Santa Fe Institute Events Wiki - User contributions [en]

"Invent and define a new word."

2013-09-02T22:05:45Z

Seoane: /* What follows is a little bit pretentious: */

Paratational- of, or related to inverse photography.

=== What follows is a little bit pretentious: ===

I was thinking precisely about that word ("pretentious") and I was amazed by the following: It
is not necessarily a wrong thing per se that something is pretentious. Not if you take its barest
meaning: your work pretends to accomplish something big, thus it's pretentious. Lucky us!! If not,
your work might not be so worthy! You really give a damn thing because it tries to reach beyond what
already exists!

But that word connotes not only its barest meaning. We perceive it as negative somehow. It has
got a slight odd sense, a subtle taste to failure. If someone calls your work pretentious it is also
very likely that you didn't succeed, that your product just gets to be kind of mediocre.

What really amused me was the ability of that word to reach through the semantic network those
subtle meanings behind the big thing (as every word shall do). So I wish to conceive a new word, and
the new word is a node of the semantic network. Here it is:

[[File:NewWord1.png]]

and it reaches subtly to its many endings, its many nuances:

[[File:NewWord2.png]]

Of course it refers to itself, just as the word "pretentious" represents itself being a word. But we
don't draw that to make things simpler. And finally, there it goes:

[[File:NewWord3.png]]

my new word in its vicinity, within the semantic network. It feeds on and is fed by so many other words! My word is a neuron.
Might my new word help you sail through the meanings of all this mess!

"Invent and define a new word."

2013-09-02T22:05:24Z

Seoane:

Paratational- of, or related to inverse photography.

= What follows is a little bit pretentious: =

I was thinking precisely about that word ("pretentious") and I was amazed by the following: It
is not necessarily a wrong thing per se that something is pretentious. Not if you take its barest
meaning: your work pretends to accomplish something big, thus it's pretentious. Lucky us!! If not,
your work might not be so worthy! You really give a damn thing because it tries to reach beyond what
already exists!

But that word connotes not only its barest meaning. We perceive it as negative somehow. It has
got a slight odd sense, a subtle taste to failure. If someone calls your work pretentious it is also
very likely that you didn't succeed, that your product just gets to be kind of mediocre.

What really amused me was the ability of that word to reach through the semantic network those
subtle meanings behind the big thing (as every word shall do). So I wish to conceive a new word, and
the new word is a node of the semantic network. Here it is:

[[File:NewWord1.png]]

and it reaches subtly to its many endings, its many nuances:

[[File:NewWord2.png]]

Of course it refers to itself, just as the word "pretentious" represents itself being a word. But we
don't draw that to make things simpler. And finally, there it goes:

[[File:NewWord3.png]]

my new word in its vicinity, within the semantic network. It feeds on and is fed by so many other words! My word is a neuron.
Might my new word help you sail through the meanings of all this mess!

File:NewWord3.png

2013-09-02T22:03:19Z

Seoane:

File:NewWord2.png

2013-09-02T22:02:51Z

Seoane:

File:NewWord1.png

2013-09-02T22:01:46Z

Seoane:

Presentations 2013

2013-06-26T17:57:47Z

Seoane:

{{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, 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

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 (Vanessa, Alastair, Stephane, Matteo, Melinda, Hua, Nix)

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

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

11:30 - 11:45: "Complexity of Cities" (Abundo, Bodnar, Driscoll, Hatton, Schweizer, Smerlak, Wright)

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

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

1:15 - 1:30:

1:30 - 1:45:

2:00 - 2:15:

2:15 - 2:30:

2:30 - 2:45: Whales (Melinda, Lauren, Cesar, Mauricio, Ren)

2:45 - 3:00: BREAK

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

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

Presentations 2013

2013-06-26T17:56:41Z

Seoane:

{{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, 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

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 (Vanessa, Alastair, Stephane, Matteo, Melinda, Hua, Nix)

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

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

11:30 - 11:45: "Complexity of Cities" (Abundo, Bodnar, Driscoll, Hatton, Schweizer, Smerlak, Wright)

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

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

1:15 - 1:30:

1:30 - 1:45:

2:00 - 2:15:

2:15 - 2:30:

2:30 - 2:45: Whales (Melinda, Lauren, Cesar, Mauricio, Ren)

2:45 - 3:00: BREAK

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

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

2013-06-19T02:30:01Z

Seoane: /* Tent Rocks National Monument on Saturday 22nd */

{{Complex Systems Summer School 2013}}

==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.

1. Elisa 
2. Bapu 
3. Luíño 

==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. Joana 
5.Filipe 

'''JP's Car''' 
1.JP 
2.Max 
3.Carol 
4.Mengsen 
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. Amara 
2. Agam 
3. Cesar 
4. Jody 
5. Melinda 
6. Elisa 
7. Luíño 
8. Molly 
9. Regina 
10. Andrea 
11. Jim 
12. Kevin 

==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

==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]]

Unfolding History

2013-06-17T18:26:32Z

Seoane: /* Tools */

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

==Brainstorming==

Some of the ideas after today's meeting:
*History Epistasis:
**How does an event affect previously existing events?
**Can we make a network and check out how deep a wave of modifications propagates.
*Reaction time after an event happens.
*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

Also, Joshua proposed some tools that can be handy to detect a change in the editing regime of an event. I just post some key-words I could catch up. If someone could add some description or some bibliography on that?

==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]]

Hey Luiño, I wrote something to parse txt data into dictionary. [https://www.dropbox.com/sh/wigwizffvcmf7l6/xxnew5I1VQ] Please check... (minimal programing experience) Thanks! - Mengsen.

==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?

=Natural Language Processing tools=

Carol made some literature review on Natural Language Processing tools with the idea that peering inside the meaning of the texts can also be helpful for our task. I paste here her results:

Natural Language Processing (NLP) Survey of Tools & Resources
[http://emerge.mc.vanderbilt.edu/natural-language-processing-nlp-survey-tools-resources]

Natural Language Toolkit
NLTK is a leading platform for building Python programs to work with human language data. It provides easy-to-use interfaces to over 50 corpora and lexical resources such as WordNet, along with a suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning.
(python)
[http://nltk.org]

The Stanford Natural Language Processing Group makes parts of our Natural Language Processing software available to everyone. These are statistical NLP toolkits for various major computational linguistics problems. They can be incorporated into applications with human language technology needs.
(java)
[http://nlp.stanford.edu/software/]

CRAN Task View: Natural Language Processing
Natural language processing has come a long way since its foundations were laid in the 1940s and 50s (for an introduction see, e.g., Jurafsky and Martin (2008): Speech and Language Processing, Pearson Prentice Hall). This CRAN task view collects relevant R packages that support computational linguists in conducting analysis of speech and language on a variety of levels - setting focus on words, syntax, semantics, and pragmatics.
In recent years, we have elaborated a framework to be used in packages dealing with the processing of written material: the package tm. Extension packages in this area are highly recommended to interface with tm's basic routines and developers are cordially invited to join in the discussion on further developments of this framework package.
(tm])
[http://cran.r-project.org/web/views/NaturalLanguageProcessing.html]

The SPECIALIST Natural Language Processing (NLP) Tools have been developed by the The Lexical Systems Group of The Lister Hill National Center for Biomedical Communications to investigate the contributions that natural language processing techniques can make to the task of mediating between the language of users and the language of online biomedical information resources. The SPECIALIST NLP Tools facilitate natural language processing by helping application developers with lexical variation and text analysis tasks in the biomedical domain. The NLP Tools are open source resources distributed subject to these terms and conditions.
[http://lexsrv3.nlm.nih.gov/Specialist/Home/index.html]

Basic NLP tools
[http://adimen.si.ehu.es/~rigau/research/Doctorat/LSKBs/00-NLP-tools.pdf]

Software Tools for NLP
[http://www-a2k.is.tokushima-u.ac.jp/member/kita/NLP/nlp_tools.html]

Natural Language Processing
[http://www.cs.cofc.edu/~manaris/ai-education-repository/nlp-tools.html]

Natural Language Processing-(NLP) Tools
[http://sqnco.com/2012/12/natural-language-processing-nlp-tools/]

==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 project by [[Carol_Strohecker | Carol Strohecker]] on narrative unfolding: [http://www.carolstrohecker.info/ProjectPages/togi.html Tired of Giving In].
* 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
* Herman & Chomsky's [http://en.wikipedia.org/wiki/Propaganda_model Propaganda model] developed in [http://en.wikipedia.org/wiki/Manufacturing_Consent:_The_Political_Economy_of_the_Mass_Media Manufacturing Consent (1988)]. A really great documentary roughly based on the book is also available on [http://www.youtube.com/watch?v=3AnB8MuQ6DU youtube].

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? Elisa

Synchrony on Networks

2013-06-17T18:07:42Z

Seoane: /* Time Tweetered Average ;) */

Below are my initial impressions about the project. These are just a sketch, and open to change!

==Useful Tools==

The Enthought Scientific Python package is [https://www.enthought.com/products/canopy/ here].

One of the key texts in theoretical / computational neuroscience is Dayan and Abbott's [http://www.amazon.com/Theoretical-Neuroscience-Computational-Mathematical-Modeling/dp/0262541858 Theoretical Neuroscience]. I just uploaded the first chapter of this book onto my dropbox's public folder. You can get it following [https://www.dropbox.com/s/fziug8a9r4z3ng7/ChaptI.pdf this link].

==To Do==

Put your email here, or if you'd rather not have your email address online, email me at ddarmon at math dot umd dot edu and I'll put together a mailing list. I'll email out a Dropbox link with some preliminary code and some sample data.

Elisa elisa.omodei@gmail.com
[[Luís_Seoane | Luíño]] luis.seoane@upf.edu [[Cesar_Flores_Garcia|Cesar]] cesar7@gmail.com
[[Regina_Martinez | Regina]] Reginaram76@yahoo.es [[Jody_Wright | Jody]] jjwright49@me.com
[[Cheryl_Abundo | Cheryl]] che.abundo@gmail.com

Read Aram et al.'s [http://arxiv.org/pdf/1110.2724v1.pdf paper].

Play around with the code in the Dropbox folder, especially generate_poisson.py. This script generates samples from an inhomogeneous Poisson process.

==Basic (Toy) Model==

Throughout, I'll use the word 'spike' interchangeably with 'tweet.'

The basic skeleton is based off of the [http://arxiv.org/pdf/1110.2724v1.pdf paper] by Aram et al. We consider a network of users which we'll model as a graph with a vertex for each user and an edge denoting a connection between each user. For Twitter data, these edges might indicate follower/followee relationships. Directedness of these edges is an open question. This gives us the basic structural model.

The dynamics occurring on top of this network will take the form of coupled inhomogeneous Poisson processes. That is, each vertex will have a [http://en.wikipedia.org/wiki/Poisson_process Poisson process] on top of it, and the rate of the process will depend on the behavior of the other nodes connected to it. An inhomogeneous Poisson process model is a common (though very rough) approximation of neural behavior. It captures the notion of 'completely random.'

Aram's model sets the instantaneous rate of each user to be a (constant) base rate, plus terms that depend on the behavior of the neighbors of a given user (if a neighbor has recently tweeted, and the user is dynamically connected to that user, they are more likely to tweet). The constant base rate is open to change.

==Community Detection==

A standard approach to finding communities within a network is to look at the network structure alone. We attempt to partition the nodes in the network such that there are many more edges within a community than between communities. A popular method for doing this is the [http://www.ece.unm.edu/ifis/papers/community-moore.pdf fast-greedy algorithm] developed by Clauset, Newman, and Moore.

[http://arxiv.org/pdf/cond-mat/0404652.pdf Another algorithm] developed by some colleagues from Granada.

==Toy Network==

One of our first tasks is to design a reasonable (small) network to run the toy model on top of. This network should presumably have apparent community structure, and then we can design on top of this a weighted network that incorporates the notion of dynamical community. These weights would essentially correspond to the weights in Equation 4 of Aram et al.' paper. One option for designing realistic network structure is to use a small network within the Twitter network I have available.

==Tweet-Triggered Average ;) ==

I am trying to get a nice summary of Spike Triggered Average from Dayan&Abbott's book. By now I leave here the [http://en.wikipedia.org/wiki/Spike-triggered_average wikipedia site] for it, where the idea is more or less clear. In the first chapters of Dayan&Abbott's book you can also find very basics about Poisson processes and such. I will upload it soon!

Written at the top, but I write it again: we just got ready the first chapter of the Dayan & Abbott book on Theoretical Neuroscience. Just use [https://www.dropbox.com/s/fziug8a9r4z3ng7/ChaptI.pdf this link] to get it from my dropbox. It is not like you need to learn it by heart, but the techniques used there (spike-triggered average and many others) seem very useful to me for our current problem. I believe we can make use of them.

What about a meeting? I (Luíño) will be busy tomorrow with the physics lab and the discussion about History (anyone is invited, by the way, at 8:00 pm), but what about meeting on Tuesday?

Meeting on Tuesday sounds like a great idea. If anyone is available and would like to meet Monday during the lab time, I'm available. Hopefully once more people sign up for the Google Group, we can send these sort of organizational things through that.

I made a [https://www.dropbox.com/s/6pewpuey6ty2b00/spikeParse.py brief script] you can get here from my dropbox. Also, I wrote a very short report ([[File:BriefReport_ITI.pdf]]) outlining the results, in case you wish to take a look. -- [[Luís_Seoane | Luíño]]

I updated the scripts a little bit. Now it is possible to produce autocorrelation plots of the tweets of single users. To advance in the direction of Tweet-Triggered Average more detailed data sets will be needed, but I think the idea remains feasible. -- [[Luís_Seoane | Luíño]]

Synchrony on Networks

2013-06-13T20:54:53Z

Seoane: /* Time Tweetered Average ;) */

Below are my initial impressions about the project. These are just a sketch, and open to change!

==Useful Tools==

The Enthought Scientific Python package is [https://www.enthought.com/products/canopy/ here].

One of the key texts in theoretical / computational neuroscience is Dayan and Abbott's [http://www.amazon.com/Theoretical-Neuroscience-Computational-Mathematical-Modeling/dp/0262541858 Theoretical Neuroscience]. I just uploaded the first chapter of this book onto my dropbox's public folder. You can get it following [https://www.dropbox.com/s/fziug8a9r4z3ng7/ChaptI.pdf this link].

==To Do==

Put your email here, or if you'd rather not have your email address online, email me at ddarmon at math dot umd dot edu and I'll put together a mailing list. I'll email out a Dropbox link with some preliminary code and some sample data.

Elisa elisa.omodei@gmail.com
[[Luís_Seoane | Luíño]] luis.seoane@upf.edu [[Cesar_Flores_Garcia|Cesar]] cesar7@gmail.com
[[Regina_Martinez | Regina]] Reginaram76@yahoo.es [[Jody_Wright | Jody]] jjwright49@me.com
[[Cheryl_Abundo | Cheryl]] che.abundo@gmail.com

Read Aram et al.'s [http://arxiv.org/pdf/1110.2724v1.pdf paper].

Play around with the code in the Dropbox folder, especially generate_poisson.py. This script generates samples from an inhomogeneous Poisson process.

==Basic (Toy) Model==

Throughout, I'll use the word 'spike' interchangeably with 'tweet.'

The basic skeleton is based off of the [http://arxiv.org/pdf/1110.2724v1.pdf paper] by Aram et al. We consider a network of users which we'll model as a graph with a vertex for each user and an edge denoting a connection between each user. For Twitter data, these edges might indicate follower/followee relationships. Directedness of these edges is an open question. This gives us the basic structural model.

The dynamics occurring on top of this network will take the form of coupled inhomogeneous Poisson processes. That is, each vertex will have a [http://en.wikipedia.org/wiki/Poisson_process Poisson process] on top of it, and the rate of the process will depend on the behavior of the other nodes connected to it. An inhomogeneous Poisson process model is a common (though very rough) approximation of neural behavior. It captures the notion of 'completely random.'

Aram's model sets the instantaneous rate of each user to be a (constant) base rate, plus terms that depend on the behavior of the neighbors of a given user (if a neighbor has recently tweeted, and the user is dynamically connected to that user, they are more likely to tweet). The constant base rate is open to change.

==Community Detection==

A standard approach to finding communities within a network is to look at the network structure alone. We attempt to partition the nodes in the network such that there are many more edges within a community than between communities. A popular method for doing this is the [http://www.ece.unm.edu/ifis/papers/community-moore.pdf fast-greedy algorithm] developed by Clauset, Newman, and Moore.

[http://arxiv.org/pdf/cond-mat/0404652.pdf Another algorithm] developed by some colleagues from Granada.

==Toy Network==

One of our first tasks is to design a reasonable (small) network to run the toy model on top of. This network should presumably have apparent community structure, and then we can design on top of this a weighted network that incorporates the notion of dynamical community. These weights would essentially correspond to the weights in Equation 4 of Aram et al.' paper. One option for designing realistic network structure is to use a small network within the Twitter network I have available.

==Time Tweetered Average ;) ==

I am trying to get a nice summary of Spike Triggered Average from Dayan&Abbott's book. By now I leave here the [http://en.wikipedia.org/wiki/Spike-triggered_average wikipedia site] for it, where the idea is more or less clear. In the first chapters of Dayan&Abbott's book you can also find very basics about Poisson processes and such. I will upload it soon!

Written at the top, but I write it again: we just got ready the first chapter of the Dayan & Abbott book on Theoretical Neuroscience. Just use [https://www.dropbox.com/s/fziug8a9r4z3ng7/ChaptI.pdf this link] to get it from my dropbox. It is not like you need to learn it by heart, but the techniques used there (spike-triggered average and many others) seem very useful to me for our current problem. I believe we can make use of them.

What about a meeting? I (Luíño) will be busy tomorrow with the physics lab and the discussion about History (anyone is invited, by the way, at 8:00 pm), but what about meeting on Tuesday?

Meeting on Tuesday sounds like a great idea. If anyone is available and would like to meet Monday during the lab time, I'm available. Hopefully once more people sign up for the Google Group, we can send these sort of organizational things through that.

I made a [https://www.dropbox.com/s/6pewpuey6ty2b00/spikeParse.py brief script] you can get here from my dropbox. Also, I wrote a very short report ([[File:BriefReport_ITI.pdf]]) outlining the results, in case you wish to take a look. -- [[Luís_Seoane | Luíño]]

File:BriefReport ITI.pdf

2013-06-13T20:48:29Z

Seoane: Brief report on parsing and analyzing plain tweet raster plots.

Brief report on parsing and analyzing plain tweet raster plots.

Unfolding History

2013-06-13T03:08:10Z

Seoane: /* Literature */

Unfolding History

2013-06-13T03:07:48Z

Seoane: /* Literature */

Unfolding History

2013-06-13T01:02:27Z

Seoane: /* Brainstorming */

Synchrony on Networks

2013-06-12T22:39:29Z

Seoane: /* Statistics part */

Below are my initial impressions about the project. These are just a sketch, and open to change!

==Useful Tools==

The Enthought Scientific Python package is [https://www.enthought.com/products/canopy/ here].

One of the key texts in theoretical / computational neuroscience is Dayan and Abbott's [http://www.amazon.com/Theoretical-Neuroscience-Computational-Mathematical-Modeling/dp/0262541858 Theoretical Neuroscience]. I just uploaded the first chapter of this book onto my dropbox's public folder. You can get it following [https://www.dropbox.com/s/fziug8a9r4z3ng7/ChaptI.pdf this link].

==To Do==

Put your email here, or if you'd rather not have your email address online, email me at ddarmon at math dot umd dot edu and I'll put together a mailing list. I'll email out a Dropbox link with some preliminary code and some sample data.

Elisa elisa.omodei@gmail.com
[[Luís_Seoane | Luíño]] luis.seoane@upf.edu [[Cesar_Flores_Garcia|Cesar]] cesar7@gmail.com
[[Regina_Martinez | Regina]] Reginaram76@yahoo.es [[Jody_Wright | Jody]] jjwright49@me.com
[[Cheryl_Abundo | Cheryl]] che.abundo@gmail.com

Read Aram et al.'s [http://arxiv.org/pdf/1110.2724v1.pdf paper].

Play around with the code in the Dropbox folder, especially generate_poisson.py. This script generates samples from an inhomogeneous Poisson process.

==Basic (Toy) Model==

Throughout, I'll use the word 'spike' interchangeably with 'tweet.'

The basic skeleton is based off of the [http://arxiv.org/pdf/1110.2724v1.pdf paper] by Aram et al. We consider a network of users which we'll model as a graph with a vertex for each user and an edge denoting a connection between each user. For Twitter data, these edges might indicate follower/followee relationships. Directedness of these edges is an open question. This gives us the basic structural model.

The dynamics occurring on top of this network will take the form of coupled inhomogeneous Poisson processes. That is, each vertex will have a [http://en.wikipedia.org/wiki/Poisson_process Poisson process] on top of it, and the rate of the process will depend on the behavior of the other nodes connected to it. An inhomogeneous Poisson process model is a common (though very rough) approximation of neural behavior. It captures the notion of 'completely random.'

Aram's model sets the instantaneous rate of each user to be a (constant) base rate, plus terms that depend on the behavior of the neighbors of a given user (if a neighbor has recently tweeted, and the user is dynamically connected to that user, they are more likely to tweet). The constant base rate is open to change.

==Community Detection==

A standard approach to finding communities within a network is to look at the network structure alone. We attempt to partition the nodes in the network such that there are many more edges within a community than between communities. A popular method for doing this is the [http://www.ece.unm.edu/ifis/papers/community-moore.pdf fast-greedy algorithm] developed by Clauset, Newman, and Moore.

[http://arxiv.org/pdf/cond-mat/0404652.pdf Another algorithm] developed by some colleagues from Granada.

==Toy Network==

One of our first tasks is to design a reasonable (small) network to run the toy model on top of. This network should presumably have apparent community structure, and then we can design on top of this a weighted network that incorporates the notion of dynamical community. These weights would essentially correspond to the weights in Equation 4 of Aram et al.' paper. One option for designing realistic network structure is to use a small network within the Twitter network I have available.

==Time Tweetered Average ;) ==

I am trying to get a nice summary of Spike Triggered Average from Dayan&Abbott's book. By now I leave here the [http://en.wikipedia.org/wiki/Spike-triggered_average wikipedia site] for it, where the idea is more or less clear. In the first chapters of Dayan&Abbott's book you can also find very basics about Poisson processes and such. I will upload it soon!

Written at the top, but I write it again: we just got ready the first chapter of the Dayan & Abbott book on Theoretical Neuroscience. Just use [https://www.dropbox.com/s/fziug8a9r4z3ng7/ChaptI.pdf this link] to get it from my dropbox. It is not like you need to learn it by heart, but the techniques used there (spike-triggered average and many others) seem very useful to me for our current problem. I believe we can make use of them.

What about a meeting? I (Luíño) will be busy tomorrow with the physics lab and the discussion about History (anyone is invited, by the way, at 8:00 pm), but what about meeting on Tuesday?

Meeting on Tuesday sounds like a great idea. If anyone is available and would like to meet Monday during the lab time, I'm available. Hopefully once more people sign up for the Google Group, we can send these sort of organizational things through that.

Unfolding History

2013-06-12T18:08:02Z

Seoane: /* 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-Tutorials

2013-06-12T16:40:54Z

Seoane: /* Genetic Algorithms and Multi-Objective Optimization */

{{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 [https://gephi.org/ Gephi]==
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]]

This tutorial will be held on Wednesday (June 12th) at 1:30 (after lunch) at the main lecture hall. Stephan and I will show step by step network visualization and analysis in the tutorial. If you want to play with Gephi hands on during the tutorial, please download and install Gephi ahead of time. Link to Download [https://gephi.org/ Gephi]. The example we will use can be downloaded from [http://gephi.org/datasets/airlines.gexf.zip here].

* I'm in -- Mauricio
* Hua, thanks!. I'm in! [[Regina_Martinez | Regina]]
* I will attend- Susanne

==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]]

* Max and I will probably schedule this tutorial for next week (after my lecture). [[Nix_Barnett | Nix]]

==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]]

* I will come, Susanne

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]]

Material: 

Some material from the presentation:
*Sildes, [[File:MOGA.pdf]]: These are from a larger, previously existing presentation; so you will find more stuff in there than I gave in the presentation. Feel free to come and ask about anything you want!
*Websites:
**The infamous [http://boxcar2d.com/ evolving car] that takes away attention from the speaker.
**Website to [http://picbreeder.org/ evolve pictures] after successive selection.
**[http://rogeralsing.com/2008/12/07/genetic-programming-evolution-of-mona-lisa/ This one] uses a genotype that encodes for polygons and evolve the Mona Lisa. You can find a gallery with other pictures evolved and an applet in [http://alteredqualia.com/visualization/evolve/ here]. By the way, I used this polygon genetic algorithm for my project on [http://briganraman.blogspot.com/2012/09/images-from-mind.html EEG-based image reconstruction], so you never now when something turns out useful in really distant parts of science.
**You can find plenty of resources similar to these by just googling!
*Some literature on the topic:
**Nice, classic [http://www.astro.cornell.edu/~cordes/A6523/stephanie.forrest.pdf Science paper] on genetic algorithms by Stefanie Forrest (external SFI).
**Does nature use MOO? Some answers [http://link.springer.com/article/10.1007%2Fs11284-009-0658-6#page-1 here] and [http://www.engr.colostate.edu/~krapf/biophysics/BPJC/FA2012/SauerScience2012.pdf here].
*Code (in C++): I am not going to post it because I never made it thinking that someone but me could use... and my code is a relative mess. I will provide it to whoever requires it, specially if you are doing a CSSS project that would enjoy MOO. Just come talk to me! Most surely we would have to talk through some details about how it works, but I assure that it is very easy, it should be platform independent, and it should be trivial to make it work together with any arbitrary programming language that supports file I/O--i.e. any decent programming language... but please don't use [http://en.wikipedia.org/wiki/Whitespace_(programming_language) something like this].

==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
Okay, I'll try to cover info theory, hidden markof model inference, and bayesian inference next week. Some of this will be covered this week in Jim's lectures and my labs. [[Nix_Barnett | Nix]]

==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].

2013-06-11T06:16:42Z

Seoane: /* June 21 Madrid to see Juniper's Brother's band and to dance with hippies */

{{Complex Systems Summer School 2013}}

==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]]

==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!==

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)
* [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)

==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

==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]]

==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

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]]

==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 :?

2013-06-09T22:53:29Z

Seoane:

{{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'''

-----
TIE DYE OUR OWN SHIRTS!

How is it we must limit ourselves to just two solid colors? I say no!! Let's purchase 62 white standard Santa Fe Institute shirts and [http://en.wikipedia.org/wiki/Tie-dye tie-dye] them!!

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

For the picture above I just picked real tie-dyed shirts and put the SFI logo in them. I figure out that the logo will not be in the center, but slightly at the left and a little bit higher. It is very easy to make our shirts have the focus of the spiral in there, or to use the SFI as the center of successive tie-dyed circles. I also propose to write in the back part a brief text to get us identified with the CSSS. A very schematic view in the following drawing:

[[File:Tie-dyeII.png|661px]]

Of course, each one chooses the pattern (s)he wishes. [https://www.google.com/search?q=tie-dye+patterns&safe=off&source=lnms&tbm=isch&sa=X&ei=dwa1UZ7gIMmpiALfqYH4Cg&ved=0CAoQ_AUoAQ&biw=1366&bih=609 There are plenty of them!] Before voting for this possibility beware that we will have to spend maybe a whole afternoon working on that, and that the results can be different from the expected... Tie-dye is a quite stochastic and stuff!!

-----s
I made a wordcloud of our respective fields of study using Sanders statistics. I think the wordcloud could be combined with another design e.g. Manishs Poincarè pickle or Vanessas I <3 complexity. Also the wordcloud font & style can be changed.- Susanne

[[File:SFI wordcloud t-shirt.png|661px]]

-----

[[File:picklegrid_03.png|661px]]

Never forget the [http://www.amazon.com/Accoutrements-11761-Yodelling-Pickle/dp/B0010VS078/ref=sr_1_1?s=toys-and-games&ie=UTF8&qid=1370726588&sr=1-1&keywords=yodeling+pickle yodelling pickle]. Never.

--Manish

It`s great, good laugh! - Susanne

Updated the text on the header to include mention of CSSS. --Manish

Question: Should "Yo Delay" be moved to the back of the shirt? --Manish

-----

[[File:ShirtFront_Todd.gif|200px|left]]
[[File:ShirtBack_Todd.gif|200px]]

I thought it would be interesting to use something we learned in class for the T-shirt. I'm trying to use a genetic algorithm to evolve the SFI logo. On the back are population samples from various time steps.

(This is a work in progress, and I'll keep improving the GA/shirt up until the voting on tuesday. - [[Todd_Bodnar | Todd]])

-----

[[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]]

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]]

* [[Giuliano_Andrea_Pagani | Andrea]], it looks good! Could you kindly include Madrid (center of Spain)? Thanks! [[Regina_Martinez | Regina]]
* [[Giuliano_Andrea_Pagani | Andrea]], I like your design! Could you please include lebanon (east of the mediterenean)? thnx :) [[AmaraAl_Sayegh |amara]]

Sure, thanks for the feedback. I will include the nodes where missing in the case it goes through the selection process, the current version is only a prototype ;-)

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

-----

Here's a prototype, combining Vanessa's front, with my Game of Life back. The real one will either say SFI CSSS 2013, or I'll use the entire logo (with nice font).--[[Nix_Barnett | Nix]]

Really cool Nix, what about putting a reference to CSSS 2013, so that we/they remember this year? -- [[Giuliano_Andrea_Pagani | Andrea]]

Okay, I updated the shirt. The logo looks fuzzy in this version, but it will be slightly larger and crisper in the final. [[Nix_Barnett | Nix]]

[[File:nix_shirt_2.jpg]]

-----

[[File:Clanshirt.png]]

Not sure of a design, but something with '''Phase Space Camp'''?
-----
*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 :)--[[AmaraAl_Sayegh | Amara]]
[[File:CROSS_WORDS.pdf]]

----

My suggestion is actually inspired by Susanne's design with the Mandelbrot clouds. If lots of folks like it, perhaps this could be made into a bumper sticker? A plain Mandelbrot would also do; I just grabbed this one because the <3 is more obvious. --[[Vanessa_Schweizer | Vanessa]] 
[[File:heart_complexity.png]]

Ha! this is great—
I <3 the Edge of Chaos would be cool too.
John D,

This one really clicked with me immediately. I was expecting more "complex" designs, but I really love how simple and to the point it is. I wonder if we could maybe collaborate? I'd like to maybe design the back like I described earlier. Basically something like "SFI CSSS 2013" and the SFI logo, with Conway's Game of Life growing from the letters and logo... [[Nix_Barnett| Nix]]

'''SFI solar system t-shirt. The color or symbols can be changed. If any of you have ideas for other symbols to put as planets, please let me know. I can also remove the pi symbols if this would look nicer. peace! :-) - Susanne'''

[[File:T-shirt SFI solar system.png]]

-----
 
'''Chaotic warning t-shirt. --[[Hua_Cai | Hua]] 
Ideally I would like to have only the circular SFI logo on the shirt (instead of a sqaure). But I don't know how to get rid of the white background of the logo.''' 
[[File:T-shirt_HC.jpg|400px]] 

*This reminds me of the series of warning t-shirts that Despair, Inc. made a few years ago. I like the idea of a warning, but maybe we could make it more visually appealing? I'm not good with graphics, but the idea would be to have a clear warning symbol on the front of the shirt (a yellow triangle with symbol inside, like the example below) adapted to reflect chaotic systems (maybe the Lorenz butterfly?). I think the text could still say WARNING across the top, show the symbol, and perhaps CHAOTIC SYSTEM INSIDE across the bottom. The additional text, "Be careful with inputs," could be a second line on the bottom, or perhaps on the back. With this design, I recommend putting the SFI logo and CSSS 2013 on the back. --[[Vanessa_Schweizer | Vanessa]] 
[[File:T-shirt_warn_ex.jpg]]

File:Tie-dyeII.png

2013-06-09T22:47:12Z

Seoane:

File:Many TieDye.png

2013-06-09T22:38:35Z

Seoane: Random examples with several tie-dyed shirts.

Random examples with several tie-dyed shirts.

File:Tie-dye.png

2013-06-09T22:38:00Z

Seoane: Idea of how a tie-dyed SFI shirt could look like!

Idea of how a tie-dyed SFI shirt could look like!

Complex Systems Summer School 2013-After Hours

2013-06-09T07:14:00Z

Seoane: /* Mafia/Werewolf */

{{Complex Systems Summer School 2013}}

==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!

==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.

==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")

==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]]

==Santa Fe on Sunday==

Anyone interested in going down to Santa Fe on Sunday to look at shops? Molly and I have talked about heading down, don't have a time yet, but let me know if there is interest! While I do plan on taking my car, would love for people to meet us either via bus or walking -Brady

Brady's car 
1) Brady 
2) Molly 
3) Cheryl 
4) 
5) 

A couple of us are talking about doing that as well. So I guess I will start the walking group here: 
1) Hua 
2) Vanessa (cell for when we have reception: 845-270-9330) 

* Thanks for organizing! I may join but I am not sure yet. If I end up going, I will go in either car (wherever there is a space available)-- Regina

==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]]

Or basketball? Anybody want to play a pickup game?

==Yoga on Sunday==

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]]

Synchrony on Networks

2013-06-07T21:10:33Z

Seoane:

Synchrony on Networks

2013-06-07T20:56:06Z

Seoane: /* To Do */

Complex Systems Summer School 2013-Projects & Working Groups

2013-06-07T17:32:17Z

Seoane: /* PRISM / NSA */

[[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'''==

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: Let's convene tonight after SFI, 8:30ish Friday June 7th, to put our brains together & focus project scope with beer & wine in Ariel (lower dorms).

==
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]]

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]]

=='''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

=='''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]]

=='''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

Synchrony on Networks

2013-06-07T17:21:02Z

Seoane: /* Community Detection */

Below are my initial impressions about the project. These are just a sketch, and open to change!

==Basic (Toy) Model==

Throughout, I'll use the word 'spike' interchangeably with 'tweet.'

The basic skeleton is based off of the [http://arxiv.org/pdf/1110.2724v1.pdf paper] by Aram et al. We consider a network of users which we'll model as a graph with a vertex for each user and an edge denoting a connection between each user. For Twitter data, these edges might indicate follower/followee relationships. Directedness of these edges is an open question. This gives us the basic structural model.

The dynamics occurring on top of this network will take the form of coupled inhomogeneous Poisson processes. That is, each vertex will have a [http://en.wikipedia.org/wiki/Poisson_process Poisson process] on top of it, and the rate of the process will depend on the behavior of the other nodes connected to it. An inhomogeneous Poisson process model is a common (though very rough) approximation of neural behavior. It captures the notion of 'completely random.'

Aram's model sets the instantaneous rate of each user to be a (constant) base rate, plus terms that depend on the behavior of the neighbors of a given user (if a neighbor has recently tweeted, and the user is dynamically connected to that user, they are more likely to tweet). The constant base rate is open to change.

==Community Detection==

A standard approach to finding communities within a network is to look at the network structure alone. We attempt to partition the nodes in the network such that there are many more edges within a community than between communities. A popular method for doing this is the [http://www.ece.unm.edu/ifis/papers/community-moore.pdf fast-greedy algorithm] developed by Clauset, Newman, and Moore.

[http://arxiv.org/pdf/cond-mat/0404652.pdf Another algorithm] developed by some colleagues from Granada.

==Toy Network==

One of our first tasks is to design a reasonable (small) network to run the toy model on top of. This network should presumably have apparent community structure, and then we can design on top of this a weighted network that incorporates the notion of dynamical community. These weights would essentially correspond to the weights in Equation 4 of Aram et al.' paper. One option for designing realistic network structure is to use a small network within the Twitter network I have available.