miles with 20 million people (a density of ~4600 people/sq. mile). Under the same interpretation, Jakarta spans only 1075 sq. miles with 25 million people (a density of ~25,000 people/sq. mile!!!). The point of my comment is that I wonder how well the scaling findings of West et al. hold up for cities in developing countries (that do not include China). It seems possible that there are scaling patterns there as well, but they might be different. By the way, I got my numbers for population densities from [http://www.newgeography.com/content/002808-world-urban-areas-population-and-density-a-2012-update Demographia]. --[[Vanessa_Schweizer | Vanessa]]

- Because of national differences, there's certainly no consensus yet on how to define the boundaries of a city. Even [http://unstats.un.org/unsd/demographic/sconcerns/densurb/densurbmethods.htm UN] recognizes this and suggests following the boundaries established by individual countries. On the point of whether scaling patterns will be the same for developed and developing countries, the scaling patterns might still be the same (wealth creation leads to superlinear scaling while economies of scale results to sublinear scaling) but the actual value of the scaling exponents might vary. It would be interesting to see whether such two sets of exponents exist as it might explain why the experience of living in two cities of the same density can be different (case in point Manila with a pop'n density of 21.9 M vs Shanghai or NY with 20.9 M). To quantify the living conditions/living experience of cities, we can use the [http://www.businessweek.com/news/2012-08-15/melbourne-remains-most-liveable-city-in-the-world Economist Intelligence Unit’s 2012 Global Liveability Survey]. If data is now available for developing countries, it wouldn't be hard to check this. But having lived in Manila and seeing how inefficient collection of census data in such cities can be, I doubt if we can have a substantial sample of developing countries with complete data. We can probably check [http://www.quandl.com/ here].

As for setting the thresholds in computing for the maximal city size, we can use the parameter values for Melbourne as according to the EIU survey, it is the most livable city in the world. If somehow we decide that using this is not a good way of defining the thresholds and there's no other way of setting them, jumping off from Vanessa's point, what we can also do is have several sets of parameter constraints and say that if city A falls under category A with parameter constraints {A}, then this is the maximal size it can have. We can do some clustering analysis of the parameter space to determine the city categories. I think it would be worthwhile to talk to someone from the cities group here in SFI as they've already mentioned before how population growth behaves with the different scaling patterns.--[[Cheryl Abundo | Cheryl]]

— Maximal city size is an interesting question and hard to answer with the boundary problem mentioned by Vennesa and Cheryl— Michael Batty also talks about this problem in 'Cities and Complexity' http://www.amazon.com/Cities-Complexity-Understanding-Cellular-Agent-Based/dp/0262524791. In biological organisms the upper limit is bounded not only by the cross sectional area of bones but also by the metabolic rate which slows down as an organism increases in size to a 3/4 power law (Klieber, West et al.) Metabolism in organisms is basically how ''efficient'' an organism is. What would be the corresponding metabolism of a city? Here is an idea: What if 'urban metabolism' were to be measured as wealth distribution (correlating with the distribution of blood in an organism)? Functional organisms distribute blood to all service volumes and limit non-essential ones when in pathological states. Crime, as you mention Matteo, increases super-linearly and one might very well imagine a large city becoming too dangerous to function— such as the LA riots or something. Perhaps this is like pathology in organisms where crime is, in essence, the system attacking itself, i.e. cancer, immune disorders etc.

West et al. have also found that infrastructure increases sub-linearly with population size making a city, at least physically, more efficient the larger it becomes. Here is a quote from the paper 'A Unified Theory of Urban Living':

“Cities manifest remarkably universal, quantifiable features. This is shown by new analyses of large urban data sets, spanning several decades and hundreds of urban centres in regions and countries around the world from the United States and Europe to China and Brazil. Surprisingly, size is the major determinant of most characteristics of a city; history, geography and design have secondary roles. Three main characteristics vary systematically with population. One, the space required per capita shrinks, thanks to denser settlement and a more intense use of infrastructure. Two, the pace of all socio- economic activity accelerates, leading to higher productivity. And three, economic and social activities diversify and become more interdependent, resulting in new forms of economic specialization and cultural expression. We have recently shown that these general trends can be expressed as simple mathematical ‘laws’. For example, doubling the population of any city requires only about an 85% increase in infrastructure, whether that be total road surface, length of electrical cables, water pipes or number of petrol stations. This systematic 15% savings happens because, in general, creating and operating the same infrastructure at higher densities is more efficient, more economically viable, and often leads to higher-quality services and solutions that are impossible in smaller places. Interestingly, there are similar savings in carbon footprints7,8 — most large, developed cities are ‘greener’ than their national average in terms of per capita carbon emissions. It is as yet unclear whether this is also true for cities undergoing extremely rapid development, as in China or India, where data are poor or lacking.
Similar economies of scale are found in organisms and communities like anthills and beehives, where the savings are closer to 20%. Such regularities originate in the mathematical properties of the multiplenetworks that sustain life, from the cardiovascular to the intracellular. This suggests that similar network dynamics underlie economies of scale in cities” (West, Bettencourt, A Unified Theory of Urban Living 2010).

I have been developing a tool in NetLogo to measure the fractal dimension of cities which, together with other metrics such as density, could afford an appropriate means to gauge the efficiency of various cities with the assumption that higher fractal dimension = more efficient distribution networks. I am interested in simulating cities with genetic algorithms and dimensioning the results— this technique could possibly support an endogenous limit to growth hypothesis using some fitness criteria such as the EIU parameters. Ecological services certainly decrease with city size and has prompted West to suggest that innovation must increase at an ever faster rate to offset the negatives imposed by growth. Here is another quote from West et al.:

“Open-ended growth is the primary assumption upon which modern cities and economies are based. Sustaining that growth with limited resources requires that major innovations — such as those historically associated with iron, coal and digital technology — be made at a continuously accelerating rate. The time between the ‘Computer Age’ and the ‘Information and Digital Age’ was some 20 years, compared to thousands of years between the Stone, Bronze and Iron Ages.Making major technological paradigm shifts systematically faster is clearly not sustainable, potentially leading to collapse of the entire urbanized socio-economic fabric. Avoiding this requires understanding whether we can continue to innovate and create wealth without continuous growth and its compounded negative social and environmental impacts” (West, Bettencourt 2010).

Fractal dimension applied to cities is still in its infancy and I wonder if this metric itself is necessary to refine relative to the questions this project presents. Multi-fractals for instance are a more nuanced metric and have not been applied to cities to my knowledge. [[John Driscoll | John Driscoll]]

'''To those still interested in discussing this further, I suggest we meet at lunch time later (6 June, 12pm)''' -Cheryl

=='''PRISM / NSA'''==

New media accounts are talking about the scale of the US National Security Agency's surveillance program (Hey, NSA folks!). It looks like they're running some network analysis with >70 trillion (not a typo) edges. We've got a good group of network people here. Anyone want to do something topical and try to put together a discussion / estimation of what can and can't be done with data that big? -- David

Complex Systems Summer School 2013-Tutorials

2013-06-06T21:19:09Z

Masad:

{{Complex Systems Summer School 2013}}

CSSS participants come from a wide range of disciplines. Participants are encouraged to share their knowledge by organizing their own tutorials.

Also, please post requests for tutorials here.

This is not a Tutorial! I [[Pablo_Galindo]] had nowhere else to post it! Its an article pointing out 15 mistakes that could sink your academic careers!
http://chronicle.com/article/Self-Sabotage-in-the-Academic/138875/

'''Bayesian Modeling'''
I'd love to attend tutorials on Bayesian Modeling. I will be happy if someone can give a series of tutorials on this topic. [[Reniel_Cabral | Ren]]

I would also be interested in this! -Brady

* I might be able to help with this, though likely in more of a discussion format, perhaps with some slides stolen from a colleague :) [[Nix_Barnett | Nix]]

* Thanks [[Nix_Barnett | Nix]]! [[Reniel_Cabral | Ren]]

'''Dynamics in Networks'''

I am very interested in learning about network dynamics. Anyone else interested in having a tutorial on that? [[Regina_Martinez | Regina]]

* I'm very experienced with hidden Markov models, which are a generalization of Markov chains. These are networks with a (potentially stochastic) dynamic. Maybe this would help! [[Nix_Barnett | Nix]]

'''Cross impact balances and Markov chains'''

For anyone who could not make the tutorial, [https://docs.google.com/file/d/0B_w3ogGtuejzVG1Ma2tKenN2QjQ/edit?usp=sharing here is a copy of the slides], which provide another way of interpreting [http://www.cross-impact.de/english/CIB_e_Alg.htm web pages explaining the CIB algorithm]. Note that from the cross-impact balance analysis web site, you can download the free software to play with CIB analysis yourself. I am also happy to talk more one-on-one if needed! --[[User:Vanessas|Vanessas]] 02:24, 6 June 2013 (UTC)

As part of brainstorming for a possible project, three of us have decided to do a tutorial on [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] (delivered by [[Vanessa_Schweizer | Vanessa]]) and Markov chains (delivered by [[Alastair_Jamieson-lane | Alastair]] and [[Matteo_Smerlak | Matteo]]). We think these methods could be leveraged to research some interesting questions. All are invited to this tutorial regardless of their interest in contributing to a project using these methods. This tutorial will be Wed. June 5th at 4:00 PM in the large lecture hall. --[[Vanessa_Schweizer | Vanessa]] 
PS -- For those interested in examples of studies that have used CIB analysis, see this one on [http://iopscience.iop.org/1748-9326/7/4/044011/article century-long socioeconomic scenarios] or this abstract on a [http://link.springer.com/article/10.1007%2Fs10389-011-0473-8 qualitative model regarding obesity development and prevention].

'''Python (and MASON)'''

If anyone is interested, I'd be happy to organize and run/co-run a Python programming tutorial. If anyone needs agent-based models beyond what NetLogo can handle, I'd be happy to run a tutorial on the [http://cs.gmu.edu/~eclab/projects/mason/ MASON] framework. -- [[David_Masad]]

Although I've been programming in python, this is the first time I've heard of MASON. I'm interested in learning about your framework. -- [[Cheryl_Abundo]]

I'd very interest on such tutorials --[[Mauricio_Cantor]]

I would also be interested in something on python -Brady

'''Genetic Algorithms and Multi-Objective Optimization'''

I have seen many people interested in implementing GAs to evolve networks, which is something I have done for some of my research. I also worked with Multi-Objective Optimization (MOO), which is perfectly possible with GAs and has been around for a while; but it has not become so mainstream. I propose to make a brief tutorial of classic Genetic Algorithm vs. Multi-Objective Genetic Algorithm. Enough people interested? If we are a few of us, we could just meet up and I'll tell you the basics! -- [[Luís_Seoane | Luíño]]
I would be very interested! --[[Molly_King | Molly]]

Me too --[[Mauricio_Cantor]]

Me too --[[Elena_Stepanova | Elena]]

Me too! --[[Matteo_Smerlak | Matteo]]

Me too --[[Cheryl_Abundo | Cheryl]]

'''Nix's Bag O' Mathematical Tools'''

I'm planning on giving a number of tutorials to supplement Jim Crutchfield and I's lectures. The purpose of these should be to help you with your projects ( and encourage usage of our methods ;) ). I think it'd be cool for people to use this area to suggest topics to focus on. I started an empty bulleted list below. This will become more clear after we've given our lectures, but feel free to throw ideas out there when they come up. General topics might be: Information theory, time series analysis/modeling/prediction, symbolic dynamics (coarse-graining dynamical systems, i.e. what Liz Bradley discussed briefly), hidden Markov models, signal processing, bayesian inference, complexity measures, etc. [[Nix_Barnett | Nix]]
*Intro to information theory. There seems to be some interest in this. I'd be happy to give a tutorial, but I should note that it will be covered (at a rapid pace) in Jim Crutchfield's lecture. [[Nix_Barnett | Nix]]
* I really want to learn how to fit hidden Markov models to data. --David
*

Complex Systems Summer School 2013-Tutorials

2013-06-06T21:18:46Z

Masad:

{{Complex Systems Summer School 2013}}

CSSS participants come from a wide range of disciplines. Participants are encouraged to share their knowledge by organizing their own tutorials.

Also, please post requests for tutorials here.

This is not a Tutorial! I [[Pablo_Galindo]] had nowhere else to post it! Its an article pointing out 15 mistakes that could sink your academic careers!
http://chronicle.com/article/Self-Sabotage-in-the-Academic/138875/

'''Bayesian Modeling'''
I'd love to attend tutorials on Bayesian Modeling. I will be happy if someone can give a series of tutorials on this topic. [[Reniel_Cabral | Ren]]

I would also be interested in this! -Brady

* I might be able to help with this, though likely in more of a discussion format, perhaps with some slides stolen from a colleague :) [[Nix_Barnett | Nix]]

* Thanks [[Nix_Barnett | Nix]]! [[Reniel_Cabral | Ren]]

'''Dynamics in Networks'''

I am very interested in learning about network dynamics. Anyone else interested in having a tutorial on that? [[Regina_Martinez | Regina]]

* I'm very experienced with hidden Markov models, which are a generalization of Markov chains. These are networks with a (potentially stochastic) dynamic. Maybe this would help! [[Nix_Barnett | Nix]]

'''Cross impact balances and Markov chains'''

For anyone who could not make the tutorial, [https://docs.google.com/file/d/0B_w3ogGtuejzVG1Ma2tKenN2QjQ/edit?usp=sharing here is a copy of the slides], which provide another way of interpreting [http://www.cross-impact.de/english/CIB_e_Alg.htm web pages explaining the CIB algorithm]. Note that from the cross-impact balance analysis web site, you can download the free software to play with CIB analysis yourself. I am also happy to talk more one-on-one if needed! --[[User:Vanessas|Vanessas]] 02:24, 6 June 2013 (UTC)

As part of brainstorming for a possible project, three of us have decided to do a tutorial on [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] (delivered by [[Vanessa_Schweizer | Vanessa]]) and Markov chains (delivered by [[Alastair_Jamieson-lane | Alastair]] and [[Matteo_Smerlak | Matteo]]). We think these methods could be leveraged to research some interesting questions. All are invited to this tutorial regardless of their interest in contributing to a project using these methods. This tutorial will be Wed. June 5th at 4:00 PM in the large lecture hall. --[[Vanessa_Schweizer | Vanessa]] 
PS -- For those interested in examples of studies that have used CIB analysis, see this one on [http://iopscience.iop.org/1748-9326/7/4/044011/article century-long socioeconomic scenarios] or this abstract on a [http://link.springer.com/article/10.1007%2Fs10389-011-0473-8 qualitative model regarding obesity development and prevention].

'''Python (and MASON)'''

If anyone is interested, I'd be happy to organize and run/co-run a Python programming tutorial. If anyone needs agent-based models beyond what NetLogo can handle, I'd be happy to run a tutorial on the [http://cs.gmu.edu/~eclab/projects/mason/ MASON] framework. -- [[David_Masad]]

Although I've been programming in python, this is the first time I've heard of MASON. I'm interested in learning about your framework. -- [[Cheryl_Abundo]]

I'd very interest on such tutorials --[[Mauricio_Cantor]]

I would also be interested in something on python -Brady

'''Genetic Algorithms and Multi-Objective Optimization'''

I have seen many people interested in implementing GAs to evolve networks, which is something I have done for some of my research. I also worked with Multi-Objective Optimization (MOO), which is perfectly possible with GAs and has been around for a while; but it has not become so mainstream. I propose to make a brief tutorial of classic Genetic Algorithm vs. Multi-Objective Genetic Algorithm. Enough people interested? If we are a few of us, we could just meet up and I'll tell you the basics! -- [[Luís_Seoane | Luíño]]
I would be very interested! --[[Molly_King | Molly]]

Me too --[[Mauricio_Cantor]]

Me too --[[Elena_Stepanova | Elena]]

Me too! --[[Matteo_Smerlak | Matteo]]

Me too --[[Cheryl_Abundo | Cheryl]]

'''Nix's Bag O' Mathematical Tools'''

I'm planning on giving a number of tutorials to supplement Jim Crutchfield and I's lectures. The purpose of these should be to help you with your projects ( and encourage usage of our methods ;) ). I think it'd be cool for people to use this area to suggest topics to focus on. I started an empty bulleted list below. This will become more clear after we've given our lectures, but feel free to throw ideas out there when they come up. General topics might be: Information theory, time series analysis/modeling/prediction, symbolic dynamics (coarse-graining dynamical systems, i.e. what Liz Bradley discussed briefly), hidden Markov models, signal processing, bayesian inference, complexity measures, etc. [[Nix_Barnett | Nix]]
*Intro to information theory. There seems to be some interest in this. I'd be happy to give a tutorial, but I should note that it will be covered (at a rapid pace) in Jim Crutchfield's lecture. [[Nix_Barnett | Nix]]
* I really want to learn how to fit data to hidden Markov models. --David
*

Complex Systems Summer School 2013-TShirts

2013-06-06T19:30:43Z

Masad:

{{Complex Systems Summer School 2013}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

'''Designs will be voted on June 11th at 2:45p.m.'''

Have fun and be creative!

'''Do note that T-shirts need to be limited to two solid colors, so things like color scaling will not work well because of the screen printing process. If you would like a high-resolution .PSD file, please see JP'''

[[File:SantaFe_Institute.png]]

[[File:CSSSshirt.png]]

[[File:T-SHIRT2.png]]

'''The landscape are the mountains behind St.Johns, and the mandelbrot fractals are the clouds. I can make the landscape less detailed and more simple, uploads will follow - Susanne'''
[[File:SFI t-shirt Mountains & Mandelbrot.png]]

What do you think about this? -- [[Giuliano_Andrea_Pagani | Andrea]]
I have created a cross words from all our names, so maybe we can print this on one sides of the T-shirt. you can find your name, let me know if i skipped any name :)- amara
[[File:CROSS_WORDS.pdf]]

Two things:

- the color could (should) be different than simple white...maybe light gray

- the network on the back has to be carefully drawn since the idea is to have a node for each of us and place it where we come from/study. The edges can then be more or less randomly assigned to have a connected net ;-)

* [[Giuliano_Andrea_Pagani | Andrea]], if you will revise the back drawing, kindly include Philippines =). This is a good design.=) [[Reniel_Cabral | Ren]]

[[File:TshirtAndrea.png]]
[[File:TshirtAndreaback.png]]

[[File:Clanshirt.png]]

Not sure of a design, but something with '''Phase Space Camp'''?

Complex Systems Summer School 2013-TShirts

2013-06-06T19:30:27Z

Masad:

{{Complex Systems Summer School 2013}}

Every year we have a T-shirt design contest, where CSSS Students create designs (relevant to the summer school) and during the end of the second week we vote on the one we will print and distribute to the cohort. Please post your T-shirt design below. The design will be printed on a single colored T-shirt (keep in mind which color T-shirt you would like to print on while planning your design). The print that will go on the T-shirt is limited to a two color back and a one color front.

'''Designs will be voted on June 11th at 2:45p.m.'''

Have fun and be creative!

'''Do note that T-shirts need to be limited to two solid colors, so things like color scaling will not work well because of the screen printing process. If you would like a high-resolution .PSD file, please see JP'''

[[File:SantaFe_Institute.png]]

[[File:CSSSshirt.png]]

[[File:T-SHIRT2.png]]

'''The landscape are the mountains behind St.Johns, and the mandelbrot fractals are the clouds. I can make the landscape less detailed and more simple, uploads will follow - Susanne'''
[[File:SFI t-shirt Mountains & Mandelbrot.png]]

What do you think about this? -- [[Giuliano_Andrea_Pagani | Andrea]]
I have created a cross words from all our names, so maybe we can print this on one sides of the T-shirt. you can find your name, let me know if i skipped any name :)- amara
[[File:CROSS_WORDS.pdf]]

Two things:

- the color could (should) be different than simple white...maybe light gray

- the network on the back has to be carefully drawn since the idea is to have a node for each of us and place it where we come from/study. The edges can then be more or less randomly assigned to have a connected net ;-)

* [[Giuliano_Andrea_Pagani | Andrea]], if you will revise the back drawing, kindly include Philippines =). This is a good design.=) [[Reniel_Cabral | Ren]]

[[File:TshirtAndrea.png]]
[[File:TshirtAndreaback.png]]

Not sure of a design, but something with '''Phase Space Camp'''?

[[File:Clanshirt.png]]

Complex Systems Summer School 2013-Blog

2013-06-06T16:49:47Z

Masad:

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-05T22:27:57Z

Masad: /* 2) co-evolution of a network and attacker */

[[Link title]]{{Complex Systems Summer School 2013}}

==Project Proposals==

=='''MOOCs'''==
I have had an interest in MOOCs and their potential role in the future of education/ as a means of providing education to non-traditional students. This has been in the back of my mind for some time, but I have no experience dealing with real social data (including how to access it) and was hoping other people might be interested. I did a brief search and found that it may be possible to use twitter data. The questions I am interested in are where MOOCs are popular (globally), how it spread, what kind of topics, etc. Anyone else interested?

-Swati

=='''Food webs'''==
It seems like there is A LOT of interest in food webs amongst this group. Since there are so many people, maybe it would be worth coming together and dividing into smaller groups based on the questions (there are many!) people are interested in addressing and skills. I think it would good be to have some coordinated effort, for efficiency and productivity. We could divide questions, or parts of bigger questions, or approach the same questions, using different methods and then compare results and try to understand the similarities and differences. Maybe we could meet at 3 pm today (Wed) or at dinner.

-Swati

=='''A Midsummer Night's Project: Comedy and Tragedy in Shakespeare'''==

Max Kleiman-Weiner and I have a corpus of all the Shakespeare plays and have been talking (with many of you, too!) about building a system to automatically classify Shakespeare plays as either comedy or tragedy. A simple approach would be to just use a bag of words to see if the plays can be classified based on lexical content alone. We have also been discussing building social networks for each play based on which characters interact (i.e., who speaks before and after whom). We suspect that the social network structure of a comedy and tragedy should look different from each other. Do characters in comedies have more connections? Do tragedies and comedies start off the same and then have networks that evolve differently over the course of the play? Or are they different from Act I? This may be an opportunity to look at how social networks change over time in a specific domain. We could also look at the different roles of men and women in the social networks of the plays.

-Kyle M

This sounds interesting and doable. I've done a work on author attribution of opinion articles before using only syntactic (function words like prepositions and articles, punctuations), structural (sentence length, paragraph length) and lexical (other non-specific words) features. It'd be nice to see if the same thing will work for this. I think it will be more fascinating to explore the social network approach and we should definitely give it a shot if there's still time.

-Cheryl

Stories are always good. Incidentally, are you familiar with Kurt Vonnegut's commentary on the shapes of stories? If not, it's not hard to find. If so, there may be something to be said for attempting to determine whether a story conforms to more specific tropes (e.g. Cinderella stories and "The Chosen One"). Moreover, if enough distinct patterns do emerge out Shakespeare's plays, it may prove interesting to compare these to other stories (e.g. novels available on Project Gutenberg).

-Eitan

There is now a DropBox with the corpus and some preliminary Python scripts - so come find me if you're interested in getting linked in.

-Max

=='''Recursive Agents'''==

A common theme that I've seen in complexity is that you can represent many different systems (cells, agents, civilizations, for example) with more or less the same rules. I'm wondering if anyone would be interested in modeling this? Essentially we develop a recursive rule set: agents' behavior are based on a set of their 'inner agents,' which also follow similar rules.

-Todd

=='''Global Emergent Risk'''==

In the current phase of globalization, networks in logistics, travel, finance, disease, energy, and ecology are growingly increasingly interconnected on a global scale. Hence, situations arise where mortgage defaults in the US bring down the Icelandic pension system, and a volcano in Iceland disrupts global air traffic. Given the scale of interconnectedness, can complexity science help develop a sense of how small perturbations in one global network might cascade into large unforeseen failures in another network? I'm wondering if we can help build a more generic grammar for describing interconnected networks and the risks posed by such systems. Would it be possible to mitigate risk at smaller local levels of scale, or do small corrections of local risk inevitably cascade into larger risks that we lack the ability to respond to (think wildfires in the Southwest where more frequent small fires would help reduce the chance of large scale fires that cannot be controlled.) I'd love to talk with anyone interested in ecology, globalization, risk, and network modelling.

My advisor at Princeton is already funded for a three year interdisciplinary symposium on Global Emergent Risk, so if people are interested, we have resources to carry on a larger research engagement.

--[[Manish_Nag | Manish]]

- I don't know if large risk cascades are inevitable, but these are timely questions. I have colleagues at the [http://gcrinstitute.org/ Global Catastrophic Risk Institute] who are also interested in this topic. I'm not sure what building a "more generic grammar" means, but the cross-impact balance method is pretty generic. Hopefully you can make our [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]]! Our group is kicking around methods for a project at the moment and have not decided on research questions, so perhaps we can join forces. --[[Vanessa_Schweizer | Vanessa]]

- To clarify, what I meant by "generic grammar" is some way to describe a set of networks and cross network dependencies that can be decoupled from the content of the network. We could use this language to describe interconnections between hypothetical logistics, travel, financial networks for example, and then use simulations to understand the conditions where risks might be amplified and/or jump across from one network to another. --[[Manish_Nag | Manish]]

- I'd love to join discussions on this as I agree that there's a need to start thinking about network of networks and not just networks in isolation. The [http://arxiv.org/abs/1010.5829 paper by Gao, Stanley et al.] on the robustness of a network of networks might be useful. --[[Cheryl_Abundo | Cheryl]]

--I'm in .[[Reniel_Cabral | Ren]]

=='''Alcohol Consumption and Language Fluency'''==
 
''(This is just one of my random thoughts, don't take it too seriously. I'm bringing it up in case it would actually add interesting noises to anyone's thought process)'' 
There's a interesting thing about me and some of my friends who speak a foreign language. There seems to be a kind of non-linear curve that depicts my blood alcohol concentration and the fluency of my speaking English (Chinese is my native language). For example, usually after one beer, I start to talk faster, and semantically relevant words pop up in my mind more fluently or spontaneously. Or say, I express the same idea with less stuttering and in shorter time. But after some point, i.e. 32 oz of beer, even it might still sound fluent, regarding the physical property of the speech, the grammatical structure of the sentences start to break down. Ultimately, i.e. half bottle of rum, I only repeat 2-3 very short sentences/phrases independent of the presence or the identity of my audience(s) (i.e. murmuring in English for hours to a group of Chinese friends). 
We know that alcohol can influence our behavior by, among other things, binding to certain neural receptors (like GABAa?). I just thought it might be interesting to model how alcohol intake influences the dynamics of language production via regulating neuron signaling. I'm also wondering about what it might imply about our brain dynamics when we're silent. 
Welcome to talk to me if you find this interesting, or silly, or you simply want to correct my grammar. Thanks! 
-Mengsen Zhang

@Mengsen I'd be very interested in doing some empirical work on this topic.
-Max Kleiman-Weiner

I've experienced this same thing with Spanish, Bahasa Indonesia, and playing billiards/pool. Sadly, my math skills do not improve with drinking, and math could arguably be considered a language. This is a creative topic with solid scientific underpinnings that nicely lend themselves to complex systems modeling, I suspect. Fun! – [[Kristen_Honey | Kristen Honey]]

On a related note:
http://xkcd.com/323/

-Eitan

=='''How the ocean can help us heal complex chronic disease'''==

The human body is its own ecosystem -- much like the ocean -- with resilience, hysteresis, synergistic properties, and multi-system dynamics that depend on matrix conditions. Can we use our understanding of the ocean and ecosystems to help us heal? Can we model different scales -- an ocean, a human body, and a microbial community -- to explore ecosystem/human/microbial health in a holistic context that depends on shared key elements like flow & trace minerals as building blocks for function? As one example to think about, chronic illnesses like HIV/AIDS or Lyme disease disrupt the immune system and human body functions (e.g., methylation pathways, detox pathways), preventing optimal function that weakens the human body and makes it vulnerable to other infections. It’s a downward spiral of negative feedbacks, analogous to a backed-up, atrophying ocean or estuary that causes fish kills, destroys coral reefs, etc... analogous to microbial communities that shift when environmental/matrix condition change. I suspect our knowledge of the ocean & large ecosystems, which we can see and visualize, can inform new thinking about system dynamics for health & recovery at the scale of a human body and at the scale of individual microbes & microbial communities...

Anyone else interested? – [[Kristen_Honey | Kristen Honey]]

- This sounds like a really nice idea. It would be interesting to understand how the disease-mediated degradation of immune/metabolic networks (the loss or alteration of edges and nodes?) affects the response of these networks to further perturbations (e.g. asymptotic stability and resilience, [http://www.jstor.org/stable/2266047 transient reactivity], cascading effects of node loss, etc.). I have little knowledge of the medical literature, but I am experienced in ecological network analysis including information theoretic analyses of weighted food webs. -- [[Ashkaan_Fahimipour | Ashkaan]]

- I liked the idea very much. In fact I am looking at similar issues related to management of ecosystems which display hysteresis and [http://arno.uvt.nl/show.cgi?fid=121389 regime shifts]. Here is some pertinet information related to [http://www.esajournals.org/doi/abs/10.1890/1051-0761%281999%29009%5B0751%3AMOEFLS%5D2.0.CO%3B2 shallow lakes] and its [http://ideas.repec.org/p/att/wimass/200026.html complex dynamics]. Your idea of scaling down to human level is interesting -- [[Puduru Reddy | Vishwa]]

- Sounds interesting. I have experience in microbial oceanography, but not so much with infectious disease. I'll be there for the dinner meeting. - [[Jody_Wright | Jody Wright]]

==
Join us for project discussion & brainstorming ideas, Wednesday June 5th dinner at 5:00. Everyone welcome! ==

=='''GDELT'''==

[[David_Masad | I'd]] love to play around with the new [http://gdelt.utdallas.edu/ Global Data on Events, Location and Tone (GDELT)] dataset, which has 200+ million timestamped and geocoded political events. Here's a [http://ideas.foreignpolicy.com/posts/2013/04/10/what_can_we_learn_from_the_last_200_million_things_that_happened_in_the_world writeup of it in Foreign Policy] -- David

=='''Research Network Formation'''==

I'd be interested in collecting some data from CSSS attendants. Some kind of way to study social network formation. -- [[Todd_Bodnar | Todd]]

Perhaps we could collect survey questions people might be interested in looking at in a [https://docs.google.com/document/d/1h_8TUyuDNT1DhPIyZuGwuvrqSExLgwoocsKZl4jFSk8/edit?usp=sharing Google Doc]? --[[Molly_King | Molly]]

My new crazy idea, inspired by [http://blog.premise.is/blog/2013/5/5/mapping-the-produce-manifold these guys], is doing something with computer vision. Maybe there's a way to photograph sitting arrangements and extract data from that? -- David

Project meeting after the lab Wednesday 6/5 for all those interested.

=='''Self-consistent networks for socio-economic institutions'''==

[[Pablo_Galindo | Pablo]] and [[Vanessa_Schweizer | I]] started to discuss a project where we could use [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] to investigate the implications of alternative hypotheses for interrelationships between various socio-economic/political factors. We began discussing this from the perspective of testing competing political economic theories to see what types of institutions (e.g. styles and stability of governance) would be self-consistent according to the theories. However, I would be open to other topics, including research questions inspired by GDELT. If there is interest to learn more about the CIB technique, I could put together a tutorial. --[[Vanessa_Schweizer | Vanessa]]

- There's a paper written by Brian Arthur here at the SFI that might help us frame our topic. Its called Complexity Economics. Basically sets the "rules" for thinking about economics in a whole different way.
It is a very good starting point so we don't go any further wasting time taking into account economic models that are vague, non-accurate and out of date. [[Pablo_Galindo | Pablo]] [?]

Elaborating more on the idea. If we focus on human action as the essence of culture. Understanding human action as the use of beliefs, attitudes and resources (which are scarce) pursuing a state of higher satisfaction. And culture as the sum of all beliefs, attitudes and unintentional consequences of the human action. We can state that the emergence of socio-econmic/political factors are the unintentional consequence of intentional individual actions that at the same time affect the way people act, in what they believe and what attitude they'll have toward the satisfaction of their needs. (Theres a loop between human action and culture - culture affects human action and human action affects culture and so forth)
Some "institutions" will emerge as a consequence of human action but not human design. That is one of the characteristics of a "good" type of institution. (e.g. Money, language, private property, contracts, a certain type of government) and it would be interesting to test the robustness of that spontaneously emerged institution against human designed institution who's robustness is just that is law enforced.
I dunno If you get my point? Compare the qualities of spontaneously emerged institutions against human designed institutions. Its more or less comparing spontaneously emerged institutions (no leader needed to coordinate like the birds flocking) vs. human designed institutions (leader needed to coordinate al human actions).

==
A [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]] on cross-impact balances and Markov chains is scheduled for Wed. June 5 at ~4:15. Everyone is welcome, even if your project interests lie elsewhere. ==

=='''Genetic algorithms to evaluate network formation or real-world data'''==
I have an ill-defined, wacky idea to possibly use genetic algorithms to evaluate the formation of networks as either following preferential attachment or homophily (aka similarity) rules. This [http://www.nature.com/doifinder/10.1038/nature11459 short Nature paper] looks at the debate between preferential attachment and similarity/homophily dynamics. I don't have a clear idea of what this would look like, but I think it might be fun to think about ways to use genetic algorithms to solve network problems. Talk to me if you think this remotely interesting and we can evolve an idea together? --[[Molly_King | Molly]]

Another possibility would be using genetic algorithms or attachment algorithms to compare to models of real-world data to understand how these networks likely formed and predict future edges.

Molly, I would like to investigate using GA to create an organizational network structure (think org chart or military chain of command or even project groups at the CSSS) and then compare it to existing structures. Let's talk! -John L

Some people were also talking about co-evolution of a network and an attacker that disconnects nodes or edges. -- David

Everyone interested in this and related meet Wed 6/5 at 4pm in main lecture hall - group of folks interested in studying network evolution/fitness/information/energy spread meeting. --Molly

Seem to be two branches of this: 
1) network evolution toward a predefined fitness function (energy, information efficiency, etc.) via genetic algorithms - what structures evolve? 
2) co-evolution of a network and attacks of different forms - what structural changes take place? which structures are robust to attacks?

===1) network evolution toward a predefined fitness function===

=== 2) co-evolution of a network and attacker ===

Interested members: Elena, Andrea, Stephan, Bruno, Johannes, David M., Holly

We're thinking about co-evolving a network and an attacker agent. The network's fitness is robustness (to be defined later) to attack, and the attacker's fitness is disruption of the network. Both also need to be subject to some sort of resource constraint -- otherwise the optimal network is fully-connected, and the attacker's optimal strategy is just disconnecting all of the nodes.

Some background reading:
http://www.talkorigins.org/faqs/tierra.html

http://www.researchgate.net/publication/220841044_Formal_Methods_for_Modeling_Socio-technical_Innovation_between_Adversaries?ev=prf_pub

Tools:
Probably Java or Python. We need something that has network metrics already, so we don't need to code them ourselves. Possibly use a GA package / library as well.

=='''Caribou Management Dynamics'''==

This project would model caribou management dynamics in a prototype NW Alaska community during a caribou shortage. Agents in the model would be informed by data from household subsistence surveys and from management history. The goal would be to evaluate the abilities of different management strategies to achieve biological harvest goals while maximizing economic efficiencies in the community. This is a real-world problem with near-term applications. Caribou cycle on 30-to-50 year periods. The Western Arctic Caribou Herd is currently in decline. During the last caribou “crash” in this region, the state management system attempted to reorganize caribou production, which generated considerable political and social disruption, precipitated widespread passive resistance among Native peoples, and left a legacy of contempt for both management (among some Inuit) and for Inuit hunters (among some sport users). The hope is to reduce conflicts during the expected nadir of the population. Comments and cooperators welcome! [[James Magdanz | Jim]]

Neat topic with data, I assume! I'm interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Evolving synchronized flashes in fireflies, and other polymorphic traits'''==

[[Bryn_Gaertner | I ]] was thinking about how some, but not all, species of fireflies can synchronize their flashes, as was mentioned in both lectures today (June 4). The mechanism is fairly simple, it seems, so we should be able to evolve it using a simple genetic algorithm, right? This is only half-baked at the moment, and I haven't checked to see if it has been done already, but I thought it would be neat to explore the space around these biological phenomena. More of a fun project than a serious "lets publish this!" type of project. Bonus points if we can work some neural network stuff into it. [[Bryn_Gaertner]]. -- EDIT -- Upon further discussion with [[Rebecca_Mease | Rebecca]] and [[Holly_Arnold | Holly]], we would like to extend this. Still using genetic algorithms, under what conditions can we evolve a stable polymorphic trait in a population, and under what conditions does a monomorphic trait evolve? This is applicable for traits in a population, but we would like to use the same model to evolve (for example) multiple or novel sensory modalities in a species, number of members in a food web, predation strategies, etc. Interested? Find us at lunch!

=='''How do historic facts collapse into written history?'''==

Let's begin with a nice example: [http://en.wikipedia.org/wiki/Gilgamesh Gilgamesh], the fifth king of Uruk, decided to gather together some stories that local tribes and surrounding cultures had been telling for years, along with things that previous kings had done. This became the [http://en.wikipedia.org/wiki/Epic_of_Gilgamesh Epic of Gilgamesh]. Someone later does a cover of the original book with some new contributions and turns it into what nowadays is the bible and the torah. Another remake of the tale turns these books into the quran, and until today... you know the rest of the story already. Peer reviewed quality, just like Nature or PNAS.

It might be interesting to study how history goes from facts to a written, definitive form which is not (and maybe cannot be) completely faithfully to the actual events. There is huge room to use, for example, models of agents that contribute to form a History with pieces of information that sums up, sometimes with contradicting versions, sometimes with hidden interests, etc etc. Furthermore, we have a great tool in the wikipedia!! We can track, for example, how many changes are made on different entries over time. We can check whether there are some generalities, how the number of edits depends on the time gone after the historic event, maybe we can quantify how successive stories differ from each other and whether there are turning points that dramatically change the whole thing...

So this is the general framework. I think this is a very exciting topic and I'd be glad to talk about this with anyone!! Just contact me! -- [[Luís_Seoane | Luíño]]

=='''Meta Food Webs'''==

I'd like to throw out an idea I've had for a while: Most animals use space in very important ways -- predators encounter and consume prey in both 2D and 3D environments, birds and fish migrate across continents in search of resources and mates, and plant pollinators fly or walk from flower to flower, in turn providing an indispensable economic service to humans. The study of food webs attempts to understand how networks of species that eat each other persist in the face of (sometimes constant) external perturbations. Yet, network-level food web studies seldom address the dynamics of animal movement, and I see this as a fundamental shortcoming in our understanding of nature. Recently, scientists in fields like computer science, physics and neurobiology have begun to model and explore [http://www.nature.com/srep/2012/120831/srep00620/full/srep00620.html?WT.ec_id=SREP-20120904 multi-level or multiplex networks] -- networks of nested networks. This seems like a reasonable candidate for the theoretical study of multiple food webs that are linked by spatial networks of animal movement. One preliminary question that comes to mind: How do the number of "mobile" species and the "speed of movement" alter important dynamical properties of complex food webs at larger spatial scales (i.e. at the meta-food web scale)? I am not dead set on answering this question, and I look forward to gaining insight from scientists who study other types of networks. I'm also not set on the multiplex network framework. Potential alternatives that come to mind are IBMs, PDEs on graphs or integrodifference equations. I look forward to any suggestions or bright ideas! --[[Ashkaan_Fahimipour | Ashkaan]]

Very cool topic. Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''(Evolution of) Aging'''==
Sorry that this one is a bit long. I'd like to brainstorm with anybody interested to see if there could be a viable project in the following direction.

Let me first define aging: deterioration that happens as an organism, e.g. a human being, gets physiologically older, eventually leading to increased mortality and/or decreased fecundity.

Some background into the 'classic' theory: Evolution is about getting to be there in the future, that is, you and/or related organisms, for instance offspring. Increased mortality and decreased fecundity as such are clearly unfavorable to getting to be there in the future. Then why could it evolve? Well, evolution tends to become less sensitive to anything happening to an organism as time progresses, because events that take place at some point in time can affect only events that are future to that event. All offspring that an organism already has at some point cannot be affected anymore, and this is a non-decreasing function of time. This can be formalized, and I'd be happy to write down the math if anybody wonders.

It has, however, limited value to theorize too much about age-specific events, while in fact events at different ages are tied together in pathways of causality, dynamic change and so on; age per se is not a cause of anything, and changes at some age do not happen independent of changes at other ages. There are a number of sufficient arguments why the 'age-specific' picture does not capture this reality. I'm skipping these arguments for now, but ask if you are interested.

We have two things that matter for the evolution of aging. 1. The declining sensitivity of fitness to age-specific changes (of some standardized magnitude). 2. The fact that there are constraints that make that what happens at age x is not independent from what happens at the ages in its neighborhood. Thus, the trick is to figure out what the constraints are - this is where complexity may come in - and to combine these with the effect on fitness that age-related change has. The effect on fitness may be solved analytically, but there are various reasons why computation may be preferable, specifically the not always realistic assumptions that are necessary to allow for analytical solutions.

Mechanistically, people tend to think about aging in two ways. The first is that aging is caused by the accumulation of damage. If this damage were all repaired, aging would not occur. People then try to think of reasons why repair would be imperfect. The second way to think about it is as a gradual loss of robustness/control, sometimes in the context of reliability engineering (is anybody familiar with that?). Beautiful medical example: old people need more insulin to process a standardized dose of sugar, and their regulation shows more peaks, especially upward peaks, than that of young people, who tend to need less insulin to process the standardized dose of sugar. Of course, if you consider loss of control as a type of damage, the two are the same, but the distinction is perhaps helpful because the way people tend to think about damage is not in a dynamical way, but just as protein aggregates sitting in the brain, inhibiting the function, cartilage that looses its suspension, etcetera. Again of course, both may influence each other.

Now toward a project proposal. If I think about how complexity may (in part) determine physiological constraints, I think of the following. Usually people tend to think of repair being limited by available energy. But to repair something, the body needs to have available somewhere the information necessary to restore the initial state, and use that information at the place where the damage has occurred to be able to repair. This is where I hypothesize complexity comes in. The necessity of different components of the body to interact may put constraints on repair other than just energetic, it is also a question of whether the energy can actually be used for the repair (flow through the system in the necessary way). That may require space, a certain chemical environment, hormonal setting etcetera that may be incompatible with the proper function of an organism. (Can you repair a car when it is driving?) Also in the 'control/robustness thinking', you have to get back to the original situation to avoid aging. Is that compatible with the best evolutionary outcome?

These are just some ideas I'm throwing at you, as you see it's not perfectly fleshed out yet, which is good, because it should benefit from your perspective. So anybody interested, please let me know!

Cheers,
Maarten

Neat ideas & I welcome more discussion around these topics. Aging is cool from the academic science side, if not from the personal experience side, lol. It seems to me that these same models/concepts for aging also apply to loss of functionality from chronic illness... illness expedites aging? – [[Kristen_Honey | Kristen Honey]]

==Quantifying Synchrony in Dynamics Occuring on Networks==

[http://arxiv.org/pdf/1110.2724v1.pdf Recent work] has focused on developing information theoretic measures for quantifying directed information transfer, with particular applications to social media. These metrics are motivated by the work being done in theoretical / computational neuroscience on the analysis of spike trains. To do this analysis, the behavior of users on a social media platform like Twitter are treated as point processes, where we only keep track of when a tweet occurs, and ignore its content. That is, we treat a user's behavior over time as 'spikes.' Despite the simplicity of the approach, it was found to be successful in identifying key actors within real social networks.

I am interested in applying a similar methodology, but using a [http://arxiv.org/abs/q-bio/0609008 different measure] of synchrony motivated by computational mechanics. This method seeks to learn the hidden states that generate a user's behavior (very much in the flavor of a Hidden Markov Model, but with a few key twists), and then considers the mutual information between the state sequences of the two users.

A first step for this project would be implementing the methodology proposed by Shalizi, et al., on the toy model proposed by Steeg, et al.

If that is successful (and completed quickly), I have a data set (network connections and behavior) of fifteen thousand Twitter users collected over a three month period. We are interested in using this approach to identify dynamical communities (not only users who are connected, but users who behave in synchrony) within the social network. This takes us beyond typical structural community detection that has had great success in the past decade.

These approaches should work with any sort of dynamics occurring on top of a network-type structure, so if you have a different system you would like to use as a test case, I would be very interested to hear about it!

[[David_Darmon | Dave Darmon]]

===A spin off?===

Sorry for editing in your proposal, Dave, but I wanted to comment an idea I have been interested in for a time now. There is this great technique used in neuroscience to pin down the most effective time-course excitation that a neuron can get so that it fires. It basically averages the input a neuron had been getting before each of its spikes. You can find a thorough description in the very popular [http://www.amazon.com/Theoretical-Neuroscience-Computational-Mathematical-Modeling/dp/0262541858 Dayan & Abbott] book on neuroscience. Since you mention the abstraction from tweets to spikes, I would be very interesting in applying such neuro-inspired analysis to this social interactions. Neuroscience has got many more techniques, so I do not pose it as a closed matter. Just open for discussion, but seems like everybody is sleeping by now ;) -- [[Luís_Seoane | Luíño]]

You're referring to the spike-triggered average? I hadn't thought of that!

All of the work I've done has only considered a single user's time series for prediction. I would certainly be interested in looking at how including the 'inputs' to the user (or at least the inputs that occur on Twitter) impact this process. The spike-triggered average seems like a great first start. Computational mechanics also has some tricks in its toolbox that could be used for this sort of input-output problem. -- [[David_Darmon | Dave D]]

===comment on spin off===
Hi, I used spike-triggered averaging (and higher-dimensional extensions, which might be useful in your case) during my thesis, so I would be interested in talking about the application to other systems. [[Rebecca_Mease| Rebecca]]

Great! The folks interested in this project will be meeting during the 3pm time slot today. We don't have a formal meeting place planned: the best I can say is to look for me!

[[David_Darmon | Dave D]]

=='''Energy resources supply patterns from biological systems to humans'''==

My idea is to start a brainstorming, it is nothing more than some disjoints thoughts!!! And many questions without an answer so far!! :-)

I would like to investigate how biological systems obtain their energy requirements. Are there patterns or network structure that evolution has developed and that are efficient for animals/plants?
Can we replicate these structures/networks/patterns in the way we (humans) obtain our energy? Can we learn something from the evolution of the energy provisioning of other species? Is that feasible?
My primary idea (given my research bias) is to then apply the findings to the structure of the electrical system. Is the current centralized generation and long distance distribution something that appears in nature? Is there a more efficient way that emerged from evolution in biological context that we can use for future provisioning?

We can apply this not only to electrical systems but more in general to the way we use our resources.

Anyone interested with ideas, feedbacks, thoughts? – [[Giuliano_Andrea_Pagani | Andrea]]

Ecological networks are, indeed, finely structured both topologically and energetically. I'd very much like to talk to you about this idea in more detail. --[[Ashkaan_Fahimipour | Ashkaan]]

Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Cellular morphogenesis - The evolution of organisms' shape'''==

I am interested in genetic design, not as much the modifications of already existing plants and animals but rather the capabilities of from-the-ground-up design of completely new organisms. One of the most basic question when it comes to multicellular organisms is how they end up with their particular shape and how it is a product of cell growth, membrane adhesion, chemical signalling etc. I suggest a project where we explore what types of shapes can emerge in simple cell growth models and how the shape can be controlled by tuning the organisms genes, the interactions. When we have something running, one interesting continuation would be to apply genetic algorithms on the growth parameters and se what happens with the emerging shape if we for example assign high fitness to high surface area but low volume, high moment of inertia or maybe concentric shells of different cell types. We can also compare our results with simple, real organisms and se if nature found similar solutions (shapes).

There are different cellular models we could use, most reasonable would be a cellular potts model (B) or a vertex dynamic model (D) [http://ars.els-cdn.com/content/image/1-s2.0-S0070215309890042-gr4.jpg], depending on what type of details we want to include. I suggest we start out with 2D simulations.

I also believe this project can steer into many different directions, so if you like parts of the premise and have ideas on other directions we could take this, say hi.

Max Planck instutute with a group on this subject: [http://www.mpipz.mpg.de/smith]

A vertex dynamics model investigating how a specific cell morphogenesis could occur: [http://dev.biologists.org/content/113/4/1231.full.pdf+html]

[[Oskar_Lindgren | Oskar]] email me at oskarxvi at gmail dot com

=='''How big can a city be?'''==

West et al. have discovered striking—and universal—patterns in the way cities scale with size (see [http://www.ted.com/talks/geoffrey_west_the_surprising_math_of_cities_and_corporations.html West's Ted talk], [http://www.nature.com/nature/journal/v467/n7318/abs/467912a.html short Nature paper], [http://www.pnas.org/content/104/17/7301.short longer PNAS paper]). Do these scaling laws allow us to predict how big a city can be?

Here's a motivating analogy. The mass of an animal grows scales the cube of its size L, but the cross-sectional area of its leg bones scales only like the square of L. This implies that bigger animals must have bulkier leg bones in order to sustain their own weight. (Think of the legs of a mouse versus the legs of an elephant.) Since the bones can never get bigger than the animal itself, this immediately tells you that land animals cannot be arbitrarily large: they must have a maximum size. If you plug in the numbers and estimate this maximum size, you find a value consistent with the largest known dinosaurs. In fact, with similar reasonings—which were discovered by Galileo, by the way—you can easily find how tall trees can be, how high animals can jump, etc [http://galileo.phys.virginia.edu/classes/304/scaling.pdf].

Now, to run a similar argument for cities, we should understand what constraints would limit their size (the equivalent of "the legs of an animal can never be larger than the animal itself"). These constraints may be technical, social—I'm not sure. (Crimes are perhaps an example. West et al. show that the number of crimes committed in a city grows faster than the number of inhabitants. Clearly then, at some point the likelihood to get shot the next day will get too high, and people will start leaving the city.) I wonder if the social scientists among us have any insight about such constraints, and whether we can actually come up with a prediction for the maximal size of a city based on them. – [[Matteo_Smerlak | Matteo]]

- Scaling patterns for cities are fascinating, but a potential data limitation to the PNAS paper is that the study was applied to cities in the US, EU and China. It can be argued that these economies have particular similarities that may not be transferable to cities in developing countries that are not China (e.g. Jakarta, Delhi, Manila). To complicate matters a bit more, there is little consensus on what a city is -- is it defined by the political boundary? What about the economic boundary determined by bedroom communities (suburbs)? If one takes the latter view of a metropolitan area, the population densities of some "cities" in developing countries is truly astounding. The New York metropolitan area can be interpreted as spanning 4500 sq. miles with 20 million people (a density of ~4600 people/sq. mile). Under the same interpretation, Jakarta spans only 1075 sq. miles with 25 million people (a density of ~25,000 people/sq. mile!!!). The point of my comment is that I wonder how well the scaling findings of West et al. hold up for cities in developing countries (that do not include China). It seems possible that there are scaling patterns there as well, but they might be different. By the way, I got my numbers for population densities from [http://www.newgeography.com/content/002808-world-urban-areas-population-and-density-a-2012-update Demographia]. --[[Vanessa_Schweizer | Vanessa]]

- Because of national differences, there's certainly no consensus yet on how to define the boundaries of a city. Even [http://unstats.un.org/unsd/demographic/sconcerns/densurb/densurbmethods.htm UN] recognizes this and suggests following the boundaries established by individual countries. On the point of whether scaling patterns will be the same for developed and developing countries, the scaling patterns might still be the same (wealth creation leads to superlinear scaling while economies of scale results to sublinear scaling) but the actual value of the scaling exponents might vary. It would be interesting to see whether such two sets of exponents exist as it might explain why the experience of living in two cities of the same density can be different (case in point Manila with a pop'n density of 21.9 M vs Shanghai or NY with 20.9 M). To quantify the living conditions/living experience of cities, we can use the [http://www.businessweek.com/news/2012-08-15/melbourne-remains-most-liveable-city-in-the-world Economist Intelligence Unit’s 2012 Global Liveability Survey]. If data is now available for developing countries, it wouldn't be hard to check this. But having lived in Manila and seeing how inefficient collection of census data in such cities can be, I doubt if we can have a substantial sample of developing countries with complete data. We can probably check [http://www.quandl.com/ here].

As for setting the thresholds in computing for the maximal city size, we can use the parameter values for Melbourne as according to the EIU survey, it is the most livable city in the world. If somehow we decide that using this is not a good way of defining the thresholds and there's no other way of setting them, jumping off from Vanessa's point, what we can also do is have several sets of parameter constraints and say that if city A falls under category A with parameter constraints {A}, then this is the maximal size it can have. We can do some clustering analysis of the parameter space to determine the city categories. I think it would be worthwhile to talk to someone from the cities group here in SFI as they've already mentioned before how population growth behaves with the different scaling patterns.--[[Cheryl Abundo | Cheryl]]

Bandelier 2013

2013-06-05T21:43:04Z

Masad: /* JP's Volunteer Camry: 5 Seats */

{{Complex Systems Summer School 2013}}

Please sign up here so we know who's going. 
Also: If you have a car, please put it down. The more cars we have, the more people we can take. 

We'll meet Saturday at 10:00am in the parking circle.

Please remember to bring a hat, sunscreen, water, hiking shoes, and anything else you'll need for a day out in the field.

If you would like to rent a car please visit the [http://santafe.edu/about/contact/ground/ SFI website] for more info

==Cars:==

===Tom's Sedan, 5 Seats===
1.Tom Carter 
2. Kristen Honey 
3. Jody Wright 
4. Kerstin Damerau 
5. Elisa Omodei 

===JP's Volunteer Camry: 5 Seats===
Note: This car needs a volunteer driver 
1. David M. (willing to drive) 
2. 
3. 
4. 
5. 

===JP's Other Car: 2 Seats===
1. JP 
2.

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-05T16:18:07Z

Masad: /* Genetic algorithms to evaluate network formation or real-world data */

[[Link title]]{{Complex Systems Summer School 2013}}

==Project Proposals==

=='''Recursive Agents'''==

A common theme that I've seen in complexity is that you can represent many different systems (cells, agents, civilizations, for example) with more or less the same rules. I'm wondering if anyone would be interested in modeling this? Essentially we develop a recursive rule set: agents' behavior are based on a set of their 'inner agents,' which also follow similar rules.

-Todd

=='''Global Emergent Risk'''==

In the current phase of globalization, networks in logistics, travel, finance, disease, energy, and ecology are growingly increasingly interconnected on a global scale. Hence, situations arise where mortgage defaults in the US bring down the Icelandic pension system, and a volcano in Iceland disrupts global air traffic. Given the scale of interconnectedness, can complexity science help develop a sense of how small perturbations in one global network might cascade into large unforeseen failures in another network? I'm wondering if we can help build a more generic grammar for describing interconnected networks and the risks posed by such systems. Would it be possible to mitigate risk at smaller local levels of scale, or do small corrections of local risk inevitably cascade into larger risks that we lack the ability to respond to (think wildfires in the Southwest where more frequent small fires would help reduce the chance of large scale fires that cannot be controlled.) I'd love to talk with anyone interested in ecology, globalization, risk, and network modelling.

My advisor at Princeton is already funded for a three year interdisciplinary symposium on Global Emergent Risk, so if people are interested, we have resources to carry on a larger research engagement.

--[[Manish_Nag | Manish]]

- I don't know if large risk cascades are inevitable, but these are timely questions. I have colleagues at the [http://gcrinstitute.org/ Global Catastrophic Risk Institute] who are also interested in this topic. I'm not sure what building a "more generic grammar" means, but the cross-impact balance method is pretty generic. Hopefully you can make our [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]]! Our group is kicking around methods for a project at the moment and have not decided on research questions, so perhaps we can join forces. --[[Vanessa_Schweizer | Vanessa]]

- To clarify, what I meant by "generic grammar" is some way to describe a set of networks and cross network dependencies that can be decoupled from the content of the network. We could use this language to describe interconnections between hypothetical logistics, travel, financial networks for example, and then use simulations to understand the conditions where risks might be amplified and/or jump across from one network to another. --[[Manish_Nag | Manish]]

- I'd love to join discussions on this as I agree that there's a need to start thinking about network of networks and not just networks in isolation. The [http://arxiv.org/abs/1010.5829 paper by Gao, Stanley et al.] on the robustness of a network of networks might be useful. --[[Cheryl_Abundo | Cheryl]]

=='''Alcohol Consumption and Language Fluency'''==
 
''(This is just one of my random thoughts, don't take it too seriously. I'm bringing it up in case it would actually add interesting noises to anyone's thought process)'' 
There's a interesting thing about me and some of my friends who speak a foreign language. There seems to be a kind of non-linear curve that depicts my blood alcohol concentration and the fluency of my speaking English (Chinese is my native language). For example, usually after one beer, I start to talk faster, and semantically relevant words pop up in my mind more fluently or spontaneously. Or say, I express the same idea with less stuttering and in shorter time. But after some point, i.e. 32 oz of beer, even it might still sound fluent, regarding the physical property of the speech, the grammatical structure of the sentences start to break down. Ultimately, i.e. half bottle of rum, I only repeat 2-3 very short sentences/phrases independent of the presence or the identity of my audience(s) (i.e. murmuring in English for hours to a group of Chinese friends). 
We know that alcohol can influence our behavior by, among other things, binding to certain neural receptors (like GABAa?). I just thought it might be interesting to model how alcohol intake influences the dynamics of language production via regulating neuron signaling. I'm also wondering about what it might imply about our brain dynamics when we're silent. 
Welcome to talk to me if you find this interesting, or silly, or you simply want to correct my grammar. Thanks! 
-Mengsen Zhang

@Mengsen I'd be very interested in doing some empirical work on this topic.
-Max Kleiman-Weiner

I've experienced this same thing with Spanish, Bahasa Indonesia, and playing billiards/pool. Sadly, my math skills do not improve with drinking, and math could arguably be considered a language. This is a creative topic with solid scientific underpinnings that nicely lend themselves to complex systems modeling, I suspect. Fun! – [[Kristen_Honey | Kristen Honey]]

=='''How the ocean can help us heal complex chronic disease'''==

The human body is its own ecosystem -- much like the ocean -- with resilience, hysteresis, synergistic properties, and multi-system dynamics that depend on matrix conditions. We can use our understanding of the ocean and ecosystems to help us heal? Can we model different scales -- an ocean, a human body, and a microbial community -- to explore ecosystem/human/microbial health in a holistic context that depends on shared key elements like flow & trace minerals as building blocks for function? As one example to think about, chronic illnesses like HIV/AIDS or Lyme disease disrupt the immune system and human body functions (e.g., methylation pathways, detox pathways), preventing optimal function that weakens the human body and makes it vulnerable to other infections. It’s a downward spiral of negative feedbacks, analogous to a backed-up, atrophying ocean or estuary that causes fish kills, destroys coral reefs, etc... analogous to microbial communities that shift when environmental/matrix condition change. I suspect our knowledge of the ocean & large ecosystems, which we can see and visualize, can inform new thinking about system dynamics for health & recovery at the scale of a human body and at the scale of individual microbes & microbial communities...

Anyone else interested? – [[Kristen_Honey | Kristen Honey]]

- This sounds like a really nice idea. It would be interesting to understand how the disease-mediated degradation of immune/metabolic networks (the loss or alteration of edges and nodes?) affects the response of these networks to further perturbations (e.g. asymptotic stability and resilience, [http://www.jstor.org/stable/2266047 transient reactivity], cascading effects of node loss, etc.). I have little knowledge of the medical literature, but I am experienced in ecological network analysis including information theoretic analyses of weighted food webs. -- [[Ashkaan_Fahimipour | Ashkaan]]

- I liked the idea very much. In fact I am looking at similar issues related to management of ecosystems which display hysteresis and [http://arno.uvt.nl/show.cgi?fid=121389 regime shifts]. Here is some pertinet information related to [http://www.esajournals.org/doi/abs/10.1890/1051-0761%281999%29009%5B0751%3AMOEFLS%5D2.0.CO%3B2 shallow lakes] and its [http://ideas.repec.org/p/att/wimass/200026.html complex dynamics]. Your idea of scaling down to human level is interesting -- [[Puduru Reddy | Vishwa]]

==
Join us for project discussion & brainstorming ideas, Wednesday June 5th dinner at 5:00. Everyone welcome! ==

=='''GDELT'''==

[[David_Masad | I'd]] love to play around with the new [http://gdelt.utdallas.edu/ Global Data on Events, Location and Tone (GDELT)] dataset, which has 200+ million timestamped and geocoded political events. Here's a [http://ideas.foreignpolicy.com/posts/2013/04/10/what_can_we_learn_from_the_last_200_million_things_that_happened_in_the_world writeup of it in Foreign Policy] -- David

=='''Research Network Formation'''==

I'd be interested in collecting some data from CSSS attendants. Some kind of way to study social network formation. -- [[Todd_Bodnar | Todd]]

Perhaps we could collect survey questions people might be interested in looking at in a [https://docs.google.com/document/d/1h_8TUyuDNT1DhPIyZuGwuvrqSExLgwoocsKZl4jFSk8/edit?usp=sharing Google Doc]? --[[Molly_King | Molly]]

My new crazy idea, inspired by [http://blog.premise.is/blog/2013/5/5/mapping-the-produce-manifold these guys], is doing something with computer vision. Maybe there's a way to photograph sitting arrangements and extract data from that? -- David

Project meeting after the lab Wednesday 6/5 for all those interested.

=='''Self-consistent networks for socio-economic institutions'''==

[[Pablo_Galindo | Pablo]] and [[Vanessa_Schweizer | I]] started to discuss a project where we could use [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] to investigate the implications of alternative hypotheses for interrelationships between various socio-economic/political factors. We began discussing this from the perspective of testing competing political economic theories to see what types of institutions (e.g. styles and stability of governance) would be self-consistent according to the theories. However, I would be open to other topics, including research questions inspired by GDELT. If there is interest to learn more about the CIB technique, I could put together a tutorial. --[[Vanessa_Schweizer | Vanessa]]

There's a paper written by Brian Arthur here at the SFI that might help us frame our topic. Its called Complexity Economics. Basically sets the "rules" for thinking about economics in a whole different way.
It is a very good starting point so we don't go any further wasting time taking into account economic models that are vague, non-accurate and out of date. [[Vanessa_Schweizer | Vanessa]].

Elaborating more on the idea. If we focus on human action as the essence of culture. Understanding human action as the use of beliefs, attitudes and resources (which are scarce) pursuing a state of higher satisfaction. And culture as the sum of all beliefs, attitudes and unintentional consequences of the human action. We can state that the emergence of socio-econmic/political factors are the unintentional consequence of intentional individual actions that at the same time affect the way people act, in what they believe and what attitude they'll have toward the satisfaction of their needs. (Theres a loop between human action and culture - culture affects human action and human action affects culture and so forth)
Some "institutions" will emerge as a consequence of human action but not human design. That is one of the characteristics of a "good" type of institution. (e.g. Money, language, private property, contracts, a certain type of government) and it would be interesting to test the robustness of that spontaneously emerged institution against human designed institution who's robustness is just that is law enforced.
I dunno If you get my point? Compare the qualities of spontaneously emerged institutions against human designed institutions. [[Vanessa_Schweizer | Vanessa]].? Its more or less comparing spontaneously emerged institutions (no leader needed to coordinate like the birds flocking) vs. human designed institutions (leader needed to coordinate al human actions).

==
A [[Complex_Systems_Summer_School_2013-Tutorials | tutorial]] on cross-impact balances and Markov chains is scheduled for Wed. June 5 at ~4:15. Everyone is welcome, even if your project interests lie elsewhere. ==

=='''Genetic algorithms to evaluate network formation or real-world data'''==
I have an ill-defined, wacky idea to possibly use genetic algorithms to evaluate the formation of networks as either following preferential attachment or homophily (aka similarity) rules. This [http://www.nature.com/doifinder/10.1038/nature11459 short Nature paper] looks at the debate between preferential attachment and similarity/homophily dynamics. I don't have a clear idea of what this would look like, but I think it might be fun to think about ways to use genetic algorithms to solve network problems. Talk to me if you think this remotely interesting and we can evolve an idea together? --[[Molly_King | Molly]]

Another possibility would be using genetic algorithms or attachment algorithms to compare to models of real-world data to understand how these networks likely formed and predict future edges.

Molly, I would like to investigate using GA to create an organizational network structure (think org chart or military chain of command or even project groups at the CSSS) and then compare it to existing structures. Let's talk! -John L

Some people were also talking about co-evolution of a network and an attacker that disconnects nodes or edges. -- David

=='''Caribou Management Dynamics'''==

This project would model caribou management dynamics in a prototype NW Alaska community during a caribou shortage. Agents in the model would be informed by data from household subsistence surveys and from management history. The goal would be to evaluate the abilities of different management strategies to achieve biological harvest goals while maximizing economic efficiencies in the community. This is a real-world problem with near-term applications. Caribou cycle on 30-to-50 year periods. The Western Arctic Caribou Herd is currently in decline. During the last caribou “crash” in this region, the state management system attempted to reorganize caribou production, which generated considerable political and social disruption, precipitated widespread passive resistance among Native peoples, and left a legacy of contempt for both management (among some Inuit) and for Inuit hunters (among some sport users). The hope is to reduce conflicts during the expected nadir of the population. Comments and cooperators welcome! [[James Magdanz | Jim]]

Neat topic with data, I assume! I'm interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Evolving synchronized flashes in fireflies'''==

[[Bryn_Gaertner | I ]] was thinking about how some, but not all, species of fireflies can synchronize their flashes, as was mentioned in both lectures today (June 4). The mechanism is fairly simple, it seems, so we should be able to evolve it using a simple genetic algorithm, right? This is only half-baked at the moment, and I haven't checked to see if it has been done already, but I thought it would be neat to explore the space around these biological phenomena. More of a fun project than a serious "lets publish this!" type of project. Bonus points if we can work some neural network stuff into it. [[Bryn_Gaertner]]

=='''How do historic facts collapse into written history?'''==

Let's begin with a nice example: [http://en.wikipedia.org/wiki/Gilgamesh Gilgamesh], the fifth king of Uruk, decided to gather together some stories that local tribes and surrounding cultures had been telling for years, along with things that previous kings had done. This became the [http://en.wikipedia.org/wiki/Epic_of_Gilgamesh Epic of Gilgamesh]. Someone later does a cover of the original book with some new contributions and turns it into what nowadays is the bible and the torah. Another remake of the tale turns these books into the quran, and until today... you know the rest of the story already. Peer reviewed quality, just like Nature or PNAS.

It might be interesting to study how history goes from facts to a written, definitive form which is not (and maybe cannot be) completely faithfully to the actual events. There is huge room to use, for example, models of agents that contribute to form a History with pieces of information that sums up, sometimes with contradicting versions, sometimes with hidden interests, etc etc. Furthermore, we have a great tool in the wikipedia!! We can track, for example, how many changes are made on different entries over time. We can check whether there are some generalities, how the number of edits depends on the time gone after the historic event, maybe we can quantify how successive stories differ from each other and whether there are turning points that dramatically change the whole thing...

So this is the general framework. I think this is a very exciting topic and I'd be glad to talk about this with anyone!! Just contact me! -- [[Luís_Seoane | Luíño]]

=='''Meta Food Webs'''==

I'd like to throw out an idea I've had for a while: Most animals use space in very important ways -- predators encounter and consume prey in both 2D and 3D environments, birds and fish migrate across continents in search of resources and mates, and plant pollinators fly or walk from flower to flower, in turn providing an indispensable economic service to humans. The study of food webs attempts to understand how networks of species that eat each other persist in the face of (sometimes constant) external perturbations. Yet, network-level food web studies seldom address the dynamics of animal movement, and I see this as a fundamental shortcoming in our understanding of nature. Recently, scientists in fields like computer science, physics and neurobiology have begun to model and explore [http://www.nature.com/srep/2012/120831/srep00620/full/srep00620.html?WT.ec_id=SREP-20120904 multi-level or multiplex networks] -- networks of nested networks. This seems like a reasonable candidate for the theoretical study of multiple food webs that are linked by spatial networks of animal movement. One preliminary question that comes to mind: How do the number of "mobile" species and the "speed of movement" alter important dynamical properties of complex food webs at larger spatial scales (i.e. at the meta-food web scale)? I am not dead set on answering this question, and I look forward to gaining insight from scientists who study other types of networks. I'm also not set on the multiplex network framework. Potential alternatives that come to mind are IBMs, PDEs on graphs or integrodifference equations. I look forward to any suggestions or bright ideas! --[[Ashkaan_Fahimipour | Ashkaan]]

Very cool topic. Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''(Evolution of) Aging'''==
Sorry that this one is a bit long. I'd like to brainstorm with anybody interested to see if there could be a viable project in the following direction.

Let me first define aging: deterioration that happens as an organism, e.g. a human being, gets physiologically older, eventually leading to increased mortality and/or decreased fecundity.

Some background into the 'classic' theory: Evolution is about getting to be there in the future, that is, you and/or related organisms, for instance offspring. Increased mortality and decreased fecundity as such are clearly unfavorable to getting to be there in the future. Then why could it evolve? Well, evolution tends to become less sensitive to anything happening to an organism as time progresses, because events that take place at some point in time can affect only events that are future to that event. All offspring that an organism already has at some point cannot be affected anymore, and this is a non-decreasing function of time. This can be formalized, and I'd be happy to write down the math if anybody wonders.

It has, however, limited value to theorize too much about age-specific events, while in fact events at different ages are tied together in pathways of causality, dynamic change and so on; age per se is not a cause of anything, and changes at some age do not happen independent of changes at other ages. There are a number of sufficient arguments why the 'age-specific' picture does not capture this reality. I'm skipping these arguments for now, but ask if you are interested.

We have two things that matter for the evolution of aging. 1. The declining sensitivity of fitness to age-specific changes (of some standardized magnitude). 2. The fact that there are constraints that make that what happens at age x is not independent from what happens at the ages in its neighborhood. Thus, the trick is to figure out what the constraints are - this is where complexity may come in - and to combine these with the effect on fitness that age-related change has. The effect on fitness may be solved analytically, but there are various reasons why computation may be preferable, specifically the not always realistic assumptions that are necessary to allow for analytical solutions.

Mechanistically, people tend to think about aging in two ways. The first is that aging is caused by the accumulation of damage. If this damage were all repaired, aging would not occur. People then try to think of reasons why repair would be imperfect. The second way to think about it is as a gradual loss of robustness/control, sometimes in the context of reliability engineering (is anybody familiar with that?). Beautiful medical example: old people need more insulin to process a standardized dose of sugar, and their regulation shows more peaks, especially upward peaks, than that of young people, who tend to need less insulin to process the standardized dose of sugar. Of course, if you consider loss of control as a type of damage, the two are the same, but the distinction is perhaps helpful because the way people tend to think about damage is not in a dynamical way, but just as protein aggregates sitting in the brain, inhibiting the function, cartilage that looses its suspension, etcetera. Again of course, both may influence each other.

Now toward a project proposal. If I think about how complexity may (in part) determine physiological constraints, I think of the following. Usually people tend to think of repair being limited by available energy. But to repair something, the body needs to have available somewhere the information necessary to restore the initial state, and use that information at the place where the damage has occurred to be able to repair. This is where I hypothesize complexity comes in. The necessity of different components of the body to interact may put constraints on repair other than just energetic, it is also a question of whether the energy can actually be used for the repair (flow through the system in the necessary way). That may require space, a certain chemical environment, hormonal setting etcetera that may be incompatible with the proper function of an organism. (Can you repair a car when it is driving?) Also in the 'control/robustness thinking', you have to get back to the original situation to avoid aging. Is that compatible with the best evolutionary outcome?

These are just some ideas I'm throwing at you, as you see it's not perfectly fleshed out yet, which is good, because it should benefit from your perspective. So anybody interested, please let me know!

Cheers,
Maarten

Neat ideas & I welcome more discussion around these topics. Aging is cool from the academic science side, if not from the personal experience side, lol. It seems to me that these same models/concepts for aging also apply to loss of functionality from chronic illness... illness expedites aging? – [[Kristen_Honey | Kristen Honey]]

==Quantifying Synchrony in Dynamics Occuring on Networks==

[http://arxiv.org/pdf/1110.2724v1.pdf Recent work] has focused on developing information theoretic measures for quantifying directed information transfer, with particular applications to social media. These metrics are motivated by the work being done in theoretical / computational neuroscience on the analysis of spike trains. To do this analysis, the behavior of users on a social media platform like Twitter are treated as point processes, where we only keep track of when a tweet occurs, and ignore its content. That is, we treat a user's behavior over time as 'spikes.' Despite the simplicity of the approach, it was found to be successful in identifying key actors within real social networks.

I am interested in applying a similar methodology, but using a [http://arxiv.org/abs/q-bio/0609008 different measure] of synchrony motivated by computational mechanics. This method seeks to learn the hidden states that generate a user's behavior (very much in the flavor of a Hidden Markov Model, but with a few key twists), and then considers the mutual information between the state sequences of the two users.

A first step for this project would be implementing the methodology proposed by Shalizi, et al., on the toy model proposed by Steeg, et al.

If that is successful (and completed quickly), I have a data set (network connections and behavior) of fifteen thousand Twitter users collected over a three month period. We are interested in using this approach to identify dynamical communities (not only users who are connected, but users who behave in synchrony) within the social network. This takes us beyond typical structural community detection that has had great success in the past decade.

These approaches should work with any sort of dynamics occurring on top of a network-type structure, so if you have a different system you would like to use as a test case, I would be very interested to hear about it!

[[David_Darmon | Dave Darmon]]

===A spin off?===

Sorry for editing in your proposal, Dave, but I wanted to comment an idea I have been interested in for a time now. There is this great technique used in neuroscience to pin down the most effective time-course excitation that a neuron can get so that it fires. It basically averages the input a neuron had been getting before each of its spikes. You can find a thorough description in the very popular [http://www.amazon.com/Theoretical-Neuroscience-Computational-Mathematical-Modeling/dp/0262541858 Dayan & Abbott] book on neuroscience. Since you mention the abstraction from tweets to spikes, I would be very interesting in applying such neuro-inspired analysis to this social interactions. Neuroscience has got many more techniques, so I do not pose it as a closed matter. Just open for discussion, but seems like everybody is sleeping by now ;) -- [[Luís_Seoane | Luíño]]

You're refering to the spike-triggered average? I hadn't thought of that!

All of the work I've done has only considered a single user's time series for prediction. I would certainly be interested in looking at how including the 'inputs' to the user (or at least the inputs that occur on Twitter) impact this process. The spike-triggered average seems like a great first start. Computational mechanics also has some tricks in its toolbox that could be used for this sort of input-output problem. -- [[David_Darmon | Dave D]]

=='''Energy resources supply patterns from biological systems to humans'''==

My idea is to start a brainstorming, it is nothing more than some disjoints thoughts!!! And many questions without an answer so far!! :-)

I would like to investigate how biological systems obtain their energy requirements. Are there patterns or network structure that evolution has developed and that are efficient for animals/plants?
Can we replicate these structures/networks/patterns in the way we (humans) obtain our energy? Can we learn something from the evolution of the energy provisioning of other species? Is that feasible?
My primary idea (given my research bias) is to then apply the findings to the structure of the electrical system. Is the current centralized generation and long distance distribution something that appears in nature? Is there a more efficient way that emerged from evolution in biological context that we can use for future provisioning?

We can apply this not only to electrical systems but more in general to the way we use our resources.

Anyone interested with ideas, feedbacks, thoughts? – [[Giuliano_Andrea_Pagani | Andrea]]

Ecological networks are, indeed, finely structured both topologically and energetically. I'd very much like to talk to you about this idea in more detail. --[[Ashkaan_Fahimipour | Ashkaan]]

Definitely interested & would love to talk more. – [[Kristen_Honey | Kristen Honey]]

=='''Cellular morphogenesis - The evolution of organisms' shape'''==

I am interested in genetic design, not as much the modifications of already existing plants and animals but rather the capabilities of from-the-ground-up design of completely new organisms. One of the most basic question when it comes to multicellular organisms is how they end up with their particular shape and how it is a product of cell growth, membrane adhesion, chemical signalling etc. I suggest a project where we explore what types of shapes can emerge in simple cell growth models and how the shape can be controlled by tuning the organisms genes, the interactions. When we have something running, one interesting continuation would be to apply genetic algorithms on the growth parameters and se what happens with the emerging shape if we for example assign high fitness to high surface area but low volume, high moment of inertia or maybe concentric shells of different cell types and see what types of shapes emerge when under influence of external forces. We can also compare our results with simple, real organisms and se if nature found similar solutions.

There are different cellular models we could use, most reasonable would be a cellular potts model (B) or a vertex dynamic model (D) [http://ars.els-cdn.com/content/image/1-s2.0-S0070215309890042-gr4.jpg], depending on what type of details we want to include. I suggest we start out with 2D simulations.

I also believe this project can steer into many different directions, so if you like parts of the premise and have ideas on other directions we could take this, say hi.

Max Planck instutute with a group on this subject: [http://www.mpipz.mpg.de/smith]

A vertex dynamics model investigating how a specific cell morphogenesis could occur: [http://dev.biologists.org/content/113/4/1231.full.pdf+html]

[[Oskar_Lindgren | Oskar]] email me at oskarxvi at gmail dot com

=='''How big can a city be?'''==

West et al. have discovered striking—and universal—patterns in the way cities scale with size (see [http://www.ted.com/talks/geoffrey_west_the_surprising_math_of_cities_and_corporations.html West's Ted talk], [http://www.nature.com/nature/journal/v467/n7318/abs/467912a.html short Nature paper], [http://www.pnas.org/content/104/17/7301.short longer PNAS paper]). Do these scaling laws allow us to predict how big a city can be?

Here's a motivating analogy. The mass of an animal grows scales the cube of its size L, but the cross-sectional area of its leg bones scales only like the square of L. This implies that bigger animals must have bulkier leg bones in order to sustain their own weight. (Think of the legs of a mouse versus the legs of an elephant.) Since the bones can never get bigger than the animal itself, this immediately tells you that land animals cannot be arbitrarily large: they must have a maximum size. If you plug in the numbers and estimate this maximum size, you find a value consistent with the largest known dinosaurs. In fact, with similar reasonings—which were discovered by Galileo, by the way—you can easily find how tall trees can be, how high animals can jump, etc [http://galileo.phys.virginia.edu/classes/304/scaling.pdf].

Now, to run a similar argument for cities, we should understand what constraints would limit their size (the equivalent of "the legs of an animal can never be larger than the animal itself"). These constraints may be technical, social—I'm not sure. (Crimes are perhaps an example. West et al. show that the number of crimes committed in a city grows faster than the number of inhabitants. Clearly then, at some point the likelihood to get shot the next day will get too high, and people will start leaving the city.) I wonder if the social scientists among us have any insight about such constraints, and whether we can actually come up with a prediction for the maximal size of a city based on them. – [[Matteo_Smerlak | Matteo]]

- Scaling patterns for cities are fascinating, but a potential data limitation to the PNAS paper is that the study was applied to cities in the US, EU and China. It can be argued that these economies have particular similarities that may not be transferable to cities in developing countries that are not China (e.g. Jakarta, Delhi, Manila). To complicate matters a bit more, there is little consensus on what a city is -- is it defined by the political boundary? What about the economic boundary determined by bedroom communities (suburbs)? If one takes the latter view of a metropolitan area, the population densities of some "cities" in developing countries is truly astounding. The New York metropolitan area can be interpreted as spanning 4500 sq. miles with 20 million people (a density of ~4600 people/sq. mile). Under the same interpretation, Jakarta spans only 1075 sq. miles with 25 million people (a density of ~25,000 people/sq. mile!!!). The point of my comment is that I wonder how well the scaling findings of West et al. hold up for cities in developing countries (that do not include China). It seems possible that there are scaling patterns there as well, but they might be different. By the way, I got my numbers for population densities from [http://www.newgeography.com/content/002808-world-urban-areas-population-and-density-a-2012-update Demographia]. --[[Vanessa_Schweizer | Vanessa]]

- Because of national differences, there's certainly no consensus yet on how to define the boundaries of a city. Even [http://unstats.un.org/unsd/demographic/sconcerns/densurb/densurbmethods.htm UN] recognizes this and suggests following the boundaries established by individual countries. On the point of whether scaling patterns will be the same for developed and developing countries, the scaling patterns might still be the same (wealth creation leads to superlinear scaling while economies of scale results to sublinear scaling) but the actual value of the scaling exponents might vary. It would be interesting to see whether such two sets of exponents exist as it might explain why the experience of living in two cities of the same density can be different (case in point Manila with a pop'n density of 21.9 M vs Shanghai or NY with 20.9 M). To quantify the living conditions/living experience of cities, we can use the [http://www.businessweek.com/news/2012-08-15/melbourne-remains-most-liveable-city-in-the-world Economist Intelligence Unit’s 2012 Global Liveability Survey]. If data is now available for developing countries, it wouldn't be hard to check this. But having lived in Manila and seeing how inefficient collection of census data in such cities can be, I doubt if we can have a substantial sample of developing countries with complete data. We can probably check [http://www.quandl.com/ here].

As for setting the thresholds in computing for the maximal city size, we can use the parameter values for Melbourne as according to the EIU survey, it is the most livable city in the world. If somehow we decide that using this is not a good way of defining the thresholds and there's no other way of setting them, jumping off from Vanessa's point, what we can also do is have several sets of parameter constraints and say that if city A falls under category A with parameter constraints {A}, then this is the maximal size it can have. We can do some clustering analysis of the parameter space to determine the city categories. I think it would be worthwhile to talk to someone from the cities group here in SFI as they've already mentioned before how population growth behaves with the different scaling patterns.--[[Cheryl Abundo | Cheryl]]

Complex Systems Summer School 2013-Tutorials

2013-06-05T15:05:20Z

Masad:

{{Complex Systems Summer School 2013}}

CSSS participants come from a wide range of disciplines. Participants are encouraged to share their knowledge by organizing their own tutorials.

Also, please post requests for tutorials here.

'''Dynamics in Networks'''

I am very interested in learning about network dynamics. Anyone else interested in having a tutorial on that? [[Regina_Martinez | Regina]]

'''Cross impact balances and Markov chains'''

As part of brainstorming for a possible project, three of us have decided to do a tutorial on [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] (delivered by [[Vanessa_Schweizer | Vanessa]]) and Markov chains (delivered by [[Alastair_Jamieson-lane | Alastair]] and [[Matteo_Smerlak | Matteo]]). We think these methods could be leveraged to research some interesting questions. All are invited to this tutorial regardless of their interest in contributing to a project using these methods. This tutorial will be Wed. June 5th at ~4:00 PM (it looks like the regular schedule is subject to change; maybe we'll do the tutorial at 4:15 instead). Location TBD (check back on the wiki for an update). --[[Vanessa_Schweizer | Vanessa]] 
PS -- For those interested in examples of studies that have used CIB analysis, see this one on [http://iopscience.iop.org/1748-9326/7/4/044011/article century-long socioeconomic scenarios] or this abstract on a [http://link.springer.com/article/10.1007%2Fs10389-011-0473-8 qualitative model regarding obesity development and prevention].

'''Python (and MASON)'''

If anyone is interested, I'd be happy to organize and run/co-run a Python programming tutorial. If anyone needs agent-based models beyond what NetLogo can handle, I'd be happy to run a tutorial on the [http://cs.gmu.edu/~eclab/projects/mason/ MASON] framework. -- [[David_Masad]]

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-04T15:16:48Z

Masad: /* Project proposals */

{{Complex Systems Summer School 2013}}

==Project proposals==

'''GDELT'''

[[David_Masad | I'd]] love to play around with the new [http://gdelt.utdallas.edu/ Global Data on Events, Location and Tone (GDELT)] dataset, which has 200+ million timestamped and geocoded political events. Here's a [http://ideas.foreignpolicy.com/posts/2013/04/10/what_can_we_learn_from_the_last_200_million_things_that_happened_in_the_world writeup of it in Foreign Policy] -- David

'''Research Network Formation'''

I'd be interested in collecting some data from CSSS attendants. Some kind of way to study social network formation. -- Todd

My new crazy idea, inspired by [http://blog.premise.is/blog/2013/5/5/mapping-the-produce-manifold these guys], is doing something with computer vision. Maybe there's a way to photograph sitting arrangements and extract data from that? -- David

'''Self-consistent networks for socio-economic institutions'''

[[Pablo_Galindo | Pablo]] and [[Vanessa_Schweizer | I]] started to discuss a project where we could use [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] to investigate the implications of alternative hypotheses for interrelationships between various socio-economic/political factors. We began discussing this from the perspective of testing competing political economic theories to see what types of institutions (e.g. styles and stability of governance) would be self-consistent according to the theories. However, I would be open to other topics, including research questions inspired by GDELT. If there is interest to learn more about the CIB technique, I could put together a tutorial. --Vanessa

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-04T15:10:19Z

Masad: /* Project proposals */

{{Complex Systems Summer School 2013}}

==Project proposals==

'''GDELT'''

[[David_Masad | I'd]] love to play around with the new [http://eventdata.psu.edu/data.dir/GDELT.html Global Data on Events, Location and Tone (GDELT)] dataset, which has 200+ million timestamped and geocoded political events. Here's a [http://ideas.foreignpolicy.com/posts/2013/04/10/what_can_we_learn_from_the_last_200_million_things_that_happened_in_the_world writeup of it in Foreign Policy] -- David

'''Research Network Formation'''

I'd be interested in collecting some data from CSSS attendants. Some kind of way to study social network formation. -- Todd

My new crazy idea, inspired by [http://blog.premise.is/blog/2013/5/5/mapping-the-produce-manifold these guys], is doing something with computer vision. Maybe there's a way to photograph sitting arrangements and extract data from that? -- David

'''Self-consistent networks for socio-economic institutions'''

[[Pablo_Galindo | Pablo]] and [[Vanessa_Schweizer | I]] started to discuss a project where we could use [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] to investigate the implications of alternative hypotheses for interrelationships between various socio-economic/political factors. We began discussing this from the perspective of testing competing political economic theories to see what types of institutions (e.g. styles and stability of governance) would be self-consistent according to the theories. However, I would be open to other topics, including research questions inspired by GDELT. If there is interest to learn more about the CIB technique, I could put together a tutorial. --Vanessa

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-04T15:03:15Z

Masad: /* Project proposals */

{{Complex Systems Summer School 2013}}

==Project proposals==

'''GDELT'''

[[David_Masad | I'd]] love to play around with the new [http://eventdata.psu.edu/data.dir/GDELT.html Global Data on Events, Location and Tone (GDELT)] dataset, which has 200+ million timestamped and geocoded political events. Here's a [http://ideas.foreignpolicy.com/posts/2013/04/10/what_can_we_learn_from_the_last_200_million_things_that_happened_in_the_world writeup of it in Foreign Policy] -- David

'''Research Network Formation'''

I'd be interested in collecting some data from CSSS attendants. Some kind of way to study social network formation. -- Todd

My new crazy idea is doing something with computer vision. Maybe there's a way to photograph sitting arrangements and extract data from that? -- David

'''Self-consistent networks for socio-economic institutions'''

[[Pablo_Galindo | Pablo]] and [[Vanessa_Schweizer | I]] started to discuss a project where we could use [http://arxiv.org/abs/0912.5352 cross-impact balances (CIB)] to investigate the implications of alternative hypotheses for interrelationships between various socio-economic/political factors. We began discussing this from the perspective of testing competing political economic theories to see what types of institutions (e.g. styles and stability of governance) would be self-consistent according to the theories. However, I would be open to other topics, including research questions inspired by GDELT. If there is interest to learn more about the CIB technique, I could put together a tutorial. --Vanessa

Physics Lab 2013

2013-06-04T06:13:29Z

Masad: /* Wednesday June 5, 5:30 - 7:30 */

{{Complex Systems Summer School 2013}}

==Wednesday June 5, 5:30 - 7:30==

1.JP 
2. Jim Magdanz 
3.Johannes Schmidt 
4. David M. 
5. 
6. 
7. 
8. 
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15. 

==Thursday June 6, 5:30 - 7:30==

1.Mengsen Zhang 
2. 
3. 
4. 
5. 
6. 
7. 
8. 
9. 
10. 
11. 
12. 
13. 
14. 
15. 

==Monday June 10, 5:30 - 7:30==

1. 
2. 
3. 
4. 
5. 
6. 
7. 
8. 
9. 
10. 
11. 
12. 
13. 
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15. 

==Tuesday June 11, 5:30 - 7:30==

1. Kerstin Damerau 
2. Vanessa Schweizer 
3. 
4. 
5. 
6. 
7. 
8. 
9. 
10. 
11. 
12. 
13. 
14. 
15.

Complex Systems Summer School 2013-Blog

2013-06-03T16:44:37Z

Masad:

Complex Systems Summer School 2013-Participants

2013-04-23T00:31:26Z

Masad: /* Participants */

{{Complex Systems Summer School 2013}}

To post a photo, bio, and answer the questions below please email them to juniper@santafe.edu:

* What are your main interests? Feel free to include a "pie in the sky" big idea!
* What sort of expertise can you bring to the group?
* What do you hope to get out of the CSSS?
* Do you have any possible projects in mind for the CSSS?

Visit the [http://www.facebook.com/pages/SFI-Complex-Systems-Summer-School/195552467134324?sk=wall&filter=2 Facebook Complex Systems Summer School Page] to get to know each other informally.

To access a '''CSSS mobile app''' of the schedule, logistics, and faculty list please use your mobile device to visit: http://my.yapp.us/Z53CQX

==Participants==
 
[[Abigail Jacobs,]] University of Colorado 
[[Agam Gupta]], Indian Institute of Managment (IIM) Calcutta 
[[AmaraAl Sayegh]], American University of Beirut 
[[Ashkaan Fahimipour]], University of California, Riverside 
[[Bapu Vaitla]], Tufts University 
[[Brady Stoll]], University of Texas at Austin 
[[Bruno Pace]], Leipzig University 
[[Bryn Gaertner]], North Carolina State University 
[[Carol Strohecker]], University of North Carolina 
[[Cesar Flores Garcia]], Georgia Institute of Technology 
[[Cheryl Abundo]], Complexity Programme, SPMS, Nanyang Technological University 
[[David Darmon]], University of Maryland 
[[David Masad]], Department of Computational Social Science, George Mason University 
[[Eitan Pechenick]], University of Vermont 
[[Elena Stepanova]], Scuola Superiore Sant'Aanna (Italy), University of Olomouc (Czech Republic) 
[[Elisa Omodei]], École Normale Supérieure 
[[Giuliano Andrea Pagani]], University of Groningen 
[[Hassan Shafiey]], Max Planck institue for evolutionary anthropology 
[[Holly Arnold]], University of Oregon 
[[Hua Cai]], University of Michigan 
[[Ian Hatton]], McGill University 
[[Ivana Stankov]], University of South Australia 
[[James Magdanz]], University of Alaska 
[[James Walsh]], University at Albany 
[[Jian Yen]] ,Monash University 
[[Joana Patrício]], IMAR-CMA 
[[JoaoFilipe Monteiro]], Brown University 
[[Jody Wright]], University of British Columbia 
[[Johannes Schmidt]] ,University of Natural Resources and Life Sciences 
[[John Driscoll]], Systems Science 
[[CAPT John Litherland]], U.S. Naval War College 
[[Kerstin Damerau]], IIASA 
[[Kevin Stadler]], The University of Edinburgh 
[[Kristen Honey]], Stanford University 
[[Kyle Mahowald]], MIT 
[[Lauren Shoemaker]], University of Colorado at Boulder 
[[Luís Seoane]], Universitat Pompeu Fabra 
[[Maarten Wensink]], Max Planck Institute for Demographic Research 
[[Manish Nag]], Princeton University 
[[Masato Yamamichi]], Cornell University 
[[Matteo Smerlak]], Max Planck Institute for Gravitational Physics 
[[Mauricio Cantor]], Dalhousie University 
[[Max Kleiman-Weiner]], MIT 
[[Mehmet Cakir]], Interdisciplinary Centre for Bioinformatics University of Leipzig 
[[Melinda Varga]], University of Notre Dame 
[[Mengsen Zhang]], University of Pennsylvania 
[[MESUT YÜCEL]], Ege University 
[[Molly King]], Stanford University 
[[Oskar Lindgren]], Chalmers University of Technology 
[[Pablo Galindo]], Universidad Francisco Marroquín 
[[Puduru Reddy]], GERAD, HEC Montreal 
[[Rebecca Mease]], Technical University of Munich 
[[Regina Martinez]], George Washington University 
[[Reniel Cabral]], University of the Philippines Diliman 
[[Roberto Reyes Carranza]], University of Puerto Rico at Rio Piedras, American Mathematical Society Member, Campus of Mathematical Research 
[[Stephan Lehner]], German Aerospace Center (DLR) 
[[Susanne Kortsch]], University of Tromsø 
[[Swati Patel]], UC Davis 
[[Todd Bodnar]], Pennsylvania State University 
[[Urbano Franca]], IFIC 
[[Vanessa Schweizer]],National Center for Atmospheric Research 
[[Yan Xu]] , Florida State University

Complex Systems Summer School 2013-Software

2013-04-10T20:52:16Z

Masad:

{{Complex Systems Summer School 2013}}

==General Software==

R Statistical Programming Language: [http://cran.opensourceresources.org/ Download Link]

NetLogo: [http://ccl.northwestern.edu/netlogo/ Download Link]

[http://backspaces.net/wiki/NetLogo_Tutorial basic netlogo tutorial]

[http://www.python.org/ Python]

[http://ipython.org/ IPython] (includes the very useful [http://nbviewer.ipython.org/ IPython Notebook])
==CMPy Server==

The CMPy server is located '''[https://cmpy.csc.ucdavis.edu:8000/ here]'''

Complex Systems Summer School 2013-Projects & Working Groups

2013-04-10T20:02:39Z

Masad: /* Project proposals */

David Masad

2013-03-22T15:01:43Z

Masad:

{{Complex Systems Summer School 2013}}

I'm a PhD student in computational social science, interested in applying complexity tools to studying international crises and conflicts. I use network analysis, agent-based modeling, natural language processing and plain old linear regressions. I'm always excited to learn new techniques, problems, and cool trivia.

Outside of academic work I enjoy road trips, speculative fiction, bourbon, and the outdoors (in moderation).