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CSSS 2007 Santa Fe-Schedule: Difference between revisions

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Van Savage (Allometry)<br/>
Van Savage (Allometry)<br/>
Lauren Ancel-Myers (Networks, Evolution, Epidemiology)<br/>
Lauren Ancel-Myers (Networks, Evolution, Epidemiology)<br/>
'''Projects'''
Paul Dwyer - a study trying to measure diversity of thought expression in the blogosphere and the processes that explain it. </br>
Nathan Menke - Modeling the formation of an atherosclerotic plaque in the coronary arteries <br/>
Spyro Kotsovilis - Modeling the formation of an atherosclerotic plaque in the coronary arteries.</br>
Joe DeRos - I might be interested in looking at the effects of social networks in
solving problems that don't lend themselves to reductionist solutions,
i.e., if hierarchy is efficient for solving a reducible problem, what
is efficient for solving non-reducible problems?<br/>
RafalRaciborski - trying to bridge political economy models of income
redistribution with the optimal taxation literature <br/>
Olaf Bochman - I would like to kick off a project that aims to understand the dynamic structure and evolution of genetic networks <br/>
Kai Spiekerman - a.) One big question which has been on my mind for quite a while:
What is the the use of computational models in the social sciences from
a descriptive / prescriptive / philosophy of science perspective?
Maybe we can work on one aspect of this question...<br/>
b.) Recently, Geoff Brennan and Philip Pettit described the "Economy of
Esteem" (2004) as a major reason why people obey social norms. Roughly
speaking, people want other people to think well of them and adapt their
behavior accordingly. Can we think of agent-based models of esteem
exchange? Are there interesting dynamics of esteem? <br/>
Heather Beil -  I would like to do a project
that is applying complexity to a health intervention or policy problem
so that I can gain a better understanding in how it applies to my field. <br/>
Simon Angus - Something that I've been interested in lately is the ressurgence in the
'group selection' hypothesis -- (David Sloan Wilson, Elliot Sober etc.) --
many of our (read 'economic') agent models not only confound genotypic and
phenotypic selection but also only apply it at the individual level only
..  untangling these, and then introducing group selective mechanisms (or
are these emergent properties of indvidiual selection pressures?) is
something I'd like to explore, either in an abstracted (has been done a
bit lately) or applied (not so much; e.g. micro-founded human strategic
interaction..) model. <br/>
Rhonda Belue - Applying a complex
systems framework to intervention design for chronic relapsing disease in
disenfranchised populations.
I would be interested in using network
analysis to find social or community hubs that could be used to increased the
sustainability of community based interventions. <br/>
Mollie Poynton - I do have remote, IRB-approved access to electronic health records (not
de-identified, but meeting limited data set criteria) for a sample of
3000 patients coded as current or former tobacco users. I think it would
be interesting to use what we learn at CSSS to examine the effect of
different concept representations and/or changes in data quality on
feature selection or induction of models from clinical (EHR) data. It
would also be really interesting to examine preventive services delivery
from a complex systems perspective.<br/>
Chris Atwood - Yes, I suggest a project on studying whether charge transfer within/between
molecules can be chaotic in the presence of a magnetic field and gradient.
There might be regimes where an interaction between the field, gradient, and
charge motion becomes chaotic, with implications for the behavior of
biomolecules. <br/>
Aaron Frank - My hope to construct an evolving international
system out of boundedly rational agents, with the specific goal of
understanding how changes in economic and military technologies and
organization can alter the domestic/internal organization of agents
(constitutional structure and logic), and the balance of power between them
(international relations, trade, war, etc.).  At a minimum, I'm hoping for a
paper model or concept, while my more ambitious goal would be have something
computational. <br/>
Andy Bell - i'd like to look at the underlying requirements for self-governing
agricultural water systems, and how they can be represented
computationally <br/>
Amir Goldberg - I hope to find new ways of modelling social contagion and apply them to
technological diffusion such as in the case of iPod use or the exponential
growth of the blogosphere. <br/>
Monika Piotrowska - I do have a particular interest in
* modeling the cell cycle of normal and cancer cells,
* the investigation of the role of inflammation on the cancer genesis
process and tumor development. <br/>
Will Ludington -  evolutionary transition from unicellular to multicellular.; One last project I'm interested in: how can molecular motors dragging vesicles can set up bulk flow in the confined, low-Reynolds number environment of the cytosol. I am particularly thinking of the scenario in Drosophila and C. elegans oocytes where violent churning is observed inside the cell. How big do the vesicles have to be? How fast do the motors have to move? Do similar processes aid mixing without drastic bulk flow in normal cells? In the very small yeast cell? How does this flow aid mixing? <br/>
Chris Darabos - I'm currently working on analyzing the tolerance to failure
of small boolean networks that share some interesting
properties with gene regulatory networks. Another filed I'd
like to explore and maybe try to model is the regulatory
effect of micro-RNA on genes. <br/>
Johan Nystrom - I've resently found an article where the morphogenesis of slime
mold(like an amoebae) is modeled. The model consists of a cellular
automata/PDE and seems to be able to give some very interesting results, including cell sorting and cell movement, with only a very limited
number of parameters. It would be fun to use this article as a start of
a project, but I'm very open to other suggestions. Anyone interested in
PDEs, CAs or morphology in general are very welcome to send me an email
and I'll be happy to tell you more. <br/>
Gabriele Laspada - I would carry on a project about volatility and stock price random walk at tick-by-tick level. Another interesting issue could be differences and similarities  between "large tick" and "small tick" stocks. <br/>
Mike Wojnowicz - I've collected dynamical systems-inspired data demonstrating different
patterns of mouse-movement trajectories when people report that they
"like" or "dislike" different ethnic groups.  Although this data has
helped me make a particular theoretical claim, it may avail itself to new
kinds of analyses. <br/>
Elizabeth Mullane - I am interested in exploring how it is possible to use computational
modeling to  describe self-organization in human systems. <br/>
George Obernosterer -  it probably needs your help in being well
formulated. The story is the following: Around ten years ago developmental
biologists discovered by chance so called microRNAs (miRNAs). Those are
non protein coding genes, that regulate messenger RNAs by bining to their
3'UTRs (sequences after the STOP codon). Thereby they can shut-down
translation. Now there are algorithms that predict miRNA binding sites
(imperfect pattern matching) but it is known that the RNA folds back and
thereby introduces another level of complexity: secondary structure. Now,
I have started to write an algorithm that predicts "accessible regions" in
RNA molecules. This is important for miRNAs because it was just recently
shown (to be published) that secondary structures around bining sites
impair miRNA function. What I would like to build kind of an accessibility
map of genomes and see how different sequences (exons, introns, UTRs) that
have diverse sequence complexities (compression levels) differ. It would
be cool to then evaluate confirmed miRNA binding sites. <br/>
Another problem would be to reconstruct phylogenetic trees from quartets
(trees of four leaves) starting with an sequence alignment. However, here
I have not done much since a year or so. But, I brought along a lot of
litereature and I have support from Andreas Dress
(http://www.icb.ac.cn/director1.htm) who actually started this project.<br/>


== Cafeteria Meal Schedule ==
== Cafeteria Meal Schedule ==

Revision as of 04:51, 4 June 2007

CSSS Santa Fe 2007

CSSS 2007

Full Schedule

This schedule will be updated frequently. Check this page often to make sure you have the latest version.

All CSSS events are open only to invited participants.

Week One

TIME ACTIVITY

Sunday, June 3
12:00 p.m. - 5:30 p.m. Registration
5:30 p.m. - 8:00 p.m. Welcome reception & dinner

Monday, June 4
9:00 a.m. - 10:15 a.m. Opening Remarks: 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. Nonlinear Dynamics II: Liz Bradley
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. Student introductions & breaking the ice

Tuesday, June 5
9:00 a.m. - 10:15 a.m.
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Nonlinear Dynamics III: Liz Bradley
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Artificial Life I: Steen Rasmussen
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. Nonlinear Dynamics IV: Liz Bradley
7:00 pm - ?? PIZZA PARTY! (@ St. Johns)

Wednesday, June 6
All events at SFI
12:00 p.m. -1:30 p.m. Lunch
1:45 p.m. - 3:00 p.m. Artificial Life II: Steen Rasmussen
3:00 p.m. Tea with SFI community
3:30 p.m. - 4:30 p.m. Social Sciences/Modeling I: Scott Page

Thursday, June 7
9:00 a.m. - 10:15 a.m. Agent Based Modeling I: Stephen Guerin & Owen Densmore
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Nonlinear Dynamics I: Alfred Hubler
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Social Sciences/Modeling II: Scott Page
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. Social Sciences/Modeling III: Scott Page

Friday, June 8
9:00 a.m. - 10:15 a.m. Agent Based Modeling II: Stephen Guerin & Owen Densmore
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Nonlinear Dynamics II: Alfred Hubler

Week Two - NETWORKS/ECOLOGY

TIME ACTIVITY

Monday, June 11
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. Networks II: Mark Newman
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Food Webs I: Jennifer Dunne
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. Food Webs II: Jennifer Dunne

Tuesday, June 12
9:00 a.m. - 10:15 a.m.
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Paleobiology I: Doug Erwin
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Paleobiology II: Doug Erwin
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. Networks III: Mark Newman
8:00-?? CINEMA NIGHT! (@ St. Johns)

Wednesday, June 13
All events at SFI
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Paleobiology III: Doug Erwin
3:00 p.m. Tea with SFI community
3:15 p.m. - 4:30 p.m. Networks IV: Mark Newman

Thursday, June 14
9:00 a.m. - 10:15 a.m. Food Webs I: Neo Martinez
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Food Webs II: Neo Martinez
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Modeling I: Aaron Clauset

Friday, June 15
9:00 a.m. - 10:15 a.m. Computational Complexity I: Cris Moore
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Computational Complexity II: Cris Moore

Week Three - FINANCE/ECONOMY

TIME ACTIVITY

Monday, June 18
All events at SFI
9:00 a.m. - 10:15 a.m. Finance/Economics I: Eric Smith
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Finance/Economics II: Eric Smith
12:00 p.m. - 1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Finance I: Blake LeBaron
3:00 p.m. Tea with SFI community
3:15 p.m. - 4:30 p.m. Computational Complexity III: Cris Moore

Tuesday, June 19
9:00 a.m. - 10:15 a.m. Patterrn Recognition and Markets I: Greg Leibon
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Patterrn Recognition and Markets II: Greg Leibon
12:00 p.m. - 1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Finance II: Blake LeBaron
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. Evolutionary Computing I: Una-May O'Reilly
7:00 - ?? PIZZA PARTY II (@ St. Johns)

Wednesday, June 20
1:30 p.m. - 2:45 p.m. Finance III: Blake LeBaron
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. Patterrn Recognition and Markets III: Greg Leibon

Thursday, June 21
9:00 a.m. - 10:15 a.m. Finance/Economics I: Doyne Farmer
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Finance IV: Blake LeBaron
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. Evolutionary Computing II: Una-May O'Reilly
1:30 p.m. - 2:45 p.m. Evolutionary Computing III: Una-May O'Reilly

Friday, June 22
9:00 a.m. - 10:15 a.m. Finance/Economics II: Doyne Farmer
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Evolution I: David Krakauer

Week Four - BIOLOGY/BBQ!

TIME ACTIVITY

Monday, June 25
9:00 a.m. - 10:15 a.m. Allometry I: Van Savage
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Networks, Evolution, Epidemiology I: Lauren Ancel-Meyers
12:00 p.m. - 1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. OPEN
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. OPEN

Tuesday, June 26
9:00 a.m. - 10:15 a.m. Allometry II: Van Savage
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. Networks, Evolution, Epidemiology II: Lauren Ancel-Meyers
12:00 p.m. - 1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. OPEN
2:45 p.m. - 3:15 p.m. Break
3:15 p.m. - 4:30 p.m. OPEN

Wednesday, June 27
All events at SFI
1:30 p.m. - 2:45 p.m. Networks, Evolution, Epidemiology III: Lauren Ancel-Meyers
3:00 p.m. Tea with SFI community
3:15 p.m. - 4:30 p.m. Allometry III: Van Savage

Thursday, June 28
9:00 a.m. - 10:15 a.m. OPEN
10:15 a.m. - 10:45 a.m. Break
10:45 a.m. - 12:00 p.m. OPEN
12:00 p.m. -1:30 p.m. Lunch
1:30 p.m. - 2:45 p.m. OPEN

Friday, June 29: FINAL POSTER DAY

Lecturers

Week 1:

Liz Bradley (Nonlinear Dynamics)
Stephen Guerin/Owen Densmore (Agent Based Modeling)
Alfred Hubler (Nonlinear Dynamics)
Scott Page (Social Sciences/Modeling)
Steen Rasmussen (Artificial Life)

Week 2:

Mark Newman (Networks)
Cris Moore (Computational Complexity)
Jennifer Dunne (Food Webs)
Neo Martinez (Food Webs)
Doug Erwin (Paleobiology)
Aaron Clauset (Modeling)

Week 3:

Eric Smith (Finance/Economics)
Doyne Farmer (Finance/Economics)
Blake Lebaron (Finance)
Una-May O’Reilly (Evolutionary Computing)
Greg Leibon (Pattern Recognition in Market Data)
Cris Moore (Statistical Mechanics)
David Krakauer (Evolution)

Week 4:

Van Savage (Allometry)
Lauren Ancel-Myers (Networks, Evolution, Epidemiology)

Projects

Paul Dwyer - a study trying to measure diversity of thought expression in the blogosphere and the processes that explain it.
Nathan Menke - Modeling the formation of an atherosclerotic plaque in the coronary arteries
Spyro Kotsovilis - Modeling the formation of an atherosclerotic plaque in the coronary arteries.
Joe DeRos - I might be interested in looking at the effects of social networks in solving problems that don't lend themselves to reductionist solutions, i.e., if hierarchy is efficient for solving a reducible problem, what is efficient for solving non-reducible problems?
RafalRaciborski - trying to bridge political economy models of income redistribution with the optimal taxation literature
Olaf Bochman - I would like to kick off a project that aims to understand the dynamic structure and evolution of genetic networks
Kai Spiekerman - a.) One big question which has been on my mind for quite a while: What is the the use of computational models in the social sciences from a descriptive / prescriptive / philosophy of science perspective? Maybe we can work on one aspect of this question...

b.) Recently, Geoff Brennan and Philip Pettit described the "Economy of Esteem" (2004) as a major reason why people obey social norms. Roughly speaking, people want other people to think well of them and adapt their behavior accordingly. Can we think of agent-based models of esteem exchange? Are there interesting dynamics of esteem?

Heather Beil - I would like to do a project that is applying complexity to a health intervention or policy problem so that I can gain a better understanding in how it applies to my field.

Simon Angus - Something that I've been interested in lately is the ressurgence in the 'group selection' hypothesis -- (David Sloan Wilson, Elliot Sober etc.) -- many of our (read 'economic') agent models not only confound genotypic and phenotypic selection but also only apply it at the individual level only .. untangling these, and then introducing group selective mechanisms (or are these emergent properties of indvidiual selection pressures?) is something I'd like to explore, either in an abstracted (has been done a bit lately) or applied (not so much; e.g. micro-founded human strategic interaction..) model.

Rhonda Belue - Applying a complex systems framework to intervention design for chronic relapsing disease in disenfranchised populations. I would be interested in using network analysis to find social or community hubs that could be used to increased the sustainability of community based interventions.

Mollie Poynton - I do have remote, IRB-approved access to electronic health records (not de-identified, but meeting limited data set criteria) for a sample of 3000 patients coded as current or former tobacco users. I think it would be interesting to use what we learn at CSSS to examine the effect of different concept representations and/or changes in data quality on feature selection or induction of models from clinical (EHR) data. It would also be really interesting to examine preventive services delivery from a complex systems perspective.

Chris Atwood - Yes, I suggest a project on studying whether charge transfer within/between molecules can be chaotic in the presence of a magnetic field and gradient. There might be regimes where an interaction between the field, gradient, and charge motion becomes chaotic, with implications for the behavior of biomolecules.

Aaron Frank - My hope to construct an evolving international system out of boundedly rational agents, with the specific goal of understanding how changes in economic and military technologies and organization can alter the domestic/internal organization of agents (constitutional structure and logic), and the balance of power between them (international relations, trade, war, etc.). At a minimum, I'm hoping for a paper model or concept, while my more ambitious goal would be have something computational.

Andy Bell - i'd like to look at the underlying requirements for self-governing agricultural water systems, and how they can be represented computationally

Amir Goldberg - I hope to find new ways of modelling social contagion and apply them to technological diffusion such as in the case of iPod use or the exponential growth of the blogosphere.

Monika Piotrowska - I do have a particular interest in

  • modeling the cell cycle of normal and cancer cells,
  • the investigation of the role of inflammation on the cancer genesis

process and tumor development.

Will Ludington - evolutionary transition from unicellular to multicellular.; One last project I'm interested in: how can molecular motors dragging vesicles can set up bulk flow in the confined, low-Reynolds number environment of the cytosol. I am particularly thinking of the scenario in Drosophila and C. elegans oocytes where violent churning is observed inside the cell. How big do the vesicles have to be? How fast do the motors have to move? Do similar processes aid mixing without drastic bulk flow in normal cells? In the very small yeast cell? How does this flow aid mixing?

Chris Darabos - I'm currently working on analyzing the tolerance to failure of small boolean networks that share some interesting properties with gene regulatory networks. Another filed I'd like to explore and maybe try to model is the regulatory effect of micro-RNA on genes.

Johan Nystrom - I've resently found an article where the morphogenesis of slime mold(like an amoebae) is modeled. The model consists of a cellular automata/PDE and seems to be able to give some very interesting results, including cell sorting and cell movement, with only a very limited number of parameters. It would be fun to use this article as a start of a project, but I'm very open to other suggestions. Anyone interested in PDEs, CAs or morphology in general are very welcome to send me an email and I'll be happy to tell you more.

Gabriele Laspada - I would carry on a project about volatility and stock price random walk at tick-by-tick level. Another interesting issue could be differences and similarities between "large tick" and "small tick" stocks.

Mike Wojnowicz - I've collected dynamical systems-inspired data demonstrating different patterns of mouse-movement trajectories when people report that they "like" or "dislike" different ethnic groups. Although this data has helped me make a particular theoretical claim, it may avail itself to new kinds of analyses.

Elizabeth Mullane - I am interested in exploring how it is possible to use computational modeling to describe self-organization in human systems.

George Obernosterer - it probably needs your help in being well formulated. The story is the following: Around ten years ago developmental biologists discovered by chance so called microRNAs (miRNAs). Those are non protein coding genes, that regulate messenger RNAs by bining to their 3'UTRs (sequences after the STOP codon). Thereby they can shut-down translation. Now there are algorithms that predict miRNA binding sites (imperfect pattern matching) but it is known that the RNA folds back and thereby introduces another level of complexity: secondary structure. Now, I have started to write an algorithm that predicts "accessible regions" in RNA molecules. This is important for miRNAs because it was just recently shown (to be published) that secondary structures around bining sites impair miRNA function. What I would like to build kind of an accessibility map of genomes and see how different sequences (exons, introns, UTRs) that have diverse sequence complexities (compression levels) differ. It would be cool to then evaluate confirmed miRNA binding sites.

Another problem would be to reconstruct phylogenetic trees from quartets (trees of four leaves) starting with an sequence alignment. However, here I have not done much since a year or so. But, I brought along a lot of litereature and I have support from Andreas Dress (http://www.icb.ac.cn/director1.htm) who actually started this project.

Cafeteria Meal Schedule

Breakfast: Monday-Saturday 7:30am - 9:30am
Lunch: Monday-Saturday 11:30am - 1:30pm
Dinner: Monday-Sunday 5:00 pm - 6:30pm
Brunch: Sunday 10:30am - 1:30pm

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