Santa Fe Institute Events Wiki - User contributions [en]

CSSS 2008 Neuroscience Working Group

2008-06-13T17:04:18Z

Sayres:

This page describes work on a project related to neuroscience issues for the 2008 CSSS.

== What questions do we want to answer? ==
The overarching question I'd like to address is:
How do the decision-making criteria of the indivual affect the behavior of the group?

There are a lot of more specific questions we could pose related to this; for the first meeting or two, I'd like to zoom in on asking things in a more constrained way.

An initial idea for a project could be this:

Recent neuroscience studies (cited below) have modeled the representation of expected and experienced value in a dynamic foraging environment. E.g., we can model a primate facing a set of choices of where to forage; different locations have a different likelihood of providing food (=reward). Because the environment is dynamic, the reward likelihood of each location can change unpredictably in time. Corrado and colleagues propose a linear/nonlinear/Poisson model for this sort of decision making, which predicts well physiological data from a parietal region (LIP) in monkeys engaged in this task.

This model gives us a way to estimate the value associated with different locations, based on one monkey's personal experience. I'd like to add to this a representation of how monkeys (or other, more abstract agents) combine this information with information about what other monkeys are doing. The second part of the model would be based/inspired by the models Iain Couzin described on group behavior. The exact details can be open to discussion, but we could look to construct a simple model where each monkey looks at other monkeys in a given radius, sees which ones are succeeding at getting reward, and updates the estimated value of those locations, with a temporal decay signal.

So, I propose we construct a value representation with these two terms -- one reflecting an agent's individual experience and memory of reward, and one representing the agent's perception of how successful nearby agents are. We would add a weighting factor to adjust between these terms. We should have some expectations about the behavior of the set of agents at the extreme values of these weights: e.g., when the weight for information coming from other agents is turned to zero, the model should reproduce the behavior reported in the Corrado et al. papers.

== What is the relevant background? ==

Articles on the neuroscience of decision-making:
* [http://www.jneurosci.org/cgi/content/abstract/27/31/8178 short review article outlining general approaches towards modeling decision-making in neuroscience: a good place to start]
* [http://www.ncbi.nlm.nih.gov/pubmed/15205529?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Science paper presenting the initial experiments on a simplified foraging task, and trying to understand neural correlates of perceived "value"]
* [http://www.ncbi.nlm.nih.gov/pubmed/16596981?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum theory paper explaining the "LNP" (linear-nonlinear-Poisson) model used to model decision-making processes]
* [http://www.nature.com/neuro/journal/v11/n4/abs/nn2066.html;jsessionid=11EFE5AF51DC7C56D26EAAE1BA588A43 Rushworth and Behrens 2008] Review article on work in cingulate and parietal cortex of humans by the Rushworth group at Oxford.

== How shall we answer them? ==

My (Rory's) only criterion: all code will be in MATLAB. No disrespect for other languages: I think Python's great and am learning it, and NetLogo is convenient; but I know for a fact that things will get done much faster if I can code in MATLAB. I'm just that kinda guy. :)

== Logistics: when and where do we meet? ==

First meeting is at '''9pm in the Lower Dorm Common Room, Friday 6/13'''.

== People: Who's interested? ==

Please sign below if you'd like to work on this with me. I'll make an email list with names from these people. (You don't have to give me your address here; I can figure it out.)

[[Rory_Sayres]]

CSSS 2008 Neuroscience Working Group

2008-06-13T14:35:31Z

Sayres:

CSSS 2008 Santa Fe-Schedule

2008-06-12T23:39:57Z

Sayres: /* Week Two - Ecology/Evolution/Molecular Biology/Disordered Systems */

{{CSSS 2008 Santa Fe}}



== Week One: MODELING/NONLINEAR DYNAMICS ==

{| width="95%" border="1" cellpadding="4"
|- align="center"
| TIME
| ACTIVITY

|- bgcolor="#aaaaaa" align="center"
| 
| Sunday, June 1
|-
|5:30 p.m. - 8:30 p.m.
|Welcome Reception & Buffet Dinner @ St. Johns

|- bgcolor="#aaaaaa" align="center"
| 
| Monday, June 2
|-
|
|All events at St. Johns
|-
|9:00 a.m. - 10:15 a.m.
|Opening Remarks: [[Geoffrey West/Dan Rockmore]]
|-
|10:15 a.m. - 10:45 a.m.
|Break
|-
|10:45 a.m. - 12:00 p.m.
|Nonlinear Dynamics I: [[Liz Bradley]]
|-
|12:00 p.m. -1:30 p.m.
|Lunch
|-
|1:30 p.m. - 2:45 p.m.
|Agent-based Modeling: [[Stephen Guerin/Owen Densmore]]
|-
|2:45 p.m. - 3:15 p.m.
|Break
|-
|3:15 p.m. - 4:30 p.m.
|Student introductions & breaking the ice
|-
|7:30 p.m.
| Special Event: Liz Bradley/David Capps - [http://www.santafe.edu/events/abstract/1226 Con/cantation Chaotic Variations]
|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 3
|-
|9:00 a.m. - 10:15 a.m.
|Networks I: [[Mark Newman]]
|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Nonlinear Dynamics II: [[Liz Bradley]]

|-
|12:00 p.m. -1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Modeling in the Social Sciences I: [[Josh Epstein]]

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Nonlinear Dynamics III: [[Liz Bradley]]

|-
|7:00 pm - 9:00/9:30 p.m.
|Downtown for evening - one drink coupon at Coyote Cafe - shuttles back and forth

|- bgcolor="#aaaaaa" align="center"
|
| Wednesday, June 4

|-
|
|All events at SFI

|-
|12:30 p.m. -1:45 p.m.
|Lunch

|-
|2:00 p.m. - 3:15 p.m.
|Networks II: [[Mark Newman]]

|-
|3:15 p.m. - 3:45 p.m.
|Tea with SFI community

|-
|3:45 p.m. - 5:00 p.m.
|Social Sciences Modeling II: [[Josh Epstein]]

|-
|8 p.m. - ?
|[http://www.santafe.edu/events/workshops/index.php/CSSS_2008_Santa_Fe-After_Hours#Board_Game_evening_.28around_8pm.29 Board Game evening] in the [http://www.santafe.edu/events/workshops/index.php/Image:Cr_map.JPG Lower Common Room]

|- bgcolor="#aaaaaa" align="center"
|
| Thursday, June 5

|-
|9:00 a.m. - 10:15 a.m.
|Nonlinear Dynamics IV: [[Liz Bradley]]

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Networks III: [[Mark Newman]]

|-
|12:00 p.m. -1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Social Sciences/Modeling III: [[Josh Epstein]]

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Nonlinear Dynamics (in action!): [[Alfred Hubler]]

|-
|7:00 p.m. - 8:30 p.m.
|[[CSSS_2008_Santa_Fe-Tutorials#Introduction_to_the_Design_and_Analysis_of_Computer_Experiments| Introduction to the Design and Analysis of Computer Experiments]]: [[B%C3%A9la_Nagy|Béla Nagy]]

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 6

|-
|9:00 a.m. - 10:15 a.m.
|Evolution I: [[David Krakauer]]

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Networks IV: [[Mark Newman]]

|-
|12:00 p.m. -1:30 p.m.
|Lunch

|-
|1:00 p.m.- 3:00 p.m.
|Nonlinear Dynamics Lab - w/Alfred Hubler [[Friday 1:00 Lab Signup|signup]] in Evans Science Building 214

Eigenvalues tutorial (1:00-2:00)

Information Theory, measurement, models -- Tom Carter (2:00-3:00) ([http://astarte.csustan.edu/~tom/SFI-CSSS/index.html Reading material and examples])

|-
|3:00 p.m. - 5:00 p.m.
|Nonlinear Dynamics Lab - w/Alfred Hubler [[Friday 3:00 Lab Signup|signup]] in Evans Science Building 214

Evolutionary Game Theory Tutorial in the big lecture hall. ([[CSSS_2008_Santa_Fe-Tutorials#A_Crash_Course_to_Classical_and_Evolutionary_Game_Theory|more info]]) ([[Media:EGT-01.pdf|notes]])

|-
|5:00 p.m.
|Nish is going to the Outlet Mall so folks can buy stuff (Josh, Petr, Sonya)

|-
|5:00 p.m - 9:00 p.m.
|Flamenco Theme Party! @ SFI

|- bgcolor="#aaaaaa" align="center"
|
| Saturday, June 7

|-
|All day
|Hiking (Bandelier, Los Alamos)

|-
|1:00 p.m. - ?
|[http://profile.myspace.com/index.cfm?fuseaction=user.viewprofile&friendID=20756842 Sharon Gilchrist] at Cowgirl

|-
|8:00 p.m.
|Viewing of ''Ghost Dog'' starring Forest Whitaker in the Lower Common Rooms (upstairs)

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

|-
|12:45 p.m. - 2:45 p.m.
|Euro 2008 - Germany vs. Poland -- On a TV in the lower dorms

|-

|-
|2:00 p.m. - 4:00 p.m.
|Ultimate Frisbee -- Meet at the athletic field

|-
|4:20 p.m. - 6:00 p.m.
|Theory group -- Meet at coffee shop/lounge

|-
|5:00 p.m. or 6:00 p.m.
|Basketball -- Meet at the gym
|}

== Week Two - Ecology/Evolution/Molecular Biology/Disordered Systems ==

{| width="95%" border="1" cellpadding="4"
|- align="center"
| TIME
| ACTIVITY

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

|-
|9:00 a.m. - 10:15 a.m.
|Adaptationism and the Adaptive Landscape: Jon Wilkins (SFI)

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|MCMC and Complex Systems: [[Aaron Clauset]]

|-
|12:00 p.m. -1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Foodwebs I: Jennifer Dunne

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Foodwebs II: Neo Martinez

|-
|4:30 p.m. - 4:45 p.m.
|T-shirt design ( [[CSSS_2008_Santa_Fe-TShirts | TShirts page ]] )

|-
|5:00 p.m. - 6:00 p.m.
| Tutorial: [[CSSS_2008_Santa_Fe-Tutorials#Genomics_.2F_Central_dogma_overview| Central dogma / genomics tutorial ]] ([[Jean_Hausser|Jean]])

|-
|7:00 p.m. - ?? p.m.
| Tutorial: [[ Opensource software tutorial ]] (includes Python [[http://www.inf.unisi.ch/phd/ciampaglia/python.tar.gz code samples]] and R)

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 10

|-
|9:00 a.m. - 10:15 a.m.
|Food Webs III: Jennifer Dunne

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Food Webs IV: Neo Martinez

|-
|12:00 p.m. -1:30 p.m.
|Lunch - Theory Group Second Meeting: Manuel DeLanda Discussion, Part II (in Cafeteria)

|-
|1:30 p.m. - 2:45 p.m.
|Rule-based modeling for biomolecular systems I: Jean Krivine

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:00 p.m. - 4:30 p.m.
|Basketball -- Meet at the gym

|-
|3:15 p.m. - 4:30 p.m.
|Logic Tutorial, focused on human reasoning
|-
|4:30 p.m. - 6:30 p.m.
|Nonlinear Dynamics Lab - Alfred Hubler [[Tuesday 4:30 Lab Signup|signup]]
|-
|7 p.m. - 8 p.m.
|Evolutionary Game Theory Tutorial: Part II
|-
|7 p.m. - ??
|NBA Finals Game 3 -- Boston Celtics at LA Lakers
|-
|8 p.m. - 9 p.m.
|[[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Geometry_of_Fitness_Landscapes|Geometry of Fitness Landscapes]] go/no-go discussion, meet outside lecture hall
|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 11

|-
|10:30 a.m. - noon
| Tutorial: [[CSSS_2008_Santa_Fe-Tutorials#Questions_at_the_Intersection_of_Neuroscience_and_Complexity|Questions at the Intersection of Neuroscience and Complexity]] [http://www.santafe.edu/events/workshops/index.php/Image:SFI_CSSS_Tutorial_Jun08.ppt Slides]

|-
|
|All afternoon events at SFI

|-
|12:30 p.m. -1:45 p.m.
|Lunch (at SFI)

|-
|2:00 p.m. - 3:15 p.m.
|Carnot, Chemistry, and Computation: D. Eric Smith

|-
|3:00 p.m.
|Tea with SFI community

|-
|3:45 p.m. - 5:00 p.m.
|Rule-based modeling for biomolecular systems II: Jean Krivine

|-
|5:30 p.m. - ?
|Albuquerque Isotopes baseball game (game starts at 7pm)

|-
|8 p.m. - ?
|[http://www.santafe.edu/events/workshops/index.php/CSSS_2008_Santa_Fe-After_Hours#Board_Games Board Game evening] in the [http://www.santafe.edu/events/workshops/index.php/Image:Cr_map.JPG Lower Common Room upper floor]

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

|-
|9:00 a.m. - 10:15 a.m.
|Rule-based modeling for biomolecular systems III: Jean Krivine

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Complex Systems I: Dan Stein

|-
|12:00 p.m. -1:30 p.m.
|Lunch - (Theory Group Meets in Cafeteria: DeLanda Part III - Machinic Phlyum)

|-
|1:30 p.m. - 2:45 p.m.
|Group Dynamics I: Iain Couzin

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Group Dynamics II: Iain Couzin

|-
|5:00 p.m. - 6:30 p.m.
|Workshop: Modelling in virus fields (a priori in the main room)

|-
|7:00 p.m. - 9:00 p.m.
|Pizza Party @ St. Johns

|-
|8:30ish - ???.
|Tom Carter -- topics TBD

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

|-
|9:00 a.m. - 10:15 a.m.
|Complex Systems II: Dan Stein

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Complex Systems III: Dan Stein

|-
|12:00 p.m. - 1:30 p.m.
|Lunch

|-
|3:00 p.m. - 4:00 p.m.
| Tutorial: [[CSSS_2008_Santa_Fe-Tutorials#Economics_.26_Finance_101|Economics & Finance 101]]: ([[Carlos_Yepez|Carlos]])

|-
|3 p.m. (??)
|Nish's car leaves for the Grand Canyon, with Petr, Jean and Jeremie.

|-
|4:15 p.m. - 5:30 p.m.
|[[CSSS_2008_Santa_Fe-Tutorials#GIS_.2F_Spatial_Analysis| GIS / Spatial Analysis]]: [[Flavia_Feitosa| Flávia]]
|}

== Week Three - FINANCE/ECONOMY ==

{| width="95%" border="1" cellpadding="4"
|- align="center"
| TIME
| ACTIVITY

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

|-
|9:00 a.m. - 10:15 a.m.
|Finance/Economics I: [[D._Eric_Smith]]

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Statistical Learning/Markets/Complex Systems I: [[Greg_Leibon]]

|-
|12:00 p.m. - 1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Herding Behaviors: Willamien Kets

|-
|3:15 p.m. - 4:30 p.m.
|[[CSSS_2008_Santa_Fe-Tutorials#A_little_analytical_tool-box:_Non-linear_dynamics,_ODEs,_PDEs...|Analytical Toolery]]: The [[David_Foster|Brothers]] [[Jacob_Foster|Foster]]

|-
|4:30 p.m. - 6:00 p.m.

|Tutorial: [[CSSS_2008_Santa_Fe-Tutorials#Semiotics,_Sign_Systems,_and_the_Mind|Semiotics, Sign Systems, and the Mind]] - [[Christopher_Vitale|Chris]]

|-
|6:00 p.m. - 7:15 p.m.

|[[CSSS_2008_Santa_Fe-Tutorials#Theory_of_computation|Theory of computation]]: [[Adam_Campbell|Adam Campbell]]

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 17

|-
|9:00 a.m. - 10:15 a.m.
| Prehistoric Finance: Daniel Hruschka

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Statistical Learning/Markets/Complex Systems II: [[Greg_Leibon]]

|-
|12:00 p.m. - 1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Statistical Learning/Markets/Complex Systems III: [[Greg_Leibon]]

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Cellular Networks and Robustness I: Andreas Wagner

|-
|7:00 p.m.
|The Motivation and Creation of "NUMB3RS:" Julie Hebert (writer, director, consulting producer) and David Zucker (co-executive producer)

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 18

|-
|9:00 a.m. - 10:15 a.m.
|Cellular Networks and Robustness II: Andreas Wagner

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Econophysics I: Doyne Farmer

|-
|12:00 p.m. - 1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|TBA: Geoffrey West

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Group project work

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 19

|-
|9:00 a.m. - 10:15 a.m.
|Econophysics II: [[J. Doyne Farmer]]

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Climate and Diet I: Gidon Eshel

|-
|12:00 p.m. -1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Evolutionary Computing I: Melanie Mitchell

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Evolutionary Computing II: Melanie Mitchell

|-
|5 pm to 6pm
|Tutorial: [[CSSS_2008_Santa_Fe-Tutorials#Network_Economics_and_Value_Theory|Network Economics and Value Theory: From Marx to Complexity]] - [[Christopher_Vitale|Chris]]
|-
|7:00 p.m. - 9:00 p.m.
|Pizza Party @ St. Johns

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 20 - All Day at SFI 

|-
|9:00 a.m. - 10:15 a.m.
|Cellular Automata and Amorphous Computing: Melanie Mitchell

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Climate and Diet II: Gidon Eshel

|-
|12:30 a.m. - 1:30 p.m.
| Lunch (@ SFI)

|-
|1:30 p.m. - 3:00 p.m
| Communicating Complexity: Mitch Waldrop

|-
|4 p.m. (??)
|Nish driving down to White Sands for the full moon with Ruben, Jean, Sonja, Peter, Petr and Giovanni (in one car?).
|}

== Week Four ==

{| width="95%" border="1" cellpadding="4"
|- align="center"
| TIME
| ACTIVITY

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

|-
|9:00 a.m. - 10:15 a.m.
|Social Sciences/Modeling II: Scott E. Page

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Computational Complexity: Cris Moore

|-
|12:00 p.m. - 1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Group project work

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Group project work

|- bgcolor="#aaaaaa" align="center"
| 
| Tuesday, June 24

|-
|9:00 a.m. - 10:15 a.m.
|Social Sciences/Modeling II: Scott E. Page

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Quantum Computing: Cris Moore

|-
|12:00 p.m. - 1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Group project work

|-
|2:45 p.m. - 3:15 p.m.
|Break

|-
|3:15 p.m. - 4:30 p.m.
|Group project work

|- bgcolor="#aaaaaa" align="center"
| 
| Wednesday, June 25

|-
|
|All events at SFI

|-
|
|CSSS@20: Continuity and Novelty

|-
|9:00 a.m. - 9:45 a.m.
|Trans-disciplinarity and complexity - What makes SFI unique?: David Krakauer

|-
|10:00 a.m. - 10:45 a.m.
|The diffusion of statistical physics reasoning into complex phenomena: D. Eric Smith

|-
|11:00 a.m. - 11:45 p.m.
|Experimental and Empirical Data: Jessica Flack

|-
|12:00 p.m. -1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:15 p.m.
|The evolution of computational concepts and methods at SFI: Stephanie Forrest

|-
|2:30 p.m. - 3:15 p.m.
|Changing visions of society: From the many-body problem to sustainability: Luis Bettencourt

|-
|3:15 p.m.
|Tea with SFI community

|-
|4:00 p.m. - 4:45 p.m.
|The influence of SFI on the academic/business/intellectual landscape

|- bgcolor="#aaaaaa" align="center"
| 
| Thursday, June 26

|-
|9:30 a.m. - 11:00 a.m.
|Group project work

|-
|10:15 a.m. - 10:45 a.m.
|Break

|-
|10:45 a.m. - 12:00 p.m.
|Group project work

|-
|12:00 p.m. -1:30 p.m.
|Lunch

|-
|1:30 p.m. - 2:45 p.m.
|Group project work

|- bgcolor="#aaaaaa" align="center"
| 
| Friday, June 27: FINAL POSTER DAY

|-
|5:00 p.m. - 9:00 p.m.
|Farewell Party! Academy Awards Theme!

|}

CSSS 2008 Santa Fe-Tutorials

2008-06-12T23:37:16Z

Sayres: /* Questions at the Intersection of Neuroscience and Complexity */

{{CSSS 2008 Santa Fe}}



== The big opensource tutorial ==

=== Open Source research software ===

Update! [[Opensource software tutorial|Tutorial]] scheduled on Monday 9 from 7:00p

Open (no pun intended...) your eyes to the wonderful world of FOSS -- Free and Open Source Software. While the distinction between Free and Open Source is a very interesting one (and highly contentious in the right crowds), for research purposes, we want to use the best tools for the job but some of us suffer from limited income, so I would like to talk about both. At the same time, FOSS is great to use for a non-economic reason: if you find bugs, or design extensions, you can fix them yourself (in OSS, at least) or at least report the problem back to a typically active community. Some potential tools to discuss/explore: R, Octave, Scilab, Gnuplot, perhaps some of the more useful languages in the field like Python and perhaps others I don't know as much about (a quick `apt-cache` on my Ubuntu Hardy install shows RasMol, ClustalW, SeaView, Achilles, complearn, EMBOSS, GENESIS, etc...)

- I would like to give a "Brazilian" contribution. Those who are interested in GIS&Cia could have a look at [http://www.dpi.inpe.br/gilberto/software.html Free and Open Source GIS Source].
[[Flavia_Feitosa|Flavia]]

I would be happy to contribute a little bit about freely available simulation environments like ns-2 (computer networks) and omnet++ (a generic DES) -- Laura

- For Python I can offer a tutorial (see below). Nish, do you have any experience with [http://www.sagemath.org/ Sage]? [[User:Giovanni|Giovanni]]

All great ideas and I would love to have more of a "You know how to use this tool or you know of this tool, you talk about it" style of tutorial :)
Maybe we can do a general OSS tutorial/discussion and then transition to specific sub-topics in separate tutorials (Python, GIS, networks, etc)?
I've not used Sage, before, but I'm happy to take a look before the tutorial. Thanks for the info, Giovanni!

 
I'd like to learn more about open software. [[Holger_Keeler| Paul]]

Some subtopics that we'll cover:

==== R tutorial ====

I (''[[Ruben_Kubiak|Ruben]]'') know a little bit about R (basic stuff such as common plots and regression analysis) but would like to enhance my R skills. Does anybody have an interest in a R tutorial, too? Please edit this if there is more interest.

I am fairly familiar with R and could probably run a tutorial... what are you all interested in
learning? - Skyler
*I'd just like to get an understanding of some of it's practical uses. -Devin
*Do you familiar with running social network analysis package in R? I want to learn more about it. [[Jiang_Wu| Jiang]]

Interested folks
#[[Devin_Drown|Devin]]
#[[Mark_Rivera | Mark]]
#[[Jiang_Wu| Jiang]]
#[[Molly_Rorick|Molly]]
#(Soumya)
#[[Riley_Crane]]
#[[Jeremie]]
#[[Tanja_Gesell|Tanja]]

==== Python tutorial ====
Update! Thank you to everybody who showed up for the tutorial. This [http://www.inf.unisi.ch/phd/ciampaglia/python.tar.gz tarball] contains all the scripts I've shown during the tutorial plus two more that do actually something interesting. To run logistic.py you will need installed [http://numpy.org numpy], [http://scipy.org scipy] and [http://matplotlib.sourceforge.net/ matplotlib]. You can easily install all these packages using [http://peak.telecommunity.com/DevCenter/EasyInstall easy_install], a tool that lets you download, build and install python packages from the command line (e.g. try "easy_install matplotlib" from the shell)

I've (''also [[Ruben_Kubiak|Ruben]]'') interest in a Python tutorial. Please edit this if there is more interest.

I can give a tutorial on python and on scipy/numpy. I can also talk about coding in general, as python is both a languange which is object oriented, imperative and functional (somehow). We can use the [http://docs.python.org/tut/tut.html python tutorial] itself as a reference for the part about the language, and then move to the basic concepts of the duo [http://numpy.org numpy] / [http://scipy.org scipy], which form a powerful tool to manipulate n-dimensional arrays of numbers and also talk about [http://ipython.scipy.org/moin/ ipython] (the enhanced interactive shell) and the [http://matplotlib.sourceforge.net/ pylab] interface, which gives a very nice environment for interactive programming and data analysis. Since pylab has been designed to mimic MATLAB's interface (the major plotting/statistical functions work as expected in both enviroments, which saves you a lot of time if you're used to MATLAB), I can also talk a bit about MATLAB, but being not a big fan of it, it would be better if somebody else stepped in to another tutorial on that.

Leave a mark if interested! [[User:Giovanni|Giovanni]]

I'd be interested in this as well [[User: Mark | Mark]] 

I'm in. —[[User:Jreyes|Josh]]

I'm in. [[Nish_Aravamudan|Nish]]

Yes please. [[Molly_Rorick|Molly]]

Me too. [[Rory_Sayres]] [[User:Sayres|Sayres]] 23:55, 4 June 2008 (MDT)

I'd be interested in this as well [[Tanja_Gesell|Tanja]]

I'm in [[Riley_Crane]]

Another one. [[Petr Svarc|Petr]]

== Neutral models in biology ==

Already met. Big thanks to Molly!

There is an interesting [http://arxiv.org/abs/0710.4911 paper] by Cosma Shalizi of SFI about methodological problems in social sciences research in which he talks about the concept of neutral models in evolution models. I was wondering if any of the bio-people can give a tutorial on this topic as I am pretty interested in understanding the concept. [[User:Giovanni|Giovanni]]

I would be very interested in learning about neutral networks too! - Skyler

== GIS / Spatial Analysis ==

Space Matters!! Geographical information system (GIS) is a computational system (hardware + database engine) that is designed to assemble, store, update, analyze, manipulate, and display geographically referenced information (data identified by their locations).

I'm thinking about introducing some basic GIS concepts and a free GIS software known as [http://www.dpi.inpe.br/~flavia/GIS/ Terraview]. We could also explore some spatial analysis techniques (this is the best part!) using Terraview and [http://www.geoda.uiuc.edu/downloadin.php GeoDa] (also free!).

Please edit here if you are interested or send me an email. [mailto:flafeitosa@gmail.com Flávia]

Update! It has been scheduled on Friday, June 13 from 1:30 p.m. - 2:45 p.m.

I'm in [[Walter_Zesk|Walt]] 
I'd do this. —[[User:Jreyes|Josh]] 
let me know, I'm in, Sonja 
Me too. —[[User:Lfriedl|Lisa]] 
Can not wait for this! Rio 
Me too. [[Kathleen_Sprouffske|Kathleen]] 
Sounds like fun. If people are interested, I can bring some data sets to play around with. Alex

== Statistical Physics for Non-Physicists ==
Problem: Textbooks about this are written for physicists.
Solution: A Physicist (or mathematician) that would be so kind and spend few minutes (or maybe hours) to explain all that stuff to people like me(Petr):-)

[[Ruben_Kubiak|Ruben]]: Do you seek for a general introduction or something specific?

A crash course in Statistical Physics would be awesome. Let us know. — [[User:cyepez|Carlos]]

I am interested too. (Soumya)

Me too. (Jean)

Interested! [[User:Meritxell|Meritxell]]

Interested! [[User:Giovanni|Giovanni]]

Ditto - Skyler

Me too. —[[User:Lfriedl|Lisa]] 

Me three. [[User:RobMills|RobMills]]

I'd be willing to run such a tutorial. However, I would have to consult with some/all of the interested parties to find out what kind of statphys you want to learn about. There are a huge number of possible topics, one could start with basics like ensembles, or perhaps people are interested in master equation and other non-equilibrium techniques, or maybe critical phenomena is what people are interested in. I really do not know. (Orion)

Can you give us who are not physicists an introduction about a kind of special questions that you will think it from the viewpoint of physicists? Like complex network, dynamic, also something else, what is the most important measurement and dynamic process you want to observe? -[[Jiang_Wu|Jiang]]

Check out this book: http://pages.physics.cornell.edu/sethna/StatMech/ [[Petr Svarc|Petr]]

== Modern Logic and Reasoning ==
Like I mentioned in the 'ice-breaking', I could tell something about application of modern logic into human reasoning. It's a very board topic, and very new. Criticisms are welcome and needed. I would give some basic examples. On top of that, I would also say some development of logic, and how I found it useful in research, which might seem un-related to logic, esp. in social science. I am planning to give a 15 to 20 minutes presentation, UNLESS people want to hear more, in that case, please let me know.
QiQi

I'm interested! [[Kathleen_Sprouffske|Kathleen]] 
Me too! [[kolbjorn|Kolbjørn]] 
Sign me up. — [[User:Jreyes|Josh]] 
I'm interested too! (Flavia) 
I'm in! [[Srideep_Musuvathy|srideep]] 
I'm in too [[User:Giovanni|Giovanni]] 
Count me in - Skyler 
I'd be interested in this as well. [[Tanja_Gesell|Tanja]]
 Sounds great - i'll be there. [[User:RobMills|RobMills]]

Please remind by email or somhow.. and sign me up! [[User:sonotto|Sonja]]

I am in Qi, But where? Rio

Update! Time at June 10th, 03.15 p.m. - 03.35 p.m.
[[CSSS 2008 Santa Fe-Schedule]]

== Introduction to the Design and Analysis of Computer Experiments ==
How do you find "interesting" behavior when your computer model is too slow or the inputs are too many to try every possible combination? Using an Arctic sea ice simulator example, I will show you how modern statistical methods can help you explore your virtual world more efficiently. Check out this brief
[http://www.stat.sfu.ca/~dbingham/NICDS_CompExpt/research.html overview] or a more technical paper about
[http://www.schonlau.net/publication/jogo98.pdf global optimization]. Also see [http://www.gaussianprocess.org/ Gaussian Processes for Machine Learning] for a list of available resources. [[B%C3%A9la_Nagy|Béla]]

== Genomics / Central dogma overview ==
It seems like some of you might be interested in an overview of the central dogma of molecular biology to non-biologists. This could be an 1h tutorial on the major actors of gene expression: nucleus, chromosomes, chromatine, DNA, RNA (tRNA, mRNA), proteins, polymerases, ribosomes, transcription factors, and eventually a quick intro to small, non-coding RNAs as a bonus. Although being a bioinformatician by training, I'm happy to leave the way if a "hard core" biologist wants to do this tutorial (Molly ?). Edit if interested! Jean

I'd be happy to attend a tutorial in 'genomics for idiots' -- Laura

Me too. I am also interested in metagenomics if this is not too much of course. -- Francois

I'd like to go to a 'genomics for idiots' tutorial as well. -- [[Srideep_Musuavthy|srideep]]

Ok, so I'll prepare some slides. How about Monday 9th, 5p - 6p (location TBA) ? -- Jean

Nice tutorial. [[Jie_Ren | Jie]]

== Artificial Intelligence/Machine Learning ==
I (Nish) could introduce some of the basic methods in AI/ML. If there is significant interest in the two fields separately, I could do two tutorials. Would probably focus on the higher level, rather than the nitty-gritty details, as well as applications of the methods to real problems. I'm not necessarily an expert, although have a fair amount of experience in the area, so I would prefer a more interactive session, where questions can be answered by everyone.

Sign me up. — [[User:cyepez|Carlos]] 
I'm also interested. -[[Sarah_Cobey|Sarah]] 
Me too! [[Flavia_Feitosa|Flávia]]

How about "AI/MI for dummies", Nish? I've been wondering about it.... Rio

sounds good [[Riley_Crane]]

nice [[Jie_Ren | Jie]]

== A Crash Course to Classical and Evolutionary Game Theory ==
Game theory is the study of interactive decision making. Classical game theory aims to develop a general theory to describe how rational agents interact strategically. In many cases humans lack the kind of infinite computational power and time assumed by classical game theory. In the early 1970s the biologist John Maynard Smith introduced evolutionary methods to the field, dispensing with the assumption of hyper-rationality while changing many of the concepts central to the field along the way. The result was evolutionary game theory. This new framework has been used to model the behavior of fundamentally non-rational players (such as viruses) as well as humans.

In this tutorial, I'd try to introduce the basic concepts in both of these fields, namely, the definition of a game, payoffs, the Nash equilibirum and evolutionarily stable strategies, the replicator dynamics. I'll briefly mention the three basic classes of two-strategy games represented by the Prisoner's Dilemma, the Snowdrift Game (sometimes called the Hawk-Dove game or Chicken), and the Stag Hunt Game. Depending on particular interests of the group, we could prove the Bishop-Cannings theorem and give a classification of all symmetric two-strategy games; or look at updating methods and spatial chaos; reputation and image scoring; rock-paper-scissors in biological systems; or evolutionary branching and specialization.

If there's something else you'd like to know about EGT, shoot me ([mailto:joshua.reyes@removeme.gmail.com Josh]) an email, and I'll see if I can dig up something I know on your topic. I'm not going to require any fancy mathematical background. If you've seen a 2×2 matrix before, great. Otherwise, it's not a big deal. We won't multiply them or calculate their eigenvalues. They'll just serve as a means for bookkeeping.

Note: Some of us are also thinking about setting up a [[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Evolutionary_Game_Theory|working group]] as well. 
Update: The next meeting has been scheduled for Tuesday, June 10 from 7–8pm in a location TBD.

=== Lecture Notes ===
Lecture 1. [[Media:EGT-01.pdf|Classical Game Theory]]

Please let me know about any typos, errors, or flat-out lies. Suggestions are good, too. Thanks.

=== Resources ===
# Hofbauer & Sigmund '''Evolutionary Games and Population Dynamics''' [http://www.amazon.com/Evolutionary-Games-Population-Dynamics-Hofbauer/dp/052162570X]
# Cressman R '''Evolutionary Dynamics and Extensive Form Games''' [http://www.amazon.com/Evolutionary-Dynamics-Extensive-Economic-Evolution/dp/0262033054/ref=sr_1_2?ie=UTF8&s=books&qid=1213149279&sr=1-2]
# [http://www.ped.fas.harvard.edu/people/faculty/index.html Nowak, Martin] (to be found)
##[http://www.univie.ac.at/virtuallabs/ Virtuallabs]
# Sandholm, Bill (to be found -- is it this: '''Evolution in games with randomly disturbed payoffs''', J. Economic Theory?)

*I'll sign up for this. Kolbjørn
*I'm interested too! (Flavia)
*I'll be there too. Kathleen
*I'm in. Jean
*I'm interested as well. Steve
*will be there at 3 [[Walter_Zesk|Walt]]
*I'll be there, Petr
*Good stuff. I could also say a few things about [http://www.iiasa.ac.at/Research/EEP/AdaptiveDynamics.html adaptive dynamics], if there's interest. [[Sarah_Cobey|Sarah]]
*I'll be there. [[Jiang_Wu|Jiang]]
*Count me in (Chris)
*I'm in. Tanja
What a good stuff! I wanna introduce several papers of mine. Hope they are helpful. [[Jie_Ren | Jie]]

*Randomness enhances cooperation: a resonance type phenomenon in evolutionary games [http://arxiv.org/abs/cond-mat/0607457]
*Interplay between evolutionary game and network structure: the coevolution of social net, cooperation and wealth[http://arxiv.org/abs/physics/0605250]
*Memory-Based Snowdrift Game on Networks [http://arxiv.org/abs/physics/0604103]
*Emergence of cooperation induced by preferential learning [http://arxiv.org/abs/physics/0603007]

== Resilience of social-ecological systems ==
The resilience perspective is increasingly used as an approach for understanding the dynamics of social–ecological systems. Essential for the resilience perspective is the recognition that living systems are not in equilibrium but rather in a domain of attraction.
Many dynamic systems, however, have multiple domains of attraction. Moreover, self-organizing processes can create or change the shape and depth of this domain of attraction. Within the resilience perspective, new pathways of sustainable development can be represented by crossing a threshold from a domain of attraction and/or by creating new domains. Resilience is a measure of how much change or disruption is required to transform a system from being maintained by one set of mutually reinforcing processes and structures to a different set of processes and structures.
If you are interested we (Mike and Dirk) can introduce you to some of the insights developed by the [http://www.resalliance.org/1.php resiliance alliance] and the challenges we face in understanding these kind of systems.

I am interested in this too. Richard

Very interested, any idea of when you will do it? [[Walter_Zesk|Walt]]

I'm interested as well. Steve

I'm interested too. - Skyler

I think to contribute from my previous work on SES. Rio

== Introduction to classical control theory ==
I (Srideep) can offer a 'quick' tutorial on control theory/control systems. This is will be a simple introduction to the motivation, basic ideas, issues and jargon in the field. If you are interested, please let me know about your background in linear algebra, complex analysis and calculus. Depending on the background, I might spend more or less time introducing the field.

Ideally, if you know what eigenvalues and eigenvectors of a matrix are, what a pole of a complex function is and how the solution of a linear differential equation looks like, you are ready to jump right into controls. If the words above don't mean much at all, then we can run a quick 'review' of what they mean intuitively.
you can sign up here or send me an email [mailto:srideep.musuvathy@gmail.com srideep]

Update! Lets plan on discussing this early next week. Will fix up a time by the end of this week. Liz bradley will be done with her introduction to dynamics and the eigenvalue, eigenvector tutorial will be done this friday. This will make my life easier! :-)

I'd be very interested in this tutorial. I think I'm basically OK on the prerequisites,
but I wouldn't be annoyed by a review. Perhaps Monday? -- Laura

I'm in too. I guess I should be ok on linear algebra, calculus and linear ODEs, but I don't know what the pole of a complex function is. Jean

I'm in. If we can start with 'pole' thing, that would be wonderful. - Masayoshi

Hi Srideep, please put me in this group. About my background on the subjects you asked; zero!!! Sorry. Rio

Definitely interested in this. - Jacob

I'm in. Paul

Looks cool. -[[Sarah_Cobey|Sarah]]

Me too! [[Rory_Sayres|Rory]]

I'm interested. Don't have any complex analysis background though. [[User:Lfriedl|Lisa]]

Sounds good. I'm in. [[Jie_Ren | Jie]]

== Topology/algebra ==
I (Srideep) will also be happy to talk about topology, introducing the concepts of point-set topology. The language of modern mathematics is enshrined in the concepts of point-set topology. I can also talk about group theory and introduce abstract algebra to those interested. In my opinion, it is the most powerful gateway into abstract thinking. sign here or email me [mailto:srideep.musuvathy@gmail.com srideep]

I'd be very interested in that. Jean

I'd be interested to see what you cover in the topology section. Algebra, however, is for the birds :) Paul

Srideep, can you do an introduction to category theory? Or would you be interested in co-organizing a tutorial with me? - Jacob

I'm very interested. Abby

Sounds like fun (Chris)

Interested. Category theory also would be fun [[User:Giovanni|Giovanni]]

== Eigenvalues - what are they and how to find them? ==
I (Kolbjørn) can put together a brief and elementary introduction to eigenvalues and eigenvectors if anyone have an urge for this. Sign up or e-mail and we'll schedule something. [mailto:kolbjorn@chalmers.se Kolbjørn]

UPDATE 06062008: SLIDES

[http://www.santafe.edu/events/workshops/images/e/e7/Linear_algebra_tutorial.pdf Tutorial slides]

UPDATE! Time: Friday June 6th, 01.00 p.m. - 03.00 p.m. If this collides with other stuff, please yell out! [[CSSS 2008 Santa Fe-Schedule]]

Yes please. [[Kathleen_Sprouffske|Kathleen]]

I am also very interested [[Walter_Zesk|Walt]]

I'm in as well [[ Mark_Rivera|Mark]]

Please - have always been kind of confusing to me. [[Jonathan_Zelner|Jon]]

Let me in - Masayoshi

I'm also interested! [[ Flavia_Feitosa|Flavia]]

I'll be there. -[[Molly_Rorick|Molly]]

I'm in as well. -[[Tanja_Gesell|Tanja]]

Me too! '''Just to remind'''; I think Classical and Evolutionary Game Theory (Josh)will be started at 3 PM. Rio

== How your computer works ==

Nish and Laura can give a joint tutorial on 'how your computer works'. What happens when I type 'www.santafe.edu' in my browser? How does a web server at santafe.edu handle all those incoming requests? What happens when I use a WiFi access point? Basically, we'd be happy to take your questions about how your computer works and do our best to answer them - we're also happy to have other co-tutors.

Let us know if there's interest [mailto:lmfeeney@sics.se Laura], we'd probably schedule later next week, to not conflict with tutorials that focus on maths and other project prerequisites.

I would love this. -[[Sarah_Cobey|Sarah]]

== How your hardware works ==
Along the same lines as the computer tutorial, I've found myself discussing hardware with a number of folks. And why hardware matters from a massive parallelism perspective (which is quite common in the complex research areas I've encountered). If folks are interested, I can give a rough overview of the way hardware works in different types of computers and supercomputers (as much as I understand of it) as well as how to best leverage that knowledge.

Not sure how this differs from the the one above it, but def. interested (Chris)

== Computational Physics for Non-physicists or A small introduction into Applied Physics ==

I've seen that many people are interested in physics. I could give an introduction to "computational" physics - this means physics with a PC. Actually, it is very broad and gives some basics for simulations (interesting for all simulation-folks):

- What is a 'random number generator' and why should I know something about it?

- What are Master-equations?

- The Ising-model / Voter-model

- The Central Limit Theorem or why does it make sense to average over multiple runs of a simulation?

- ...

[[Ruben Kubiak|Ruben]]

I'm very interested [[Nish_Aravamudan|Nish]]

I'm in too. [[Jiang_Wu|Jiang]]

[[Srideep_Musuvathy|srideep]] is in.
Sounds great. [[Molly_Rorick|Molly]]

Looking forward to it. [[Petr Svarc|Petr]]

Interested [[User:Giovanni|Giovanni]]

Check out this book: http://pages.physics.cornell.edu/sethna/StatMech/ [[Petr Svarc|Petr]]

==Information Theory==
An open discussion of Shannon information theory (would like some help in presenting this part clearly) and then some newer results from its application to cellular automata (and potentially other complex systems).

Interesting. I remember something from the master course I took. [[User:Giovanni|Giovanni]] 
I'd love to participate. -[[Sarah_Cobey|Sarah]] 
I'm interested.[[Holger_Keeler|Paul]] 
I'm in. --[[User:Lfriedl|Lisa]]

I'm in. --[[User:meritxell|Meritxell]]

FYI: Tom Carter is going to be talking about Information Theory a bit tomorrow from 2-3pm, not sure of a location yet, but its on the schedule.

==Cellular Automata==
CAs (particularly ECAs) are a very interested model of computation. How do 8 rules (ECA 110, e.g.) emulate a Turing Machine? Why is that interesting? What can we learn about what defines computation given CAs? Maybe we can also discuss some simple computational (Turing) theory.

I'd go to that twice. —[[User:Jreyes|Josh]]

Sounds like fun. [[Christopher Vitale|Chris]]

==A little analytical tool-box: Non-linear dynamics, ODEs, PDEs...==
The [[David_Foster|Brothers]] [[Jacob_Foster|Foster]] would be happy to offer some tutorials on analytical methods. Depending on what Alfred Hubler covers, we can do some fraction of Strogatz (flows on the line & circle, bifurcations, maybe linear systems, index theorem, etc.), as well as offering a basic introduction to solving linear ODEs (no theorems, just techniques) and simple PDEs like the heat equation, with boundary conditions. Ideally this would come after Kolbjørn's eigen-stuff course, so we can just assume familiarity with that.

We've put a tentative time for our tutorial on the schedule: [[CSSS_2008_Santa_Fe-Schedule#Week_Three_-_FINANCE/ECONOMY|June 16 at 3:15pm]]. Let us know if this doesn't work out for some reason and we can try to change it.

These are fun topics! I never get enough of them! -- [[Srideep_Musuvathy|srideep]] 
Sounds great. [[Molly_Rorick|Molly]] 
Interesting -- sure. [[User:Lfriedl|Lisa]] 
Very useful! [[Kathleen_Sprouffske|Kathleen]] 
Need this.... Rio 
I'm in! [[Flavia_Feitosa|Flávia]]
great! [[Riley_Crane]]

Brothers Foster rulez! I'll be there. [[Petr Svarc|Petr]]
Count me in! [[User:Giovanni|Giovanni]]

==Linguistics==
Can someone (I don't know [[Peter_Graff|who]]) perhaps offer a tutorial on basic linguistics stuff? I am particularly interested in generative grammar and coverage of the Chomsky "Three Models" paper, but maybe there are more interesting topics to be discussed these days... -Jacob

I could easily do a Saussure/Pierce tutorial, along with how this has been applied from everything to kinship structure to film theory to table manners, but this is continental structural linguistics, very diff from the chomsky stuff. I think Peter Graff can do the chomsky stuff, though, perhaps we could work on this together (Chris)

Would love both tutorials. Esp. the kinship structure stuff (is this Andre Weil's algebra chapter on kinship, from Levi-Strauss I think?) -Jacob

I'd love to participate. -Tanja

==Fitting models to data==
A few people have asked me for a brief review of fitting models to data, but I'd like to know what methods interest you. I could start with least squares and progress to Bayesian approaches, maximum likelihood, and some more recent developments in methods for exploring space (GAs, particle filters, MCMC) with which I'm familiar. I'm by no means an expert in all these topics, so please add your name below if there's something you'd like to learn about (a particular method or method for a particular context) or teach. I feel like this tutorial would be most appropriate for the third or fourth week. -[[Sarah_Cobey|Sarah]]

I am really interested in this. (Soumya)

cool [[Riley_Crane]]

I am interested in this, especially in various regression approaches and Bayesian inference. [[Jie_Ren | Jie]]

==Semiotics, Sign Systems, and the Mind==

UPDATE: TUTORIAL NOW SCHEDULED MONDAY NIGHT, 4:30-6 - bring dinner with you to coffee shop!

This tutorial will be a general overview of theories of language (Saussure, Pierce, French Structuralism, Lacan) and how they impact philosophy of mind (Freud, Fodor, Minsky, Edelman, ANNs). No previous knowledge of any of this stuff needed!

Probably start off with the first real theory of language and the brain, Freud's topological theory, and then move to how this was absorbed into structuralist linguistics/semiotics in the 1950's (Saussure's theory of signifiers, Jakobsen on axes of discourse, paradigms/syntagms, metaphoric value transfer, and how this was applied to kinship structures, social institutions, etc.) From there we could look at how Jacques Lacan built upon this with his 'mathemic' algebraic notation for discourse analysis. We could then look at how networked theories of mind challenge both the Lacanian model and its American counterparts (Fodor's psychosemantics, for example), particularly in regard to connectionist architectures in artificial neural networks, and how this leads to more distributed notions of linguistic structure. These new paradigms can allow us to move beyond notions of discrete 'signs' existing somewhere in the brain to models based on research in microfeature maps, dynamic network synchronization, spreading activation, and feature vectores. When synthesized with Lacan's insights, and blended with some ideas from object-relations theory and by thinkers like Marvin Minsky and Gerald Edelman, its possible to come up with models that actually reflect the impact of complex systems theories. Likely wayy too much stuff to squeeze in, but certainly enough to get a conversation going, even if we don't get to half of it!

(-Chris)

== Questions at the Intersection of Neuroscience and Complexity ==

This tutorial met Wedenesday AM (June 11). Thanks to everyone who showed up! We'll continue the discussion of these topics as a [[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Something_in_Neuroscience |working group]].

Related to Chris' proposal above, but perhaps on the flip side, I'd be happy to give a tutorial / lead a discussion on issues where questions of complexity intersect with problems in neuroscience. I'll distinguish this topic from the idea above, in that I'll focus a bit more on bottom-up questions rather than purely theory-motivated questions. Neuroscience is a very large field, so I'll talk about some of the things I know, but encourage others to bring their own knowledge and curiosity.

I'll start with a short background on neuroanatomy of humans and other species. Then I'll do a survey of what's sometimes termed "systems neuroscience". This is the branch of neuroscience that asks about behavior roughly on the level of neural circuits -- but which often jumps up and down scales, and overlaps pretty significantly with ideas in "cognitive neuroscience" where the focus is on a lot of the interesting, higher-order behaviors unique to relatively few species. Then I'll go over a couple of papers which I think start on a road to using complex systems. Examples of what I might talk about would be:

* [http://www.ncbi.nlm.nih.gov/pubmed/17428910?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Kiani et al J. Neurophys 2007] '''Does the visual system naturally group objects into heirarchical categories?''' These authors tried to apply some dimensionality reduction techniques to neural data from monkey inferotemporal cortex. The ideas from Dr. Newman's lectures may be very appropriate here.
* [http://www.ncbi.nlm.nih.gov/pubmed/17660812?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Assisi et al. Nature Neuroscience 2007] '''Sparseness in representation of odors'''. The Laurent lab has been combining high-quality experimental methods in the insect olfactory system with computational models (including network models) to look at how the insect system (and more recently the mammalian system) represent odors. The system presents a very interesting contrast to the visual system, in terms of the sparseness of representations at the early levels. There's some elegant circuitry mapped out here. '''BONUS QUESTION!''' I remember one of the questions they investigated earlier was how locusts transition from 'happy grasshopper' mode to 'Biblical swarm' mode. This has something to do with olfaction. This population behavior is probably a very intersting bifurcation; we can dig into what this reflects.
* [http://www.ncbi.nlm.nih.gov/pubmed/18047414?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Machens and Brody, Neural Computation 2008]. [[http://www.molbio.princeton.edu/index.php?option=content&task=view&id=335 Carlos Brody]] does a lot of work on how neural circuits dynamics can allow for short term memory behavior. This includes comparing a perceived sensation to something you experienced a few seconds or minutes ago, and constructing an internal sense of how time elapses. His group uses tools like attractor networks to model this behavior.
* '''Walter Freeman's work'''. Freeman studies the mammalian visual system, but also has a background in talking about how neural circuits encode meaning. This will be an opportunity for me to go back and find some interesting results to discuss. We may also highlight the questions of information theory and oscillatory behavior in neural circuits, which covers researchers like Pascal Fries, John Huguenard, and David McCormick. I'll update this part with a more specific paper when I find a good one.

'''Timing?''' Right now I'll focus on Wednesday morning, June 11. Please let me know below if you're interested. If it's a small group we can meet in the small library next to the main room; this might encourage discussion. And of course, let me know if there's something within this area in which you're more or less interested.

Cheers, [[Rory_Sayres | Rory]]

I'll be there Wednesday AM. Teach me, oh wise Neuroscientist! [[Nish_Aravamudan|Nish]]

Hellsyeah. [[Christopher Vitale|Chris]]

cool [[User:Giovanni|Giovanni]]

Cool tutorial. By the way, who is the tutor? [[Jie_Ren | Jie]]
* I gave the tutorial. Thanks for coming! BTW, if you'd like some follow-up, I'm setting a time to talk about these things (w/o necessarily turning into a project) at the [[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Something_in_Neuroscience |working group]] page. [[User:Sayres|Sayres]] 17:37, 12 June 2008 (MDT)

==Network Economics and Value Theory: From Marx to Complexity==

What is Value? Where does Wealth come from? Does Capital really make money from nowhere, and if so, how? How does complexity studies change our picture of value theory, in economics and beyond?

We'll likely start off with Marx's three levels of value (use, exchange, surplus), move to his theories on production, formulas for capital, commodity fetishism, sticky points of his famous 'labor theory of value,' then on to his analysis of modes of production, and his thesis on the falling rate of profit that was supposed to bring down capitalism (but which obviously didn't). From there we could discuss critiques/updates of this theory via the growth of Keynesianism/Stalinism/Neoliberalism, in order to get to David Harvey's new work on how neoliberal economies largely avoid demand crises by engineering carefully managed accumulation crises whose effects can be easily passed off to poorer nations using multi-national postwar institutions like the IMF/WTO. This leads to examples of how networked models can help us understand today's economic crises (for example, how evolutionary search models can help us understand the ways in which 'overleveraging' economies via 'market derivatives' can help funnel capital to hedge funds in rich countries). From there we could look at critiques of economic theories of value, particularly Deleuze and Guattari's notion of 'desiring-production' as that which links production of commodities to the production of consumers by the social unit of production, namely, the family, and how even this model needs to be rethought in terms of shifts in mass media. Other topics could include theories of network political activism, namely those of Hardt and Negri (Empire/Multitude) and Ernesto Laclau on social dislocations and crisis management via counterhegemonic blocs.

Do you know anything about Debord's interpretation of Marxism in term of spectacle? I read the society of spectacle and the commentaries and would be cool to have a discussion [[User:Giovanni|Giovanni]]

yeah, we can discuss Debord, sure! [[User:Chris|Chris]]

== Topological and Symbolic Dynamical Systems ==

I would like to address the perceived interest among [[Jacob_Foster|few]] of us here in topics relating to the topological dynamics and symbolic dynamics. I can talk a bit about ideas relating to the topological properties of dynamical systems and systems with very little structure to them (i.e., systems whose state spaces are merely a hausdorff space and a dynamic shift which is a continuous function). The symbolic dynamics part will deal with spaces of sequences of symbols and the dynamics being a shift map. I would like to wrap things up with a powerful tool - topological conjugacy - which allows us to define an 'equivalence' between two dynamical systems, one of which might be easier to understand and analyze. Ideally, this discussion will come after my topology tutorial, but I'll spend a few minutes describing formally and intuitively, the terms I use. Alternatively, we can form small discussion groups and chat about this over a cup of tea. [[Srideep_Musuvathy|srideep]]

absolutely interested. [[Christopher Vitale|Chris]]

Interested! [[User:Giovanni|Giovanni]]

== Economics & Finance 101 ==
A 1 hour mini crash-course on the basic principles of Economics and Finance. The aim of this tutorial is -hopefully- to give a heads up for the upcoming Economics/Finance week for people who do not have a background in Economics.
I will introduce 3 simple models of microeconomics, macroeconomics and finance that can give an idea of what economists do. [[Carlos_Yepez|Carlos]]

'''Date and time:''' Friday June 13, 3:00-4:00pm.

'''Note:''' Reply to this page if you are interested in taking this tutorial.
*[[Devin_Drown|Devin]]
*[[Kolbjorn_Tunstrom|Kolbjørn]]
*[[Jacob_Foster|Jacob]]
*[[Flavia_Feitosa|Flávia]]
*[[Holger_Keeler|Paul]]
*[[Kathleen_Sprouffske|Kathleen]]
*[[User:Giovanni|Giovanni]]
*[[User:Lfriedl|Lisa]]
*[[Jiang_Wu|Jiang]]
*Justin

==Theory of computation==
[[Adam_Campbell|Adam Campbell]] will be holding a tutorial on the theoretical side of Computer Science. This will be a high level overview of the mathematical foundation on which computability theory is based and won't be a discussion on practical algorithms or programming methods. I will discuss Turing Machines, the various classes of problems (P, NP, NP-Complete, etc.), decidability, computational complexity, etc. What does it mean when an algorithm is in O(n), O(n^2), etc.? What makes a problem in NP-Complete, and how can you take your problem and prove that it is in NP-Complete or in P? What is the P = NP question all about? These questions and more will be discussed.

The tutorial is scheduled for: [[CSSS_2008_Santa_Fe-Schedule#Week_Three_-_FINANCE/ECONOMY|June 16 at 6:00pm]].

It sounds great! I would very appreaciate if you add some contents about K-SAT and CSP. Thanks. [[Jie_Ren | Jie]]

CSSS 2008 Neuroscience Working Group

2008-06-12T21:01:24Z

Sayres:

This page describes work on a project related to neuroscience issues for the 2008 CSSS.

== What questions do we want to answer? ==

== What is the relevant background? ==

== How shall we answer them? ==

My (Rory's) only criterion: all code will be in MATLAB. No disrespect for other languages: I think Python's great and am learning it, and NetLogo is convenient; but I know for a fact that things will get done much faster if I can code in MATLAB. I'm just that kinda guy. :)

== Logistics: when and where do we meet? ==

First meeting is at '''9pm in the Lower Dorm Common Room, Friday 6/13'''.

== People: Who's interested? ==

Please sign below if you'd like to work on this with me. I'll make an email list with names from these people. (You don't have to give me your address here; I can figure it out.)

[[Rory_Sayres]]

CSSS 2008 Neuroscience Working Group

2008-06-12T21:00:43Z

Sayres: /* People: Who's interested? */

== What questions do we want to answer? ==

== What is the relevant background? ==

== How shall we answer them? ==

My (Rory's) only criterion: all code will be in MATLAB. No disrespect for other languages: I think Python's great and am learning it, and NetLogo is convenient; but I know for a fact that things will get done much faster if I can code in MATLAB. I'm just that kinda guy. :)

== Logistics: when and where do we meet? ==

First meeting is at '''9pm in the Lower Dorm Common Room, Friday 6/13'''.

== People: Who's interested? ==

Please sign below if you'd like to work on this with me. I'll make an email list with names from these people. (You don't have to give me your address here; I can figure it out.)

[[Rory_Sayres]]

2008-06-06T21:02:10Z

Sayres: added neuroscience tutorial

{{CSSS 2008 Santa Fe}}



== The big opensource tutorial ==

=== Open Source research software ===

Update! [[Opensource software tutorial|Tutorial]] scheduled on Monday 9 from 7:00p

Open (no pun intended...) your eyes to the wonderful world of FOSS -- Free and Open Source Software. While the distinction between Free and Open Source is a very interesting one (and highly contentious in the right crowds), for research purposes, we want to use the best tools for the job but some of us suffer from limited income, so I would like to talk about both. At the same time, FOSS is great to use for a non-economic reason: if you find bugs, or design extensions, you can fix them yourself (in OSS, at least) or at least report the problem back to a typically active community. Some potential tools to discuss/explore: R, Octave, Scilab, Gnuplot, perhaps some of the more useful languages in the field like Python and perhaps others I don't know as much about (a quick `apt-cache` on my Ubuntu Hardy install shows RasMol, ClustalW, SeaView, Achilles, complearn, EMBOSS, GENESIS, etc...)

- I would like to give a "Brazilian" contribution. Those who are interested in GIS&Cia could have a look at [http://www.dpi.inpe.br/gilberto/software.html Free and Open Source GIS Source].
[[Flavia_Feitosa|Flavia]]

I would be happy to contribute a little bit about freely available simulation environments like ns-2 (computer networks) and omnet++ (a generic DES) -- Laura

- For Python I can offer a tutorial (see below). Nish, do you have any experience with [http://www.sagemath.org/ Sage]? [[User:Giovanni|Giovanni]]

All great ideas and I would love to have more of a "You know how to use this tool or you know of this tool, you talk about it" style of tutorial :)
Maybe we can do a general OSS tutorial/discussion and then transition to specific sub-topics in separate tutorials (Python, GIS, networks, etc)?
I've not used Sage, before, but I'm happy to take a look before the tutorial. Thanks for the info, Giovanni!

 
I'd like to learn more about open software. [[Holger_Keeler| Paul]]

=== R tutorial ===
Update! [[Opensource software tutorial|Tutorial]] scheduled on Monday 9 from 7:00p

I (''[[Ruben_Kubiak|Ruben]]'') know a little bit about R (basic stuff such as common plots and regression analysis) but would like to enhance my R skills. Does anybody have an interest in a R tutorial, too? Please edit this if there is more interest.

I am fairly familiar with R and could probably run a tutorial... what are you all interested in
learning? - Skyler
*I'd just like to get an understanding of some of it's practical uses. -Devin
*Do you familiar with running social network analysis package in R? I want to learn more about it. [[Jiang_Wu| Jiang]]

Interested folks
#[[Devin_Drown|Devin]]
#[[Mark_Rivera | Mark]]
#[[Jiang_Wu| Jiang]]
#[[Molly_Rorick|Molly]]
#(Soumya)
#[[Riley_Crane]]
#[[Jeremie]]
#[[Tanja_Gesell|Tanja]]

=== Python tutorial ===

Update! [[Opensource software tutorial|Tutorial]] scheduled on Monday 9 from 7:00p

I've (''also [[Ruben_Kubiak|Ruben]]'') interest in a Python tutorial. Please edit this if there is more interest.

I can give a tutorial on python and on scipy/numpy. I can also talk about coding in general, as python is both a languange which is object oriented, imperative and functional (somehow). We can use the [http://docs.python.org/tut/tut.html python tutorial] itself as a reference for the part about the language, and then move to the basic concepts of the duo [http://numpy.org numpy] / [http://scipy.org scipy], which form a powerful tool to manipulate n-dimensional arrays of numbers and also talk about [http://ipython.scipy.org/moin/ ipython] (the enhanced interactive shell) and the [http://matplotlib.sourceforge.net/ pylab] interface, which gives a very nice environment for interactive programming and data analysis. Since pylab has been designed to mimic MATLAB's interface (the major plotting/statistical functions work as expected in both enviroments, which saves you a lot of time if you're used to MATLAB), I can also talk a bit about MATLAB, but being not a big fan of it, it would be better if somebody else stepped in to another tutorial on that.

Leave a mark if interested! [[User:Giovanni|Giovanni]]

I'd be interested in this as well [[User: Mark | Mark]] 

I'm in. —[[User:Jreyes|Josh]]

I'm in. [[Nish_Aravamudan|Nish]]

Yes please. [[Molly_Rorick|Molly]]

Me too. [[Rory_Sayres]] [[User:Sayres|Sayres]] 23:55, 4 June 2008 (MDT)

I'd be interested in this as well [[Tanja_Gesell|Tanja]]

I'm in [[Riley_Crane]]

Another one. [[Petr Svarc|Petr]]

== Neutral models in biology ==

Already met. Big thanks to Molly!

There is an interesting [http://arxiv.org/abs/0710.4911 paper] by Cosma Shalizi of SFI about methodological problems in social sciences research in which he talks about the concept of neutral models in evolution models. I was wondering if any of the bio-people can give a tutorial on this topic as I am pretty interested in understanding the concept. [[User:Giovanni|Giovanni]]

I would be very interested in learning about neutral networks too! - Skyler

== GIS / Spatial Analysis ==

Space Matters!! Geographical information system (GIS) is a computational system (hardware + database engine) that is designed to assemble, store, update, analyze, manipulate, and display geographically referenced information (data identified by their locations).

I'm thinking about introducing some basic GIS concepts and a free GIS software known as [http://www.dpi.inpe.br/~flavia/GIS/ Terraview]. We could also explore some spatial analysis techniques (this is the best part!) using Terraview and [http://www.geoda.uiuc.edu/downloadin.php GeoDa] (also free!).

Please edit here if you are interested or send me an email. [mailto:flafeitosa@gmail.com Flávia]

Update! It has been scheduled on Friday, June 13 from 1:30 p.m. - 2:45 p.m.

I'm in [[Walter_Zesk|Walt]] 
I'd do this. —[[User:Jreyes|Josh]] 
let me know, I'm in, Sonja 
Me too. —[[User:Lfriedl|Lisa]] 
Can not wait for this! Rio 
Me too. [[Kathleen_Sprouffske|Kathleen]] 
Sounds like fun. If people are interested, I can bring some data sets to play around with. Alex

== Statistical Physics for Non-Physicists ==
Problem: Textbooks about this are written for physicists.
Solution: A Physicist (or mathematician) that would be so kind and spend few minutes (or maybe hours) to explain all that stuff to people like me(Petr):-)

[[Ruben_Kubiak|Ruben]]: Do you seek for a general introduction or something specific?

A crash course in Statistical Physics would be awesome. Let us know. — [[User:cyepez|Carlos]]

I am interested too. (Soumya)

Me too. (Jean)

Interested! [[User:Meritxell|Meritxell]]

Interested! [[User:Giovanni|Giovanni]]

Ditto - Skyler

Me too. —[[User:Lfriedl|Lisa]] 

Me three. [[User:RobMills|RobMills]]

I'd be willing to run such a tutorial. However, I would have to consult with some/all of the interested parties to find out what kind of statphys you want to learn about. There are a huge number of possible topics, one could start with basics like ensembles, or perhaps people are interested in master equation and other non-equilibrium techniques, or maybe critical phenomena is what people are interested in. I really do not know. (Orion)

Can you give us who are not physicists an introduction about a kind of special questions that you will think it from the viewpoint of physicists? Like complex network, dynamic, also something else, what is the most important measurement and dynamic process you want to observe? -[[Jiang_Wu|Jiang]]

== Modern Logic and Reasoning ==
Like I mentioned in the 'ice-breaking', I could tell something about application of modern logic into human reasoning. It's a very board topic, and very new. Criticisms are welcome and needed. I would give some basic examples. On top of that, I would also say some development of logic, and how I found it useful in research, which might seem un-related to logic, esp. in social science. I am planning to give a 15 to 20 minutes presentation, UNLESS people want to hear more, in that case, please let me know.
QiQi

I'm interested! [[Kathleen_Sprouffske|Kathleen]] 
Me too! [[kolbjorn|Kolbjørn]] 
Sign me up. — [[User:Jreyes|Josh]] 
I'm interested too! (Flavia) 
I'm in! [[Srideep_Musuvathy|srideep]] 
I'm in too [[User:Giovanni|Giovanni]] 
Count me in - Skyler 
I'd be interested in this as well. [[Tanja_Gesell|Tanja]]
 Sounds great - i'll be there. [[User:RobMills|RobMills]]

Please remind by email or somhow.. and sign me up! [[User:sonotto|Sonja]]

I am in Qi, But where? Rio

Update! Time at June 10th, 03.15 p.m. - 03.35 p.m.
[[CSSS 2008 Santa Fe-Schedule]]

== Introduction to the Design and Analysis of Computer Experiments ==
How do you find "interesting" behavior when your computer model is too slow or the inputs are too many to try every possible combination? Using an Arctic sea ice simulator example, I will show you how modern statistical methods can help you explore your virtual world more efficiently. Check out this brief
[http://www.stat.sfu.ca/~dbingham/NICDS_CompExpt/research.html overview] or a more technical paper about
[http://www.schonlau.net/publication/jogo98.pdf global optimization]. Also see [http://www.gaussianprocess.org/ Gaussian Processes for Machine Learning] for a list of available resources. [[B%C3%A9la_Nagy|Béla]]

== Genomics / Central dogma overview ==
It seems like some of you might be interested in an overview of the central dogma of molecular biology to non-biologists. This could be an 1h tutorial on the major actors of gene expression: nucleus, chromosomes, chromatine, DNA, RNA (tRNA, mRNA), proteins, polymerases, ribosomes, transcription factors, and eventually a quick intro to small, non-coding RNAs as a bonus. Although being a bioinformatician by training, I'm happy to leave the way if a "hard core" biologist wants to do this tutorial (Molly ?). Edit if interested! Jean

I'd be happy to attend a tutorial in 'genomics for idiots' -- Laura

Me too. I am also interested in metagenomics if this is not too much of course. -- Francois

I'd like to go to a 'genomics for idiots' tutorial as well. -- [[Srideep_Musuavthy|srideep]]

Ok, so I'll prepare some slides. How about Monday 9th, 5p - 6p (location TBA) ? -- Jean

== Artificial Intelligence/Machine Learning ==
I (Nish) could introduce some of the basic methods in AI/ML. If there is significant interest in the two fields separately, I could do two tutorials. Would probably focus on the higher level, rather than the nitty-gritty details, as well as applications of the methods to real problems. I'm not necessarily an expert, although have a fair amount of experience in the area, so I would prefer a more interactive session, where questions can be answered by everyone.

Sign me up. — [[User:cyepez|Carlos]] 
I'm also interested. -[[Sarah_Cobey|Sarah]] 
Me too! [[Flavia_Feitosa|Flávia]]

How about "AI/MI for dummies", Nish? I've been wondering about it.... Rio

sounds good [[Riley_Crane]]

== A Crash Course to Classical and Evolutionary Game Theory ==
Game theory is the study of interactive decision making. Classical game theory aims to develop a general theory to describe how rational agents interact strategically. In many cases humans lack the kind of infinite computational power and time assumed by classical game theory. In the early 1970s the biologist John Maynard Smith introduced evolutionary methods to the field, dispensing with the assumption of hyper-rationality while changing many of the concepts central to the field along the way. The result was evolutionary game theory. This new framework has been used to model the behavior of fundamentally non-rational players (such as viruses) as well as humans.

In this tutorial, I'd try to introduce the basic concepts in both of these fields, namely, the definition of a game, payoffs, the Nash equilibirum and evolutionarily stable strategies, the replicator dynamics. I'll briefly mention the three basic classes of two-strategy games represented by the Prisoner's Dilemma, the Snowdrift Game (sometimes called the Hawk-Dove game or Chicken), and the Stag Hunt Game. Depending on particular interests of the group, we could prove the Bishop-Cannings theorem and give a classification of all symmetric two-strategy games; or look at updating methods and spatial chaos; reputation and image scoring; rock-paper-scissors in biological systems; or evolutionary branching and specialization.

If there's something else you'd like to know about EGT, shoot me ([mailto:joshua.reyes@removeme.gmail.com Josh]) an email, and I'll see if I can dig up something I know on your topic. I'm not going to require any fancy mathematical background. If you've seen a 2×2 matrix before, great. Otherwise, it's not a big deal. We won't multiply them or calculate their eigenvalues. They'll just serve as a means for bookkeeping.

Update! Some of us are also thinking about setting up a [[CSSS_2008_Santa_Fe-Projects_%26_Working_Groups#Evolutionary_Game_Theory|working group]] as well.

 Update 2! This has been scheduled on Friday from 3 - 5, location TBD.

*I'll sign up for this. Kolbjørn
*I'm interested too! (Flavia)
*I'll be there too. Kathleen
*I'm in. Jean
*I'm interested as well. Steve
*will be there at 3 [[Walter_Zesk|Walt]]
*I'll be there, Petr
*Good stuff. I could also say a few things about [http://www.iiasa.ac.at/Research/EEP/AdaptiveDynamics.html adaptive dynamics], if there's interest. [[Sarah_Cobey|Sarah]]
*I'll be there. [[Jiang_Wu|Jiang]]
*Count me in (Chris)
*I'm in. Tanja

== Resilience of social-ecological systems ==
The resilience perspective is increasingly used as an approach for understanding the dynamics of social–ecological systems. Essential for the resilience perspective is the recognition that living systems are not in equilibrium but rather in a domain of attraction.
Many dynamic systems, however, have multiple domains of attraction. Moreover, self-organizing processes can create or change the shape and depth of this domain of attraction. Within the resilience perspective, new pathways of sustainable development can be represented by crossing a threshold from a domain of attraction and/or by creating new domains. Resilience is a measure of how much change or disruption is required to transform a system from being maintained by one set of mutually reinforcing processes and structures to a different set of processes and structures.
If you are interested we (Mike and Dirk) can introduce you to some of the insights developed by the [http://www.resalliance.org/1.php resiliance alliance] and the challenges we face in understanding these kind of systems.

I am interested in this too. Richard

Very interested, any idea of when you will do it? [[Walter_Zesk|Walt]]

I'm interested as well. Steve

I'm interested too. - Skyler

I think to contribute from my previous work on SES. Rio

== Introduction to classical control theory ==
I (Srideep) can offer a 'quick' tutorial on control theory/control systems. This is will be a simple introduction to the motivation, basic ideas, issues and jargon in the field. If you are interested, please let me know about your background in linear algebra, complex analysis and calculus. Depending on the background, I might spend more or less time introducing the field.

Ideally, if you know what eigenvalues and eigenvectors of a matrix are, what a pole of a complex function is and how the solution of a linear differential equation looks like, you are ready to jump right into controls. If the words above don't mean much at all, then we can run a quick 'review' of what they mean intuitively.
you can sign up here or send me an email [mailto:srideep.musuvathy@gmail.com srideep]

Update! Lets plan on discussing this early next week. Will fix up a time by the end of this week. Liz bradley will be done with her introduction to dynamics and the eigenvalue, eigenvector tutorial will be done this friday. This will make my life easier! :-)

I'd be very interested in this tutorial. I think I'm basically OK on the prerequisites,
but I wouldn't be annoyed by a review. Perhaps Monday? -- Laura

I'm in too. I guess I should be ok on linear algebra, calculus and linear ODEs, but I don't know what the pole of a complex function is. Jean

I'm in. If we can start with 'pole' thing, that would be wonderful. - Masayoshi

Hi Srideep, please put me in this group. About my background on the subjects you asked; zero!!! Sorry. Rio

Definitely interested in this. - Jacob

I'm in. Paul

Looks cool. -[[Sarah_Cobey|Sarah]]

Me too! [[Rory_Sayres|Rory]]

== Topology/algebra ==
I (Srideep) will also be happy to talk about topology, introducing the concepts of point-set topology. The language of modern mathematics is enshrined in the concepts of point-set topology. I can also talk about group theory and introduce abstract algebra to those interested. In my opinion, it is the most powerful gateway into abstract thinking. sign here or email me [mailto:srideep.musuvathy@gmail.com srideep]

I'd be very interested in that. Jean

I'd be interested to see what you cover in the topology section. Algebra, however, is for the birds :) Paul

Srideep, can you do an introduction to category theory? Or would you be interested in co-organizing a tutorial with me? - Jacob

I'm very interested. Abby

Sounds like fun (Chris)

== Eigenvalues - what are they and how to find them? ==
I (Kolbjørn) can put together a brief and elementary introduction to eigenvalues and eigenvectors if anyone have an urge for this. Sign up or e-mail and we'll schedule something. [mailto:kolbjorn@chalmers.se Kolbjørn]

UPDATE 06062008: SLIDES

[http://www.santafe.edu/events/workshops/images/e/e7/Linear_algebra_tutorial.pdf Tutorial slides]

UPDATE! Time: Friday June 6th, 01.00 p.m. - 03.00 p.m. If this collides with other stuff, please yell out! [[CSSS 2008 Santa Fe-Schedule]]

Yes please. [[Kathleen_Sprouffske|Kathleen]]

I am also very interested [[Walter_Zesk|Walt]]

I'm in as well [[ Mark_Rivera|Mark]]

Please - have always been kind of confusing to me. [[Jonathan_Zelner|Jon]]

Let me in - Masayoshi

I'm also interested! [[ Flavia_Feitosa|Flavia]]

I'll be there. -[[Molly_Rorick|Molly]]

I'm in as well. -[[Tanja_Gesell|Tanja]]

Me too! '''Just to remind'''; I think Classical and Evolutionary Game Theory (Josh)will be started at 3 PM. Rio

== How your computer works ==

Nish and Laura can give a joint tutorial on 'how your computer works'. What happens when I type 'www.santafe.edu' in my browser? How does a web server at santafe.edu handle all those incoming requests? What happens when I use a WiFi access point? Basically, we'd be happy to take your questions about how your computer works and do our best to answer them - we're also happy to have other co-tutors.

Let us know if there's interest [mailto:lmfeeney@sics.se Laura], we'd probably schedule later next week, to not conflict with tutorials that focus on maths and other project prerequisites.

I would love this. -[[Sarah_Cobey|Sarah]]

== How your hardware works ==
Along the same lines as the computer tutorial, I've found myself discussing hardware with a number of folks. And why hardware matters from a massive parallelism perspective (which is quite common in the complex research areas I've encountered). If folks are interested, I can give a rough overview of the way hardware works in different types of computers and supercomputers (as much as I understand of it) as well as how to best leverage that knowledge.

Not sure how this differs from the the one above it, but def. interested (Chris)

== Computational Physics for Non-physicists or A small introduction into Applied Physics ==

I've seen that many people are interested in physics. I could give an introduction to "computational" physics - this means physics with a PC. Actually, it is very broad and gives some basics for simulations (interesting for all simulation-folks):

- What is a 'random number generator' and why should I know something about it?

- What are Master-equations?

- The Ising-model / Voter-model

- The Central Limit Theorem or why does it make sense to average over multiple runs of a simulation?

- ...

[[Ruben Kubiak|Ruben]]

I'm very interested [[Nish_Aravamudan|Nish]]

I'm in too. [[Jiang_Wu|Jiang]]

[[Srideep_Musuvathy|srideep]] is in.
Sounds great. [[Molly_Rorick|Molly]]

Looking forward to it. [[Petr Svarc|Petr]]

==Information Theory==
An open discussion of Shannon information theory (would like some help in presenting this part clearly) and then some newer results from its application to cellular automata (and potentially other complex systems).

Interesting. I remember something from the master course I took. [[User:Giovanni|Giovanni]] 
I'd love to participate. -[[Sarah_Cobey|Sarah]] 
I'm interested.[[Holger_Keeler|Paul]] 
I'm in. --[[User:Lfriedl|Lisa]]

I'm in. --[[User:meritxell|Meritxell]]

FYI: Tom Carter is going to be talking about Information Theory a bit tomorrow from 2-3pm, not sure of a location yet, but its on the schedule.

==Cellular Automata==
CAs (particularly ECAs) are a very interested model of computation. How do 8 rules (ECA 110, e.g.) emulate a Turing Machine? Why is that interesting? What can we learn about what defines computation given CAs? Maybe we can also discuss some simple computational (Turing) theory.

I'd go to that twice. —[[User:Jreyes|Josh]]

==A little analytical tool-box: Non-linear dynamics, ODEs, PDEs...==
The [[David_Foster|Brothers]] [[Jacob_Foster|Foster]] would be happy to offer some tutorials on analytical methods. Depending on what Alfred Hubler covers, we can do some fraction of Strogatz (flows on the line & circle, bifurcations, maybe linear systems, index theorem, etc.), as well as offering a basic introduction to solving linear ODEs (no theorems, just techniques) and simple PDEs like the heat equation, with boundary conditions. Ideally this would come after Kolbjørn's eigen-stuff course, so we can just assume familiarity with that.

We've put a tentative time for our tutorial on the schedule: [[CSSS_2008_Santa_Fe-Schedule#Week_Three_-_FINANCE/ECONOMY|June 16 at 3:15pm]]. Let us know if this doesn't work out for some reason and we can try to change it.

These are fun topics! I never get enough of them! -- [[Srideep_Musuvathy|srideep]] 
Sounds great. [[Molly_Rorick|Molly]] 
Interesting -- sure. [[User:Lfriedl|Lisa]] 
Very useful! [[Kathleen_Sprouffske|Kathleen]] 
Need this.... Rio 
I'm in! [[Flavia_Feitosa|Flávia]]
great! [[Riley_Crane]]

Brothers Foster rulez! I'll be there. [[Petr Svarc|Petr]]

==Linguistics==
Can someone (I don't know [[Peter_Graff|who]]) perhaps offer a tutorial on basic linguistics stuff? I am particularly interested in generative grammar and coverage of the Chomsky "Three Models" paper, but maybe there are more interesting topics to be discussed these days... -Jacob

I could easily do a Saussure/Pierce tutorial, along with how this has been applied from everything to kinship structure to film theory to table manners, but this is continental structural linguistics, very diff from the chomsky stuff. I think Peter Graff can do the chomsky stuff, though, perhaps we could work on this together (Chris)

Would love both tutorials. Esp. the kinship structure stuff (is this Andre Weil's algebra chapter on kinship, from Levi-Strauss I think?) -Jacob

I'd love to participate. -Tanja

==Fitting models to data==
A few people have asked me for a brief review of fitting models to data, but I'd like to know what methods interest you. I could start with least squares and progress to Bayesian approaches, maximum likelihood, and some more recent developments in methods for exploring space (GAs, particle filters, MCMC) with which I'm familiar. I'm by no means an expert in all these topics, so please add your name below if there's something you'd like to learn about (a particular method or method for a particular context) or teach. I feel like this tutorial would be most appropriate for the third or fourth week. -[[Sarah_Cobey|Sarah]]

I am really interested in this. (Soumya)

cool [[Riley_Crane]]

==Networks, Sign Systems, and the Mind==

So, as an outgrowth of the (continental) theory/philosophy working group, I've come up with two ideas for tutorial/discussion sessions on stuff people might be interested in, in which I'd likely throw some materials at the group, then see where discussion takes us. The first one would be on theories of language and the mind. Probably start off with the first real theory of language and the brain, Freud's topological theory, and then move to how this was absorbed into structuralist linguistics/semiotics in the 1950's (Saussure's theory of signifiers, Jakobsen on axes of discourse, paradigms/syntagms, metaphoric value transfer, and how this was applied to kinship structures, social institutions, etc.) From there we could look at how Jacques Lacan built upon this with his 'mathemic' algebraic notation for discourse analysis. We could then look at how networked theories of mind challenge both the Lacanian model and its American counterparts (Fodor's psychosemantics, for example), particularly in regard to connectionist architectures in artificial neural networks, and how this leads to more distributed notions of linguistic structure. These new paradigms can allow us to move beyond notions of discrete 'signs' existing somewhere in the brain to models based on research in microfeature maps, dynamic network synchronization, spreading activation, and feature vectores. When synthesized with Lacan's insights, and blended with some ideas from object-relations theory and by thinkers like Marvin Minsky and Gerald Edelman, its possible to come up with models that actually reflect the impact of complex systems theories. Likely wayy too much stuff to squeeze in, but certainly enough to get a conversation going, even if we don't get to half of it!

Anyone interested? (-Chris)

== Questions at the Intersection of Neuroscience and Complexity ==

Related to Chris' proposal above, but perhaps on the flip side, I'd be happy to give a tutorial / lead a discussion on issues where questions of complexity intersect with problems in neuroscience. I'll distinguish this topic from the idea above, in that I'll focus a bit more on bottom-up questions rather than purely theory-motivated questions. Neuroscience is a very large field, so I'll talk about some of the things I know, but encourage others to bring their own knowledge and curiosity.

I'll start with a short bacgkround on neuroanatomy of humans and other species. Then I'll do a survey of what's sometimes termed "systems neuroscience". This is the branch of neuroscience that asks about behavior roughly on the level of neural circuits -- but which often jumps up and down scales, and overlaps pretty significantly with ideas in "cognitive neuroscience" where the focus is on a lot of the interesting, higher-order behaviors unique to relatively few species. Then I'll go over a couple of papers which I think start on a road to using complex systems. Examples of what I might talk about would be:

* [http://www.ncbi.nlm.nih.gov/pubmed/17428910?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Kiani et al J. Neurophys 2007] '''Does the visual system naturally group objects into heirarchical categories?''' These authors tried to apply some dimensionality reduction techniques to neural data from monkey inferotemporal cortex. The ideas from Dr. Newman's lectures may be very appropriate here.
* [http://www.ncbi.nlm.nih.gov/pubmed/17660812?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Assisi et al. Nature Neuroscience 2007] '''Sparseness in representation of odors'''. The Laurent lab has been combining high-quality experimental methods in the insect olfactory system with computational models (including network models) to look at how the insect system (and more recently the mammalian system) represent odors. The system presents a very interesting contrast to the visual system, in terms of the sparseness of representations at the early levels. There's some elegant circuitry mapped out here. '''BONUS QUESTION!''' I remember one of the questions they investigated earlier was how locusts transition from 'happy grasshopper' mode to 'Biblical swarm' mode. This has something to do with olfaction. This population behavior is probably a very intersting bifurcation; we can dig into what this reflects.
* '''Walter Freeman's work'''. Freeman studies the mammalian visual system, but also has a background in talking about how neural circuits encode meaning. This will be an opportunity for me to go back and find some interesting results to discuss. We may also highlight the questions of information theory and oscillatory behavior in neural circuits, which covers researchers like Pascal Fries, John Huguenard, and David McCormick. I'll update this part with a more specific paper when I find a good one.

'''Timing?''' Right now I'll focus on Wednesday morning, June 11. Please let me know below if you're interested. If it's a small group we can meet in the small library next to the main room; this might encourage discussion. And of course, let me know if there's something within this area in which you're more or less interested.

Cheers, [[Rory_Sayres | Rory]]

==Network Economics and Value Theory==

So, for the third week of CSSS, I'm thinking of maybe doing a session on 'Network Economics and Value Theory' for whoever's interested. Likely start off with Marx's three levels of value (use, exchange, surplus), move to his theories on production, formulas for capital, commodity fetishism, sticky points of his famous 'labor theory of value,' then on to his analysis of modes of production, and his thesis on the falling rate of profit that was supposed to bring down capitalism (but which obviously didn't). From there we could discuss critiques/updates of this theory via the growth of Keynesianism/Stalinism/Neoliberalism, in order to get to David Harvey's new work on how neoliberal economies largely avoid demand crises by engineering carefully managed accumulation crises whose effects can be easily passed off to poorer nations using multi-national postwar institutions like the IMF/WTO. This leads to examples of how networked models can help us understand today's economic crises (for example, how evolutionary search models can help us understand the ways in which 'overleveraging' economies via 'market derivatives' can help funnel capital to hedge funds in rich countries). From there we could look at critiques of economic theories of value, particularly Deleuze and Guattari's notion of 'desiring-production' as that which links production of commodities to the production of consumers by the social unit of production, namely, the family, and how even this model needs to be rethought in terms of shifts in mass media. Other topics could include theories of network political activism, namely those of Hardt and Negri (Empire/Multitude) and Ernesto Laclau on social dislocations and crisis management via counterhegemonic blocs.

Anyone interested in any of this stuff, lemme know! (-Chris)

CSSS 2008 Santa Fe-Projects & Working Groups

2008-06-06T20:41:28Z

Sayres: /* "Speculative" Neuroscience */

CSSS 2008 Santa Fe-Projects & Working Groups

2008-06-06T20:40:01Z

Sayres: /* Financial crisis in Housing Markets */

CSSS 2008 Santa Fe-Projects & Working Groups

2008-06-06T20:39:37Z

Sayres: /* Financial crisis in Housing Markets */

2008-06-05T00:39:11Z

Sayres:

I'm a postdoc at Stanford university, studying representation of the visual field, objects, and object categories. I've also long been interested in the dynamics of complex systems.

[[Image:RorySayres.jpg|thumb|That's me!]]

http://white.stanford.edu/~sayres/

I was lucky to attend a workshop at SFI in 2003, and had a great time. Now looking forward to the main course!

I'm in Calliope 14. You're always welcome to knock.

== Answers to Dan Rockmore's Questions ==

=== 1. What are your main interests? Feel free to include a "pie in the sky" big idea! ===

I've been interested in the behavior of complex systems for quite a
while now, so my main interests run wide and deep. I'm very interested
in modeling the behavior of human interactions and cultures,
particularly in examining differences and similarities in behaviors
across scales. I remember reading accounts of memetics and cultural
evolution by writers such as Dawkins, and am interested to see how far
these ideas have been taken to model behavior.

I'm also interested in understanding models of animal population
changes, but for a somewhat more sober reason. I feel that the first
half of this century will see a lot of challenges to human society in
the form of skyrocketing cost, and decreasing availability, of
resources such as cheap energy sources and clean water. I'm not sure
anyone knows exactly what will happen, but I think an understanding of
the dynamics of complex systems can be one of the most powerful tools
in preparing for what might happen.

Finally, some of my neuroscience research has focused on the problem
of object recognition and object representation: do our brains form
some sort of continuous "shape space" or "object space" to represent
different objects? Working with this question, and with
highly-parallel fMRI data, has introduced me to the ideas of
higher-dimensional space representations, and problems of
dimensionality reduction -- finding a relatively small subset of a
much larger space which can compactly describe a set of things. I hope
to see how the formulations of problems in higher-dimensional spaces
is done in complexity theory, and how people who think about these
things visualize these complex phenomena.

=== 2. What sorts of expertise can you bring to the group? ===

I have a lot of experience with biology and neuroscience, and have
reasonably good knowledge of neural anatomy and functionality. I spend
a large chunk of the day coding in, and otherwise working with,
MATLAB. I am very concerned with producing elegant data
visualizations, as well as reusable code that is well-documented.

=== 3. What do you hope to get out of the CSSS? ===

I hope to get at least two big things out of CSSS:

First, I hope this is an opportunity to meet, work, and have fun with
lots of people from different backgrounds, and get exposed to
radically different ways of thinking about problems. I really like
studying the brain and vision, but having spent so much time in this
field, I think I'm at risk of getting too narrow a perspective. My
last experience at SFI, for a short course, helped me re-expand my
perspective; I hope the Complex Systems school is similarly
reinvigorating.

Second, I hope this course provides an opportunity to flesh out my
understanding of a lot of the details about modeling complex systems,
and also about theories of computation in general. There are a lot of
trains of thought to which I've been exposed, which I think relate to
each other, but the exact details of those relationships were not
clear. For instance, I think there's a mechanistic relationship
between the way statistical mechanics can count "degenerate"
(statistically equivalent) sub-states of a system to produce something
profound like increasing entropy, and the idea that populations move
unidirectionally along a higher-dimensional fitness space. But what
this relationship is, I'm not sure. Perhaps it's really not known, but
I figure if anyone understands these issues, it's the folks at SFI!
<nowiki> :) </nowiki>

=== 4. Do you have any possible projects in mind for the CSSS? (Recall that you will all be working in groups on at least one project with the goal of presenting your progress on the last day and finishing up a paper by sumer's end.) ===

Actually, I don't have anything particular. Given that what I've
written is all pretty broad, and a month is short, I'll need to think
some more to find an appropriate-sized question to tackle. I noticed
that one other participant mentioned what is referred to as the
"credit assignment problem" in neuroscience: given a series of
decisions and delayed feedback on the decisions, how does one decide
which decisions are most likely to lead to reward?

A second idea would be modeling dominance hierarchies in primates.
Given a set of primate agents which engage in social interactions, and
in which status changes are rated by some function of the riskiness of
the animal's behavior, what stable distributions of risky behavior is
the system likely to exhibit? What behavior patterns (prior
probabilities of risk-seeking) select for higher status? (Clearly this
would be a strongly underconstrained problem; perhaps I will learn
enough to pose a particular instance of this question with some
well-founded assumptions to constrain the set of free parameters.)

== Notes from classes ==

[[Sayres logstic M-code|Here]] is a little MATLAB program I wrote to iterate a logistic measure of a population (from the first lecture). [[Sayres logistic plot M-code|Here]] is some code to visualize the iteration space.
Here are some things I played with using these tools:

<code>
% try different values for the control parameter R
figure, plot(logistic(1, 50, 0.2));
hold on, plot(logistic(2.8, 10, 0.5), 'k');
hold on, plot(logistic(3.3, 10, 0.5), 'k');
hold on, plot(logistic(3.3, 10, 0.5), 'r');
hold on, plot(logistic(4.1, 10, 0.5), 'c'); % start seeing chaos

% visualize iteration diagram for different values of R
plotLogistic(2.8, 50, .5);
plotLogistic(3.3, 50, .5);
plotLogistic(3.5, 50, .5);
plotLogistic(3.9, 50, .5);

% is it sensitive to the initial value of X?
% seems like it's on the same curve, but distributed differently...
plotLogistic(3.9, 50, .5001);
</code>

CSSS 2008 Santa Fe-Projects & Working Groups

2008-06-05T00:35:46Z

Sayres: /* if you can't grow '''Collapse''', you haven't explained it */

CSSS 2008 Santa Fe-Projects & Working Groups

2008-06-05T00:35:18Z

Sayres: /* Something in Neuroscience */ must ... match... parentheses!

CSSS 2008 Santa Fe-Projects & Working Groups

2008-06-05T00:34:30Z

Sayres: /* Something in Neuroscience */ ahem...