Santa Fe Institute Events Wiki - User contributions [en]

Presentations 2012

2012-06-28T05:11:47Z

Sepehre:

{{Complex Systems Summer School 2012}}

9:00 - 9:15: Christa Brelsford and Xin Lu: Changes in Social Network Structure in Response to Crisis: Using Twitter data to Explore the Effect of the Tōhoku Earthquake.

9:15 - 9:30: Piotr Milanowski and Georg F. Weber: Enzyme kinetics and the outcome of chemical reactions.

9:30 - 9:45: Fabio, Elena, Tom and Friederike: Collaboration in times of stress: an Agent Based Modelling approach

9:45 - 10:00: Joanne, Vikram, Matteo, Sanith: Price-time Dynamics of Contracts Traded on Prediction Markets

10:15 - 10:45: BREAK

10:45 - 11:00: Katrien, Jasmeen, Sandro, Cameron, Vanessa

11:00 - 11:15: Sepehr

11:15 - 11:30: Xue, Χλοε, Xiaoli

11:30 - 11:45: Seth, Daniel, Cameron: flocking in iterated reasoning.

12:00 - 1:00: LUNCH

1:00-1:15: Group Photo

1:15 - 1:30: Andres, Charlie, Gareth, and Nic G: We Got the Skills to Pay the Bills - Exploring the Link Between Occupation Diversity and Innovation

1:30 - 1:45: Xin and Abby: Use Entropy as a Measure of Traceability for Food Supply Networks

2:00 - 2:15: Ben, Laurent, Oscar, Georg: The Targeting and Timing of Treatment Influences the Emergence of Influenza Resistance in Structured Populations

2:15 - 2:30: Georg, Ben, Laurent, Oscar: Escaping the Poverty Trap: Modeling the Interplay Between Economic Growth and the Ecology of Infectious Disease

2:30 - 2:45: Ian, Marco, Oleksandr and Xin: Space of complex networks and robustness

2:45 - 3:00: BREAK

3:00 - 3:15: Marco and Matteo: Trade network formation: the role of technology and geography

3:15 - 3:30: Riccardo and Priya:

3:30 - 3:45: Nick A., Keegan, Matteo, Vikram, Sarah, Mark: Learning in Random Boolean Networks

3:45-4:00: Si, Miguel, Hide, Sarah: The Robustness, Stability and Persistence of Niche-Structured Food Webs

5:00: Final Remarks & Farewell Dinner

Presentations 2012

2012-06-27T18:41:06Z

Sepehre:

Complex Systems Summer School 2012-Project Presentations

2012-06-26T02:23:53Z

Sepehre:

{{Complex Systems Summer School 2012}}

Use this space to post project presentations and outlines. Include group members, a brief outline, and your slides.

=== Simple variation of the logistic map as a model to invoke questions on cellular protein trafficking ===
(Sepehr Ehsani, http://arxiv.org/abs/1206.5557)

Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown aspects of a biological system cannot provide more information about the set of biologically meaningful (e.g., 'hidden') states of the system than could be understood by the designer of the model ab initio. Here, the case is made for the utilization of such models to shift from a 'predictive' to a 'questioning' nature, and a simple natural-logarithm variation of the logistic polynomial map is presented that can invoke questions about protein trafficking in eukaryotic cells.

Experiment sign-up

2012-06-19T19:15:41Z

Sepehre:

Hi! Please sign up for one slot below. The experiment will be held in the SENIOR Common Room (again) next to the great hall (YES, JP's office). Please arrive on time! Ta.

- Katrien, Vanessa, Sandro, Cameron & Jasmeen

==Monday June 18==

Morning Break:

10.20-10.30: Piotr X

10.30-10.40: Laurent X

Lunch Break:

12.05-12.15: Chloe X

'''12.15-12.25: Andres ???'''

12.25-12.35: Xue X

12.35-12.45: Oleksandr X

12.55-1.05: Nick A X

1.05-1.15: Fabio X

1.15-1.25: Priya X

Afternoon:

5.00-5.10: Matteo X

5.10-5.20: Abby X

5.20-5.30: Elena X

5.30-5.40: Riccardo X

5.40-5.50: [[JP]]! X

6.00-6.10: [[Xin]] X

6.10-6.20: Ian X

6.20-6.30: Keegan

6.30-6.40: Aleksandra

6.40-6.50: Tom X

6.50-7.00:Christa X

==Tuesday June 19==

Morning Break:

10.20-10.30: Vikram X

10.30-10.40: Oscar

Lunch Break:

12.30-12.40: Gareth

12.40-12.50: Sanith

12.50-1.00: Nona

1.00-1.10: Ben

1.10-1.20: Sepehr

1.20-1.30: David P

Afternoon:

4.30-4.40: dan

4.40-4.50: Georg W. / Ben

4.50-5.00: Sander Bais / Sepehr

5.00-5.10: Aleksandra

5.10-5.20: Marque

5.20-5.30: Sarah

5.30-5.40: Oscar

5.40-5.50:

5.50-6.00:

6.00-6.10:

6.10-6.20:

6.20-6.30:

6.30-6.40:

6.40-6.50:

6.50-7.00:

Experiment sign-up

2012-06-19T01:03:29Z

Sepehre:

Hi! Please sign up for one slot below. The experiment will be held in the SENIOR Common Room (again) next to the great hall (YES, JP's office). Please arrive on time! Ta.

- Katrien, Vanessa, Sandro, Cameron & Jasmeen

==Monday June 18==

Morning Break:

10.20-10.30: Piotr X

10.30-10.40: Laurent X

Lunch Break:

12.05-12.15: Chloe X

'''12.15-12.25: Andres ???'''

12.25-12.35: Xue X

12.35-12.45: Oleksandr X

12.55-1.05: Nick A X

1.05-1.15: Fabio X

1.15-1.25: Priya X

Afternoon:

5.00-5.10: Matteo X

5.10-5.20: Abby X

5.20-5.30: Elena X

5.30-5.40: Riccardo X

5.40-5.50: [[JP]]! X

6.00-6.10: [[Xin]] X

6.10-6.20: Ian X

6.20-6.30: Keegan

6.30-6.40: Aleksandra

6.40-6.50: Tom X

6.50-7.00:Christa X

==Tuesday June 19==

Morning Break:

10.20-10.30: Vikram

10.30-10.40: Oscar

Lunch Break:

12.30-12.40: Gareth

12.40-12.50: Sanith

12.50-1.00: Nona

1.00-1.10: Ben

1.10-1.20: Sepehr

1.20-1.30:

Afternoon:

4.30-4.40: dan

4.40-4.50:

4.50-5.00:

5.00-5.10:

5.10-5.20:

5.20-5.30:

5.30-5.40:

5.40-5.50:

5.50-6.00:

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Complex Systems Summer School 2012-Photos

2012-06-08T04:45:24Z

Sepehre:

{{Complex Systems Summer School 2012}}

Feel free to share links to your photos here.

A photo of the transit of Venus across the Sun: [[Media:Venus-transit-2.jpg]]

[http://www.dropbox.com/gallery/1694302/1/CSSS2012?h=0d4e88 Some pictures]

[http://www.flickr.com/photos/sepehrehsani/7350419208/ Transit of Venus 2012]

[http://www.flickr.com/photos/sepehrehsani/7165200933/ Dr. Hübler's wave chaos experiment]

Complex Systems Summer School 2012-Projects & Working Groups

2012-06-05T15:31:33Z

Sepehre:

{{Complex Systems Summer School 2012}}

==Project proposals==

=== Nonequilibrium game theory ===
My hope is to adapt some SFI-based models, by people like Crutchfield and Farmer, so that they will quantitatively or qualitatively reproduce features of real human data. Of course, that is very specific, and I'm up for all kinds of ideas in the areas of game learning, game dynamics, small group collective behavior, cognitive science, nonlinear time series, non-eq time series, etc., etc.

Meet me, Seth Frey, at dinner on Thursday and Friday.

=== Enzyme kinetics – Do enzymes just accelerate equilibrium or play an active role in chemical reactions? ===
Enzyme networks (e.g. glycolysis) and catalysts in complex mixtures (e.g. Belusov-Zhabotinski reaction) can profoundly influence the outcome of a chemical reaction system. What about a single enzyme? Biochemistry textbooks uniformly say that an enzyme accelerates a reaction without altering its outcome. Yet, the set of differential equations that generically describes enzyme catalysis has remarkable resemblance to the Roessler equations (a textbook example of a non-linear, complex system). With a fixed substrate input or a steady substrate flow, a single enzyme probably cannot affect the reaction outcome. However, sinusoidal or pulsating substrate input, substrate activation or product inhibition, coupling of two enzymes could turn the reaction pattern non-linear. For this project, the sets of equations to study are quite well established – they need to be analyzed. In contrast to some of the more ambitious ideas circulated, this task is exhaustively doable in less than four weeks.

I am Georg Weber. If you are interested in studying this problem, please find me on Tuesday over lunch or dinner (or talk to me at any other unstructured time).
=== Traffic pattern analysis - Can we estimate car velocity by only observing car counts? ===
Imagine you have a monitored highway section with a start and end point. At both points you count the number of cars that pass by. The question I'd like to answer / simulate / estimate is: can we make some inference about the velocity of cars although we only have their counts? This would be very useful from an engineering / economic perspective because it's much easier / cheaper to count cars instead of actually tracking them from A to B.

I have some intuition about how to go about this, but these are purely statistical (think of it as birth and death process; or as particles in a system that have a certain lifetime - cars in the highway section are like particles in a system). I would like to see if using more physical modeling of motion and agent-based modeling of traffic flow could shed more light on this problem.

If you are interested let me know (me = (me = [http://tuvalu.santafe.edu/events/workshops/index.php/Georg_M_Goerg Georg M. Goerg]; email my_3_initials_in_lowercase@stat.cmu.edu). Let's say Wednesday for lunch (or any other time you see me around).

=== Cultural Evolution - General Meet-up ===
Attention anyone who is interested in cultural evolution or applying your models/methodologies to this fabulous topic!

Let's meet at 4:15 (June 5th) in the cafe during the first "Time to work on Projects" slot. A bunch of us coalesced there tonight and figured we should all properly meet up and then bud off into different projects. Please post your potential buds below:

=== Cultural Evolution - things that look like drift but aren't ===
Lots of cultural evolution looks like drift (Bently et al 2004 'Random drift and culture change"). But what social transmission or cognitive learning mechanisms are isomorphic to random sampling with replacement from cultural inputs? In biological evolution, drift serves as a null model of sorts - one that should be ruled out before you can claim that anything more interesting is happening. However, it's not clear what the "uninteresting" type of change is for things that replicate by passing through human cognition and human social systems - like culture does. Is there even a reasonable equivalent of drift in cultural transmission? How should we go about conceptualizing and modeling the evolutionary forces at play in culture?

One candidate for a drifty-lookin' human behavior is probability matching: when people reproduce similar distributions of variation to that which they've learned from. And probability matching is rampant in human behavior (from language learning, to decision making, and even at the neural level). But I think this is a clearly different process than drift, however it still may qualify under Bentley's vague criteria - we can test that out. And there have got to be more drift-esque processes, anyone have any ideas?

If you're interested in these issues or modeling evolution (of any type of system), please give me a shout!

Vanessa

vanferdi [at] gmail.com

==="Small Steps and Big Ideas" Group===

[http://tuvalu.santafe.edu/events/workshops/index.php/Christa_Brelsford Christa] [http://tuvalu.santafe.edu/events/workshops/index.php/Daniel_Wu Dan] [http://tuvalu.santafe.edu/events/workshops/index.php/Xin_Lu Xin] and Tom spent a while talking after dinner about a bunch of big ideas. Some things we thought about were *big data type network problems, *integrating qualitative social information with models of physical systems, *using games to understand cooperation and decision making.

=== 107 Proteins in 10-15 cubic meters ===
Cells rely on proteins to perform vital metabolic and signaling functions; however, it is unclear how proteins are successfully directed to their necessary cellular location(s) in a densely-packed macromolecular environment within the cytoplasm and on the cellular membrane in a short timescale (see for example [http://www.pnas.org/content/108/16/6438.full Weigel et al., PNAS 2011]). Using the cell as a manipulatable model of complexity, one could begin to define the parameters and questions, as they pertain to prokaryotic and eukaryotic cells. If interested, please drop me a line: Sepehr Ehsani; sepehr.ehsani[at]utoronto.ca.

=== Innovation and Technological Progress ===

I noticed that a number of people mentioned that they were interested in some way in relation to innovation. I was wondering if anyone was interested in a project looking at how particular technologies progress over time and whether charting the form of successful (and/or unsuccessful) previous technologies such as the transistor, fission reactor, mobile phone, etc. in terms of either price, efficiency, or some other variable may be useful in predicting whether a current technology such as solar PV, fuel cell, or something else is following a similar trajectory. Other possible ideas might be to look at using patent, publication, or collaboration network data to reveal certain features of innovation that are not captured by other statistics, particularly for technologies that have yet to reach the market. SFI Professor Doyne Farmer has looked at some of this already in 'The Role of Design Complexity in Technology Improvement', see link: http://adsabs.harvard.edu/abs/2009arXiv0907.0036M

This could be a jumping off point for some ideas on data, methods, models etc. Just throwing the idea out there and it's welcome to completely change but if you're interested, message me (Gareth Haslam) haslam@ias.unu.edu or find me in class.

=== Space, Stochasticity, Stability; Speciation? ===

[http://tuvalu.santafe.edu/events/workshops/index.php/Xue_Feng Xue], [http://tuvalu.santafe.edu/events/workshops/index.php/Chloe_Lewis Chloe] and [http://tuvalu.santafe.edu/events/workshops/index.php/Xiaoli_Dong Xiaoli]are all working in ecosystems that experience_ a lot of unpredictability in a limiting ecosystem variables (water and/or nutrients); we see patchiness in space and time in how organisms are arranged; and we have some ideas about how the stochasticity may cause the spatial arrangements. [http://tuvalu.santafe.edu/events/workshops/index.php/Si_Tang Si] is working on the stability and robustness of ecosystems.

With enough time, this is likely to involve speciation either to express different strategies, or as a result of spatial separation.

Find any of us walking-around, or meet in the cafeteria at 4:15 June 5th.

=== Plasticity in Neural Networks ===
I've done some modeling which shows that the amount of genetic variation that accumulates at any particular metabolic gene (enzyme) in a population at any given time is a function of the network topology in which the gene is embedded, as well as the distance of the network output from an optimum. So, for instance, in a linear metabolic network, enzymes at the beginning of a pathway will tend to be more constrained (show less variation in the population) than at the end of the pathway. This makes sense given that any changes in those first genes would ripple through the system and have a greater relative effect than mutations in later genes. However, this is only true when a population is already close to an optimum. When far from an optimum, we see the exact opposite trend with more variation in the front of the pathway. This also makes sense - when far from a goal, taking bigger steps gives individuals a better chance of achieving higher fitness. The system as a whole then uses the different relative step sizes according to pathway position to "fine tune" its output.
I think these findings are quite general - at least the model we used was simple enough that it could apply to many different types of directional developmental processes. We can conceptualize these "genes" more generally as sequential steps in a developmental process with some arbitrary goal. These could be steps in a factory assembly line, major product revisions versus minor releases, or (and this is my favorite), neurons learning about their environment. I'm curious what would happen if we took a similar approach to model neural networks. Genetic variation is the raw material for evolution while neural plasticity is the raw material for learning. The question we would be trying to answer is where, within a neural network, would we expect the most plasticity given a particular network topology and distance form a learning goal.
Please contact me (Mark Longo) if this sounds interesting. I'll be available during unstructured time, or you can email mlongo@stanford.edu.
[http://tuvalu.santafe.edu/events/workshops/index.php/Mark_D._Longo]

=== Robustness of complex networks ===
[[File:Zoo.png|thumb|Fig. 1. Zoo of complex networks (an example). Taken from Sol´e and Valverde, 2001.]]
==== Problem statement ====
Complex networks have various properties which can be measured in real networks (WWW, social networks, biological networks), e.g. degree distribution, modularity, hierarchy, assortativity etc. Robustness of complex networks is a big question, however only some progress have been done in this direction. For example, it was shown that the scale-free networks are much more topologically robust to random attacks than random networks. Many people claim that various characteristics of complex networks will influence the robustness interdependently. The question I am interested in is how?

==== Approach ====
The idea is to generate continuous topology space of various complex networks (networks with different modularity, degree distribution, hierarchy etc) and use it to measure their robustness (see Fig. 1). There are many approaches to measure the robustness of complex networks. For example we can remove edges of vertices of a complex network graph and look at the size of a giant cluster. We can discuss other possibilities.

If you are interested you can contact me directly or via my E-mail: krystoferivanov@gmail.com or via my [[Oleksandr Ivanov|discussion page in CSSS 2012 wiki]].

Complex Systems Summer School 2012-Projects & Working Groups

2012-06-05T04:31:31Z

Sepehre:

Alfred Hubler's Nonlinear Dynamics Lab 2012

2012-06-03T23:01:00Z

Sepehre:

{{Complex Systems Summer School 2012}}

==Thursday, June 7, 6:00pm==

1. Sarah Tweedt 
2. Georg F. Weber 
3. Georg M. Goerg 
4. Cameron Smith 
5. Mikkel Vestergaard 
6. Friederike Greb 
7. Fabio Cresto Aleina 
8. Benji zusman 
9. Elena del Val 
10.Riccardo Fusaroli 
11. Nick Allgaier 
12.John Long 
13. Sepehr Ehsani 
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==Friday, June 8 7:00am==
PLEASE NOTE THAT THIS IS AN EARLY MORNING CLASS! 
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==Monday, June 11, 6:00pm==
1. Hidetoshi Inamine 
2. Dan Wu 
3. Xiaoli Dong 
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==Tuesday, June 12, 6:00pm==
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Sepehr Ehsani

2012-05-29T16:43:00Z

Sepehre: Created page with ' I'm a fourth-year PhD student in the Department of Laboratory Medicine and Pathobiology at the University of Toronto. My project involves the biochemistry and evolutionary histo…'

I'm a fourth-year PhD student in the Department of Laboratory Medicine and Pathobiology at the University of Toronto. My project involves the biochemistry and evolutionary history of the prion protein, the causative agent of prion diseases such as bovine spongiform encephalopathy (aka mad cow disease) in cattle and Creutzfeldt-Jakob disease in humans.

I very much look forward to learning from the programs and activities at the Complex Systems Summer School.