Learn complex systems perspectives & methods by doing hands-on
research.
. Let me know when you
want to present. We will have 1–5 presentation per class (will try to
finish before the spring break).
Guideline for the presentation (you don't need to follow it):
The progress report will be a draft of the final paper, with
preliminary results. This is just a safeguard and I am happy to discuss
about the project anytime.
A full research paper (~10 pages) with all the details.
Prepare 10 minute presentation about your work.
You need to submit a short review of the papers by the midnight before
the class (e.g. by Monday night for the Tuesday's readings).
The review for each paper should contain
Assigned moderators will make a brief (~ 5 minutes) presentation about
the premises and the results of the paper. However, it is also possible
to have a extended presentation if you want. The format is not
constrained. Some of the important elements in the presentation are:
The principles of academic honesty and ethics will be enforced. Any
cases of academic misconduct (cheating, fabrication, plagiarism, etc)
will be thoroughly investigated and immediately reported to the
School and the Dean of Students.
You should actively discuss with others, but you should write your
own report and you should not read others' review. You should credit
all the sources (discussion with other students, using some
softwares, etc).
| Date | Readings | Presenter |
| 1/8 | Introduction and Misc. | YY |
| Schooling Flocks and Crowds |
| 1/10 |
Required:
Notable people and groups:
Further readings:
- Boids
- J. Toner and Y. Tu, Flocks, herds,
and schools: A quantitative theory of flocking, PRE 58,
4828 (1998).
- M. Nagy et al., Hierarchical
group dynamics in pigeon flocks, Nature 464, 890 (2010).
- J. Buhl et al., From
disorder to order in marching locusts, Science 312, 1402
(2006).
- Wikipedia:
Collective animal behavior
- M. Ballerini et al., Interaction
ruling animal collective behavior depends on topological
rather than metric distance: Evidence from a field study,
PNAS 105, 1232 (2008).
- H. Hildenbrandt et al., Self-organized
aerial displays of thousands of starlings: a model,
Behavioral Ecology 21, 1349 (2010).
- C.K. Hemelrijk and H. Hildenbrandt, Some
Causes of the Variable Shape of Flocks of Birds
- Y. Katz et al., Inferring
the structure and dynamics of interactions in schooling
fish, PNAS 108, 18720 (2011).
- W. Bialek et al., Statistical
mechanics for natural flocks of birds, PNAS 109, 4786
(2012).
- D.H. Kelley et al., Emergent
dynamics of laboratory insect swarms, Scientific Reports
3, 1073 (2013).
- Wired:
You May Have Been Born to Flock
- A. Berdahl et al., Emergent
Sensing of Complex Environments by Mobile Animal Groups,
Science 339, 574 (2013).
Other resources:
|
Alex |
| Traffic and Panic |
| 1/15 |
Required reading:
Notable people, groups, and collections:
Further readings:
- D. Helbing et al., The Dynamics of
Crowd Disasters: An Empirical Study, PRE 75, 046109
(2007); Science:
Modeling Mecca's crowds; Nature:
Crowd researchers make pilgrimage safer
- R. Escobar and A. De La Rosa, Architectural
design for the survival optimization of panicking fleeing
victims, Advances in Artificial Life 2801, 97 (2003).
- M. Burd et al., Nest
architecture and traffic flow: large potential effects from
small structural features, Ecological Entomology 35, 464
(2010); N. Shiwakoti et al., Animal
dynamics based approach for modeling pedestrian crowd egress
under panic conditions, Procedia - Social and Behavioral
Sciences 17, 438 (2011); ABC
catalyst: Panic Dynamic (2008).
- D. Helbing, Traffic
and related self-driven many-particle systems, RMP 73,
1067 (2001).
- D. Helbing et al., Modelling
the evolution of human trail systems, Nature 388, 47
(1997).
- D.R. Parisi et al., Financial
price dynamics and pedestrian counterflows: A comparison of
statistical stylized facts, PRE 87, 012804 (2013).
|
Paul |
| Collective Behavior and Social Segregation |
| 1/17 |
Required readings:
Further readings:
- CR Shalizi, The
Schelling Model, Notebooks
- W.A.V. Clark, Residential
Preferences and Neighborhood Racial Segregation: A Test of
the Schelling Segregation Model, Demography 28, 1
(1991).
- D. Vinkovic and A. Kirman, A
physical analogue of the Schelling model, PNAS 103, 19261
(2006).
- D. Stauffer and S. Solomon, Ising, Schelling
and Self-Organising Segregation, EPJB 57, 473
(2007).
- W.A.V. Clark and M. Fossett, Understanding
the social context of the Schelling segregation model,
PNAS 105, 4109 (2008).
- M. Lim et al., Global
Pattern Formation and Ethnic/Cultural Violence, Science
317, 1540 (2007).
- L.C. Freeman, Segregation
in social networks, Sociological Methods & Research
6, 411 (1978).
- G. Fagiolo et al., Segregation
in networks, Journal of Economic Behavior &
Organization 64, 316 (2007).
- A.D. Henry et al., Emergence
of segregation in evolving social networks, PNAS 108,
8605 (2011).
- Y. Xie and X. Zhou, Modeling
individual-level heterogeneity in racial residential
segregation, PNAS 109, 11646 (2012).
Other resources:
|
Jordan |
| Emergence of Network Communities |
| 1/22 |
Required readings:
Further readings:
- J. Davidsen et al., Emergence
of a Small World from Local Interactions: Modeling
Acquaintance Networks, PRL 88, 128701 (2002).
- K. Klemm and V.M. Equíluz, Highly
clustered scale-free networks, PRE 65, 036123
(2002).
- M. Marsili et al., The rise
and fall of a networked society: A formal model, PNAS
101, 1439 (2004).
- M.C. González et al., System
of Mobile Agents to Model Social Networks, PRL 96, 088702
(2006).
- N.F. Johnson et al., Human
group formation in online guilds and offline gangs driven by
a common team dynamic, PRE 79, 066117 (2009).
- A.D. Henry et al., Emergence
of segregation in evolving social networks, PNAS 108,
8605 (2011).
- J.P. Bagrow and D. Brockmann, Natural emergence of
clusters and bursts in network evolution, arXiv:1209.3307
[physics.soc-ph] (2012)
- J.-J.E. Slotine and W. Lohmiller, Modularity,
evolution, and the binding problem: a view from stability
theory, Neural Networks 14, 137 (2001).
- E.A. Variano et al., Networks,
Dynamics, and Modularity, PRL 92, 188701 (2004).
- N. Kashtan and U. Alon, Spontaneous
evolution of modularity and network motifs, PNAS 102,
13773 (2005).
- J. Sun and M.W. Deem, Spontaneous
Emergence of Modularity in a Model of Evolving
Individuals, PRL 99, 228107 (2007).
- G.P. Wagner et al., The
road to modularity, Nature Reviews Genetics 8, 921
(2007).
- A. Kreimer et al., The
evolution of modularity in bacterial metabolic networks,
PNAS 105, 6976 (2008).
- D.M. Lorenz et al., The Emergence of
Modularity in Biological Systems, Physics of Life Reviews
8, 129 (2011).
- J. Clune et al., The evolutionary
origins of modularity, arXiv:1207.2743 [q-bio.PE]
|
Jaimie |
| Threshold Model and Information Diffusion |
| 1/24 |
Required readings:
Further readings:
|
Karissa |
| Social Contagion and Virality |
| 1/29 |
Required readings:
Further readings:
|
Onur |
| Economic Complexity |
| 1/31 |
Required readings:
Further readings:
Other resources:
|
Nathaniel |
| Networks of Genes, Proteins, Diseases, and Drugs |
| 2/5 |
Required readings:
Further readings:
- A.-L. Barabási et al., Network
medicine: a network-based approach to human disease,
Nature Reviews Genetics 12, 56 (2011).
- A.-L. Barabási et al., Network
Medicine — From Obesity to the “Diseasome”, NEJM 357, 404
(2007).
- D.-S. Lee et al., The
implications of human metabolic network topology for disease
comorbidity, PNAS 105, 9880 (2008).
- M. Vidal et al., Interactome
Networks and Human Disease, Cell 144, 986 (2011).
- C.A. Hidalgo et al., A
Dynamic Network Approach for the Study of Human
Phenotypes, PLOS Comp. Biol 5, e1000353 (2009).
- P. Padivojac et al., An
integrated approach to inferring gene–disease associations in
humans, Proteins 72, 1030 (2008).
- J. Park et al., The
impact of cellular networks on disease comorbidity,
Molecular Systems Biology 5, 262 (2009).
- N. Gulbahce et al., Viral
Perturbations of Host Networks Reflect Disease Etiology,
PLOS Comp. Biol. 8, e1002531 (2012).
- O. Rozenblatt-Rosen et al., Interpreting
cancer genomes using systematic host network perturbations by
tumour virus proteins, Nature 487, 491 (2012).
- H. Yu et al., High-Quality
Binary Protein Interaction Map of the Yeast Interactome
Network, Science 322, 104 (2008).
- Arabidopsis Interactome Mapping Consortium, Evidence
for Network Evolution in an Arabidopsis Interactome Map,
Science 333, 601 (2011).
|
Abhik |
| Evolution: Cost Optimization in Brain |
| 2/7 |
Required readings:
Further readings:
- H.B. Barlow, The
Size of Ommatidia in Apposition Eyes, J. Exp. Biol. 29,
667 (1952).
- C. Cherniak, Neural
component placement, Trends in Neurosciences 18, 522
(1995).
- C. Cherniak et al., Large-scale
optimization of neuron arbors, PRE 59, 6001 (1999).
- D.B. Chklovskii et al., Wiring
Optimization in Cortical Circuits, Neuron 34, 341
(2002).
- R. Ferrer i Cancho and R.V. Solé, Optimization
in Complex Networks, Statistical Mechanics of Complex
Networks 625, 114 (2003).
- V.A. Klyachko and C.F. Stevens, Connectivity
optimization and the positioning of cortical areas, PNAS
100, 7937 (2003).
- C. Cherniak et al., Global
optimization of cerebral cortex layout, PNAS 101, 1081
(2004).
- Y.-Y. Ahn et al., Wiring
Cost in the Organization of a Biological Neuronal
Network, Physica A 367, 531 (2006).
- D.S. Bassett et al., Efficient
Physical Embedding of Topologically Complex Information
Processing Networks in Brains and Computer Circuits, PLOS
Comp. Biol. 6, e1000748 (2010).
|
Andrea |
| Evolution of Cooperation |
| 2/12 |
Required readings:
Recommended:
Further readings:
Other resources:
|
Ian
Proposal: Scott |
| 1/f noise and Music |
| 2/14 |
Required readings:
Further readings:
- R.F. Voss, Evolution
of long-range fractal correlations and 1/f noise in DNA base
sequences, PRL 68, 3805 (1992).
- D.J. Levitin et al., Musical
rhythm spectra from Bach to Joplin obey a 1/f power law,
PNAS 109, 3716 (2012).
- M. Gardner, White
and brown music, fractal curves and one-over-f
fluctuations, Sci. Am. (1978)
- K.J. Hsü and A.J. Hsü, Fractal
geometry of music, PNAS 87, 938 (1990).
- K.J. Hsü and A. Hsü, Self-similarity
of the "1/f noise" called music, PNAS 88, 3507
(1991).
- M. Schroeder, Is
there such a thing as fractal music?, Nature 325, 765
(2002).
- Scholarpedia: 1/f noise
- Wikipedia: Colors of
noise
|
Damion |
| Fractal |
| 2/19 |
Required readings:
Further readings:
- D. Avnir et al., Is
the geometry of nature fractal?, Science 279, 39
(1998).
- R.P. Taylor et al., Fractal
analysis of Pollock's drip paintings, Nature 399, 422
(1999); K. Jones-Smith and H. Mathur, Fractal
Analysis: Revisiting Pollock's drip paintings, Nature
444, E9 (2006).
- K. Jones-Smith et al., Drip
paintings and fractal analysis, PRE 79, 046111
(2009).
- Wikipedia: Minkowski–Bouligand
dimension (Box-counting dimension)
- Wikipedia: Hausdorff
dimension
- Wikipedia: Mandelbrot
set
- J. Leskovec et al., Realistic,
Mathematically Tractable Graph Generation and Evolution,
Using Kronecker Multiplication, PKDD'05
- J. Leskovec and C. Faloutsos, Scalable
modeling of real graphs using Kronecker
multiplication, ICML'07
- J. Leskovec et al., Kronecker
Graphs: An Approach to Modeling Networks, The Journal of
Machine Learning Research 11, 985 (2010).
- G. Palla et al., Multifractal
network generator, PNAS 107, 7640 (2009).
- G. Palla et al., Rotated
multifractal network generator, J. Stat. Mech. 2011,
P02003
- C. Song et al., Origins
of fractality in the growth of complex networks, Nature
Physics 2, 275 (2006).
- K.-I. Goh et al., Skeleton
and Fractal Scaling in Complex Networks, PRL 96, 018701
(2006).
- H.D. Rozenfeld et al., Small world-Fractal
Transition in Complex Networks: Renormalization Group
Approach, PRL 104, 025701 (2010).
- L.K. Gallos et al., A small
world of weak ties provides optimal global integration of
self-similar modules in functional brain networks, PNAS
109, 2825 (2012).
- D.S. Bassett et al., Efficient
Physical Embedding of Topologically Complex Information
Processing Networks in Brains and Computer Circuits, PLOS
Comp. Biol. 6, e1000748 (2010).
Other resources:
|
Rick |
| 2/21: Project proposal due |
| Self-organized criticality |
| 2/21 |
Required readings:
Further readings:
- D.L. Turcotte, Self-organized
criticality, Reports on Progress in Physics 62, 1377
(1999).
- J.M. Beggs and D. Plenz, Neuronal
Avalanches in Neocortical Circuits, J. Neurosci 23, 11167
(2003).
- I. Shmulevich et al., Eukaryotic
cells are dynamically ordered or critical but not
chaotic, PNAS 102, 13439 (2005).
- M. Nykter et al., Gene
expression dynamics in the macrophage exhibit
criticality, PNAS 105, 1897 (2008).
- E. Romanelli and M.L. Tushman, Organizational
transformation as punctuated equilibrium: an empirical
test, Acad. Manage. J. 37, 1141 (1994).
- J. Pu et al., Developing
neuronal networks: Self-organized criticality predicts the
future, Sci. Rep. 3, 1081 (2013).
Other resources:
|
Alex G |
| Power-law |
| 2/26 |
Required readings:
Further readings:
- C.R. Shalizi, Power
Law Distributions, 1/f Noise, Long-Memory Time Series,
Notebooks
- A. Clauset et al., Power-law distributions
in empirical data, SIAM Review 51, 661 (2009).
- M. Mitzenmacher, A
brief history of generative models for power law and
lognormal distributions
- M.V. Simkin and V.P. Roychowdhury, Re-inventing
Willis, Physics Reports 502, 1 (2011).
- L.A. Adamic, Zipf,
Power-laws, and Pareto - a ranking tutorial
- M.P.H. Stumpf and M. Porter, Critical
Truths About Power Laws, Science 335, 665 (2012).
Other resources:
|
Paul, YY |
| Common Patterns of Nature |
| 2/28 |
Required reading:
Further readings:
|
Scott
Proposal: Onur, Paul |
| Allometric Scaling |
| 3/5 |
Required readings:
Further readings:
- G.B. West et al., A
general model for the structure and allometry of plant
vascular systems, Nature 400, 664 (1999).
- P.S. Dodds et al., Re-examination
of the “3/4-law” of Metabolism, J. Theor. Biol. 209, 9
(2001).
- P.B. Reich et al., Universal
scaling of respiratory metabolism, size and nitrogen in
plants, Nature 439, 457 (2006).
- B. Mauroy et al., An
optimal bronchial tree may be dangerous, Nature 427, 633
(2003).
- F. Bokma, Evidence
against universal metabolic allometry, Functional Ecology
18, 184 (2004).
- A. Giometto et al., Scaling
body size fluctuations, PNAS (early edition).
- R.S. Balaban, Allometry
of brain metabolism, PNAS 110, 3216 (2013).
Other resources:
|
Qing
Proposal: Abhik, Jordan, AlexG |
| Proposal presentations |
| 3/7 | Proposal: Ian, Jaimie, Karissa, Damion, Andrea & Rick, Qing, Nathaniel | |
| 3/10-17: Spring break |
| Cities |
| 3/19 |
Required readings:
Further readings:
- M. Batty, The
cal
Size, Scale, and Shape of Cities, Science 319, 769
(2008).
- L. Bettencourt and G. West, A
unified theory of urban living, Nature 467, 912 (2010).
- C.R. Shalizi, Scaling and Hierarchy
in Urban Economies, arXiv:1102.4101 [stat.AP]
- L.M.A. Bettencourt, The
Origins of Scaling in Cities, SFI Working papers
- E. Arcaute et al., City boundaries and the
universality of scaling laws, arXiv:1301.1674
[physics.soc-ph]
- S.G. Ortman et al., Urban
Scaling in Prehispanic Central Mexico, SFI Working
paper
- M.T. Gastner and M.E.J. Newman, Optimal design
of spatial distribution networks, PRE 74, 016117
(2006).
- J. Um et al., Scaling
laws between population and facility densities, PNAS 106,
14236 (2009).
- W. Pan et al., Urban characteristics
attributable to density-driven tie formation,
arXiv:1210.6070v3
- H.A. Makse et al., Modelling
urban growth patterns, Nature 377, 608 (2002).
- L.M.A. Bettencourt et al., Urban
Scaling and Its Deviations: Revealing the Structure of
Wealth, Innovation and Crime across Cities, PLOS ONE 5,
e13541 (2010).
- J. Lobo et al., Urban
Scaling and the Production Function for Cities, PLOS ONE
8, e58407 (2013).
- A.F.J. van Raan, Universities
Scale Like Cities, PLOS ONE 8, e59384 (2013).
Other resources:
|
Scott
Proposal: Alex J |
| Boolean Networks |
| 3/21 |
Required readings:
Further readings:
- S.A. Kauffman, Metabolic
stability and epigenesis in randomly constructed genetic
nets, J. Theor. Biol 22, 437 (1969).
- S. Kauffman, Homeostasis
and Differentiation in Random Genetic Control Networks,
Nature 224, 177 (1969).
- S. Kauffman, Towards
a general theory of adaptive walks on rugged landscapes,
J. Theor. Biol. 128, 11 (1987).
- S. Kauffman et al., Random
Boolean network models and the yeast transcriptional
network, PNAS 100, 14796 (2003).
- G. von Dassow and G.M. Odell, Design
and constraints of the Drosophila segment polarity module:
Robust spatial patterning emerges from intertwined cell state
switches, Journal of Experimental Zoology 294, 179
(2002).
- T. Rohlf and S. Bornholdt, Morphogenesis by
coupled regulatory networks, arXiv:q-bio/0401024
[q-bio.MN]
- M. Chaves et al., Robustness
and fragility of Boolean models for genetic regulatory
networks, J. Theor. Biol, 235, 431 (2005).
- S. Li et al., Predicting
Essential Components of Signal Transduction Networks: A
Dynamic Model of Guard Cell Abscisic Acid Signaling, PLOS
Biology 4, e312 (2006).
- M. Chaves et al., Methods of
robustness analysis for Boolean models of gene control
networks, arXiv:q-bio/0605004 (2006).
- W. Ma et al., Robustness
and modular design of the Drosophila segment polarity
network, Molecular Systems Biology 2, 70 (2006).
- M.I. Davidich and S. Bornholdt, Boolean
Network Model Predicts Cell Cycle Sequence of Fission
Yeast, PLOS ONE 3, e1672 (2008).
- S. Bornholdt, Boolean
network models of cellular regulation: prospects and
limitations,
Other resources:
|
YY |
| Robustness of Regulatory Networks |
| 3/26 |
Required readings:
Further readings:
- E. Meir et al., Robustness,
Flexibility, and the Role of Lateral Inhibition in the
Neurogenic Network, Current Biology 12, 778 (2002).
- M. Aldana and P. Cluzel, A
natural class of robust networks, PNAS 100, 8710
(2003).
- J. Stelling et al., Robustness
of cellular functions, Cell 118, 675 (2004).
- S. Kauffman et al., Genetic
networks with canalyzing Boolean rules are always stable,
PNAS 101, 17102 (2004).
- S. Ciliberti et al., Robustness
Can Evolve Gradually in Complex Regulatory Gene Networks with
Varying Topology, PLOS Comp. Biol. 3, 15 (2007).
- M. Aldana et al., Robustness
and evolvability in genetic regulatory networks, J.
Theor. Biol 245, 433 (2007).
- E.H. Davidson, Emerging
properties of animal gene regulatory networks, Nature
468, 911 (2010).
- M. Marques-Pita, L.M. Rocha, Canalization and
control in automata networks: body segmentation in Drosophila
melanogaster, PLOS ONE (2013).
People
|
Alexander |
| 3/28: Project progress report |
| Control |
| 3/28 |
Required readings:
Further readings:
|
Alex G |
| Homophily and Influence |
| 4/2 |
Required readings:
Further readings:
|
Jordan |
| Laws of Mobility |
| 4/4 |
Required readings:
Further readings:
- G.M. Viswanathan et al., Lévy
flight search patterns of wandering albatrosses, Nature
381, 413 (1996).
- G.M. Viswanathan et al., Optimizing
the success of random searches, Nature 401, 911
(1999).
- A.M. Edwards et al., Revisiting
Lévy flight search patterns of wandering albatrosses,
bumblebees and deer, Nature 449, 1044 (2007).
- D.W. Sims et al, Scaling
laws of marine predator search behaviour, Nature 451,
1098 (2008).
- L. Hufnagel et al., Forecast and
control of epidemics in a globalized world, PNAS 101,
15124 (2004).
- V. Colizza et al., The role
of the airline transportation network in the prediction and
predictability of global epidemics, PNAS 103, 2015
(2006).
- D. Balcan et al., Multiscale
mobility networks and the spatial spreading of infectious
diseases, PNAS 106, 21484 (2009).
- P. Wang et al., Understanding
the Spreading Patterns of Mobile Phone Viruses, Science
324, 1071 (2009).
- C. Song et al., Limits
of Predictability in Human Mobility, Science 327, 1018
(2010).
- C. Song et al., Modelling
the scaling properties of human mobility, Nature Physics
6, 818 (2010).
- D.J. Crandall et al., Inferring
social ties from geographic coincidences, PNAS 107, 22436
(2010).
- J.P. Bagrow and Y.-R. Lin, Mesoscopic
Structure and Social Aspects of Human Mobility, PLOS ONE
7, e37676 (2012).
Other resources:
|
Clayton |
| Virtual Worlds |
| 4/9 |
Required readings:
Further readings:
- W.S. Bainbridge, The
Scientific Research Potential of Virtual Worlds, Science
317, 472 (2007).
- M. Szell and S. Thurner, Measuring
social dynamics in a massive multiplayer online game,
Social Networks 32, 313 (2010).
- N. Ducheneaut et al., "Alone
together?": exploring the social dynamics of massively
multiplayer online games, CHI'06
- N. Ducheneaut et al., The
life and death of online gaming communities: a look at guilds
in world of warcraft, CHI'07
- J. Bohannon, Slaying
Monsters for Science, Science 320, 1592 (2008).
- W. Mason and A. Clauset, Friends FTW!
Friendship, Collaboration and Competition in Halo: Reach,
CSCW'13
Other resources:
|
Paul |
| Stochastic Resonance |
| 4/11 |
Required readings:
Further readings:
- Google scholar: Stochastic
resonance
- R. Benzi et al., The
mechanism of stochastic resonance, Journal of Physics A
14, L453 (1981).
- L. Gammaitoni et al., Stochastic
resonance, RMP 70, 223 (1998).
- R. Benzi et al., Stochastic
resonance in climatic change, Tellus 34, 10 (1982).
- J.J. Collins et al., Stochastic
resonance without tuning, Nature 376, 236 (2002).
- A. Ganopolski and S. Rahmstorf, Abrupt
Glacial Climate Changes due to Stochastic Resonance, PRL
88, 038501 (2002).
|
Ian |
| Data |
| 4/16 |
Required readings:
Further readings:
|
Jaimie |
| 4/18: Project presentation (AlexG, Karissa, Abhik) |
| 4/23: Project presentation (Scott, Jordan, Onur, Paul, Clayton, Qing) |
| 4/25: Project presentation (Rick & Andrea, Nathaniel, Ian, AlexJ, Damion, Jaimie) |
| 4/30: Final paper due |