Topics in Modelling, Simulation and Optimization
Papers
- Group A: Cellular Automata
- J.Avnet.
Computation, Dynamics and the Phase Transition
Santa Fe Institute.
- M.Mitchell, J.P.Crutchfield, and P.T.Hraber.
Dynamics, computation, and the ``edge of chaos'': A re-examination.
In G. Cowan, D. Pines, and D. Melzner (editors), Complexity: Metaphors, Models, and Reality. Reading, MA: Addison-Wesley, 1994.
- J.P.Crutchfield and M.Mitchell.
The evolution of emergent computation.
PNAS, 92 (23): 10742, 1995.
- M.Alber. Cellular Automaton Appproaches to
Modeling Biological Cells.
- M.Mitchell, J.P.Crutchfield and R.Das.
Evolving cellular automata to perform computations.
In T. Back, D. Fogel, and Z. Michalewicz (editors), Handbook of Evolutionary Computation. Oxford: Oxford University Press, 1998.
- Group B: Complexity
- J.M.Carlson and J.Doyle.
Highly optimized tolerance: a mechanism for power laws in designed systems.
Phys. Rev. E 60, 1412-1427.
- J.M.Carlson and J.Doyle.
Complexity and robustness.
Proc. Nat. Acad. Sci. 99 , 2538-2545.
- D.Reynolds, J.Carlson and J.Doyle.
Design degrees of freedom and mechanisms for complexity
Phys. Rev. E 66, article 016108.
- M.E.Csete and J.Doyle.
Reverse Engineering of Biological Complexity.
Science, 295, 1664 (2002)
- C.Moore. Unpredictability and
undecidability in dynamical systems.
- A.Fabrikant. Heuristically optimized
tradeoffs: a new paradigm for power laws in the internet.
- Group C: Network theory
- M.E.J.Newman.
The structure and function of networks.
- M.E.J.Newman.
Models of the Small World: A Review
. J.Stat.Phys. Vol. 101, 2000, pp. 819-841.
- M.E.J. Newman, C.Moore and D.J.Watts.
Mean-field solution of the small-world network model.
Phys. Rev. Lett. 84, 3201-3204 (2000).
- L.Adamic et al.
Search in power-law networks
. Phy Rev E, Vol. 64, 2001.
- J.Kleinberg.
The smallworld phenomenon: an algorithmic perspective.
- A.-L. Barabási, R. Albert, and H. Jeong
Scale-free characteristics of random networks: The topology of the World Wide Web
Physica A 281, 69-77 (2000).
- R.Albert, H.Jeong, and A.-L. Barabási.
Error and attack tolerance in complex networks
Nature 406 , 378 (2000).
- A.-L.Barabási, R.Albert and H.Jeong.
Mean-field theory for scale-free random networks
Physica A 272, 173-187 (1999).
- Group D: Percolation
- R.Meester and R.Roy. Lecture notes in
percolation.
- A.Bugacov et al.
Threshold behavior in a boolean network model for SAT
. Information Sciences Institute, USC.
- C.Zou, D.Towsley and W.Gong.
Email virus propagation: modeling and analysis.
- C.Moore and M.E.J.Newman.
Exact solution of site and bond percolation on small-world networks
Phys. Rev. E 62, 7059-7064 (2000).
- N. Schwartz, R.Cohen, D.ben-Avrahm, A.-L.Barabási and S.Havlin.
Percolation in directed scale-free networks.
Physical Review E 66, 015104(R) (2002).
- Group E: Boolean networks
- R.Albert and A.Barabási.
Dynamics of complex systems: Scaling laws for the period of Boolean Networks.
Physical Review Letters 84, 5660-5663 (2000).
- B.Luque and R.Sole.
Phase transitions in random networks: simple analytic determination of critical points.
Phy Rev E, Jan 1997.
- B.Luque. Measuring mutual information in
random boolean networks.
- H.Oktem et al.
A computational model for simulating continuous time boolean networks
.
- S.Huang and D.E.Ingber. Shape-dependent
control of cell growth, differentiation, and apoptosis: switching
between attractors in cell regulatory networks.
Experimental Cell Research, Vol. 261, 2000, pp.91-103.
- S.Bornholdt and T.Rohlf.
Topological evolution of dynamical networks: Global criticality from local dynamics.
Phys. Rev. Lett. 84 (2000) 6114-6117.
- Group F: Network theory applications
- R.Pastor-Satorras and A.Vespignani.
Epidemic spreading in scale-free networks.
Phy. Rev. Letters, Vol.86, No. 14, 2001.
- X.Zhang, G.Neglia, J.Kurose and D. Towsley.
Performance Modeling of Epidemic Routing
UMass CMPSCI Technical Report 05-44, 2005.
- R.Milo, S.Shen-Orr, S.Itzkovitz, N.Kashtan, D.Chklovskii and U.Alon.
Network Motifs: Simple Building Blocks of Complex Networks.
Science, 298:824-827 (2002).
- S.Shen-Orr, R.Milo, S.Mangan and U.Alon.
Network motifs in the transcriptional regulation network of Escherichia coli.
Nature Genetics, 31:64-68 (2002).
- R.Dobrin, Q.K.Beg and A.-L.Barabási.
Aggregation of topological motifs in the Escherichia coli tranascriptional.
BMC Bioinformatics 5: 10 (2004).
- I.Farkas, H.Jeong, T.Vicsek, A.-L.Barabási and Z.N.Oltvai.
The topology of transcription regulatory network in the yeast, Saccharomyces cerevisiae.
Physica A 318, 601-612 (2003).
- A.Vazquez, R.Dobrin, D.Sergi, J.-P.Eckmann, Z.N.Oltvai and A.-L.Barabási.
The topological relationship between the large-scale attributes and local interactions patterns of complex networks.
PNAS, 17940-17945 (2004).
- R.Milo, S.Itzkovitz, N.Kashtan, R.Levitt, S.Shen-Orr, I.Ayzenshtat, M.Sheffer and U.Alon.
Superfamilies of designed and evolved networks.
Science, 303:1538-42 (2004).
- P.Fernandez and R.Sole.
The role of computation in complex regulatory networks.
- Group G: Network dynamics
- N.Barkai et al.
Robustness in simple biochemical networks. Nature, Vol 387,
June 1997.
- H.Ebel and S.Bornholdt.
Evolutionary games and the emergence of complex networks.
- S.Bornholdt.
Modeling Genetic Networks and Their Evolution: A Complex Dynamical Systems Perspective.
Biological Chemistry 382 (2001) 1289-1299.
- R.Sole and P.Fernandez.
Modularity for free in genome networks.
Santa Fe Institute.
- J.C.Liao, R.Boscolo, Y-L.Yang, L.M.Tran, C.Sabatti and V.Roychowdhury.
Network component analysis: reconstruction of regulatory signals
in biological systems.
PNAS, Vol.100, No.26, Dec 2003.
- B.Skyrms and R.Pemantle.
A dynamic model of social network formation.
PNAS, Aug 2000, Vol. 97, No. 16, pp. 9340-46.
- T.Kaizoji, S.Bornholdt and Y.Fujiwara.
Dynamics of price and trading volume in a spin model of stock markets with heterogeneous agents.
Physica A 316 (2002) 441-452.
- C.Kamp and S.Bornholdt.
From HIV infection to AIDS: A dynamically induced percolation transition?
Proc. R. Soc. London B 269 (2002) 2035-2040.
- E.Almaas, B.Kovacs, T.Vicsek, Z.N.Oltvai and A.-L.Barabási.
Global organization of metabolic fluxes in the bacterium Escherichia coli.
Nature 427, 839-843 (2004).
- R.Hanel, S.Kauffman and S.Thurner.
The phase transition in random catalytic sets.
Santa Fe Institute.
- S.Bornholdt and T.Roehl.
Self-organized critical neural networks.
Phys. Rev. E 67 (2003).
- Group H: Miscellaneous
- E.Drinea et al. Balls and bins models with feedback.
- I.Welch. Sequential sales, learning and cascades.
- H.E.Stanley et al.
Self-organized complexity in economics and finance.
PNAS, Feb. 2002, pp.2561-2565.
- Molecular
information theory.
- W.Harrison. An entropy-based measure of software complexity.
IEEE. Trans. Soft. Engg. Vol. 18, No. 11, Nov 1992, pp. 1025-1029.
- Group I: Network comparison
- B.McKay.
Practical graph isomorphism.
See also the NAUTY algorithm.
- J-L.Faulon. Isomorphism, automorphism partitioning and
canonical labeling can be solved in polynomial-time for molecular graphs.
- R.T.Faizullin. Heuristic algorithm for
solving the graph isomorphism problem.
- J.Siek. An implementation of graph
isomorphism testing.
- J.Corneil et al. An efficient algorithm
for graph isomorphism.
- H.Ogata et al. A heuristic graph comparison
algorithm and its application to detect functionally related
enzyme clusters.
- Group J: Additional
- P.Cheeseman et al.
Where the really hard problems are
.
IJCAI 1991.
- Mitchell et al.
Hard and easy distributions of sat problems.
10th National conf on AI, 1992.
- A.Wuensche.
Discrete dynamical networks and their attractor basins.
Santa Fe Institute.
- T.Zhou, J.M. Carlson and J.Doyle.
Mutation, Specialization, and Hypersensitivity in Highly Optimized Tolerance.
PNAS, 2002.