Embedded Files
Instructor: Prof. INDIKA Rajapakse
Teaching Assistant: COOPER Stansbury
Class Time: Tuesday and Thursday, 8:30 AM - 10:00 AM
Office Hours:
Tuesdays (in-person), from 10:00 AM - 11:00 AM EST in DCMB (Palmer Commons) Rm. 2017A
Thursday and Friday (remote), after 2pm EST by appointment via Google Meet: meet.google.com/dnm-zipr-tsb (Links to an external site.) (note that this is a different link)
References of Interest
Recommended Reading Material
Dr. Cleve Moler's Book: Numerical Computing with MatLab
Jon Kleinberg's Book: Networks, Crowds, and Markets
NOTES, SLIDES, AND PAPERS
NOTES, SLIDES, AND PAPERS
Date: 12-09-2021
Date: 12-09-2021
Network Systems: Synchrony and its Breakdown
Papers
P. J. Mucha, T. Richardson, K. Macon, M. A. Porter, and J.-P. Onnela, “Community Structure in Time-Dependent, Multiscale, and Multiplex Networks,” Science, vol. 328, no. 5980, pp. 876–878, May 2010, doi: 10.1126/science.1184819.
Stankovski T, Pereira T, McClintock PV, Stefanovska A. Coupling functions: universal insights into dynamical interaction mechanisms. Reviews of Modern Physics. 2017 Nov 6;89(4):045001.
Date: 12-07-2021
Date: 12-07-2021
Supplementary materials that used in today's lecture
Papers
Strogatz SH. "Exploring complex networks." nature. 2001 Mar;410(6825):268-76.
Barabási, Albert-László, and Réka Albert. "Emergence of scaling in random networks." science 286, no. 5439 (1999): 509-512.
Rajapakse, Indika, and Stephen Smale. "Emergence of function from coordinated cells in a tissue." Proceedings of the National Academy of Sciences 114.7 (2017): 1462-1467.
Date: 12-02-2021
Date: 12-02-2021
Optimal Hard Threshold
Papers
Gavish, Matan, and David L. Donoho. "The optimal hard threshold for singular values is 4/sqrt(3)." IEEE Transactions on Information Theory 60.8 (2014): 5040-5053.
Date: 11-30-2021
Date: 11-30-2021
Papers
Gavish, Matan, and David L. Donoho. "The optimal hard threshold for singular values is 4/sqrt(3)." IEEE Transactions on Information Theory 60.8 (2014): 5040-5053. (Amazing Paper!)
FUN readings.....
Buchanan, Mark. "The best is yet to come." Nature 447.7140 (2007): 39-39.
More papers: Connections in 2007
Date: 11-23-2021
Date: 11-23-2021
Please read!
Benson, Austin R., David F. Gleich, and Jure Leskovec. "Higher-order organization of complex networks." Science 353.6295 (2016): 163-166.
URL: https://snap.stanford.edu/higher-order/
D. L. Barabási and A.-L. Barabási, “A Genetic Model of the Connectome,” Neuron, vol. 105, no. 3, pp. 435-445.e5, Feb. 2020, doi: 10.1016/j.neuron.2019.10.031.
Date: 11-18-2021
Date: 11-18-2021
Network Dynamics: Stability and Bifurcations cont.....
Additional Information:
Papers
Papers
Tero, Atsushi, et al. "Rules for biologically inspired adaptive network design." Science 327.5964 (2010): 439-442.
Rajapakse I, Groudine M, Mesbahi M. "What can systems theory of networks offer to biology?" PLoS Comput Biol. 2012 Jun 28;8(6):e1002543.
J. Gao, B. Barzel, and A.-L. Barabási, “Universal resilience patterns in complex networks,” Nature, vol. 530, no. 7590, pp. 307–312, Feb. 2016, doi: 10.1038/nature16948.
Date: 11-16-2021
Date: 11-16-2021
Network Dynamics: Stability and Bifurcations
Network Visualization: (Gephi)
Papers
Donnat, Claire, and Susan Holmes. "Tracking network dynamics: A survey using graph distances." The Annals of Applied Statistics 12.2 (2018): 971-1012
Surana A, Chen C, Rajapakse I. "Hypergraph Similarity Measures." arXiv preprint arXiv:2106.08206 (2021)
Date: 11-11-2021
Date: 11-11-2021
Network Neuroscience (slides)
TED Talk: I am my connectome
Papers
Restrepo, Juan G., Edward Ott, and Brian R. Hunt. "Characterizing the dynamical importance of network nodes and links." Physical review letters 97.9 (2006): 094102.
Sweeney P, Chen C, Rajapakse I, Cone R. "Network Dynamics of Hypothalamic Feeding Neurons." Proceedings of the National Academy of Sciences, 118.14 (2021).
Date: 11-09-2021
Date: 11-09-2021
Network Robustness: Network robustness is the ability of a network to survive from random failures or deliberate attacks (e.g., removal of nodes or edges). It is intimately related to the underlying network structure/topology.
Papers:
Kitano, Hiroaki. "Biological robustness." Nature Reviews Genetics 5.11 (2004): 826-837.
Chen P, Wu L, Liu S, Rajapakse I. "Fast Incremental von Neumann Graph Entropy Computation: Theory, Algorithm, and Applications." 2019 International Conference on Machine Learning (2019).
Chen C, Rajapakse I. "Tensor Entropy for Uniform Hypergraphs." IEEE Transactions on Network Science and Engineering 7.4 (2020): 2889-2900.
Book:
Network Science: Network Robustness
Date: 11-04-2021
Date: 11-04-2021
Nonlinear Dynamics of Networks
Date: 11-02-2021
Date: 11-02-2021
Nonlinear Dynamics of Networks
Date: 10-28-2021
Date: 10-28-2021
Controllability Metrics for Networks: Controllability Gramian
Papers
Data-guided Control (DGC)
Ronquist S, Patterson G, Muir LA, Lindsly S, Chen H, Brown M, Wicha MS, Bloch A, Brockett R, Rajapakse I. "Algorithm for cellular reprogramming." Proceedings of the National Academy of Sciences. 2017 Nov 7;114(45):11832-7.
Date: 10-26-2021
Date: 10-26-2021
Papers
Gavish, Matan, and David L. Donoho. "The optimal hard threshold for singular values is 4/sqrt(3)." IEEE Transactions on Information Theory 60.8 (2014): 5040-5053. (Amazing Paper!)
Book
Kutz, J. Nathan, et al. Dynamic mode decomposition: data-driven modeling of complex systems. Society for Industrial and Applied Mathematics, 2016.
Chapter 1: Dynamic Mode Decomposition: An Introduction
Date: 10-21-2021
Date: 10-21-2021
Controllability Metrics for Networks: Controllability Gramian
Papers
Timothy Gardner, Charles Cantor, and James Collins. "Construction of a genetic toggle switch in escherichiacoli." Nature, 403(6767): 339, 2000.
Michael Elowitz and Stanislas Leibler. "A synthetic oscillatory network of transcriptional regulators." Nature, 403(6767): 335, 2000.
Spencer, Sabrina L., et al. "The proliferation-quiescence decision is controlled by a bifurcation in CDK2 activity at mitotic exit." Cell 155.2 (2013): 369-383.
Rajapakse I, and Smale S. "Mathematics of the Genome." Foundations of Computational Mathematics 17.5 (2017): 1195-1217.
Can We Control the Brain Networks?
Date: 10-14-2021
Date: 10-14-2021
Papers
Data-guided Control (DGC)
Ronquist S, Patterson G, Muir LA, Lindsly S, Chen H, Brown M, Wicha MS, Bloch A, Brockett R, Rajapakse I. "Algorithm for cellular reprogramming." Proceedings of the National Academy of Sciences. 2017 Nov 7;114(45):11832-7.
Date: 10-12-2021
Date: 10-12-2021
Papers
Liu, Yang-Yu, Jean-Jacques Slotine, and Albert-László Barabási. "Controllability of complex networks." Nature 473.7346 (2011): 167-173.
Rajapakse I, Groudine M, Mesbahi M. "Dynamics and control of state-dependent networks for probing genomic organization." Proceedings of the National Academy of Sciences. 2011 Oct 18;108(42):17257-62.
Gurdon, J. B., and D. A. Melton. "Nuclear reprogramming in cells." science 322.5909 (2008): 1811-1815.
Date: 10-07-2021
Date: 10-07-2021
Extra Notes: Prof. David Bindel's Fall 2019 6210 course notes
Papers
Brin, Sergey, and Lawrence Page. "The anatomy of a large-scale hypertextual web search engine." (1998).
Bryan, Kurt, and Tanya Leise. "The $25,000,000,000 eigenvector: The linear algebra behind Google." SIAM review 48.3 (2006): 569-581.
Ng AY, Jordan MI, Weiss Y. "On spectral clustering: Analysis and an algorithm." In Advances in neural information processing systems (2002) (pp. 849-856).
Date: 10-05-2021
Date: 10-05-2021
Eckhart-Young: The Closest Rank k Matrix to A
Papers
Ng AY, Jordan MI, Weiss Y. "On spectral clustering: Analysis and an algorithm." In Advances in neural information processing systems (2002) (pp. 849-856).
Chen H, Chen J, Muir LA, Ronquist S, Meixner W, Ljungman M, Ried T, Smale S, Rajapakse I. "Functional Organization of the Human 4D Nucleome. " Proceedings of the National Academy of Sciences 112.26 (2015): 8002-8007.
Please read!
Benson, Austin R., David F. Gleich, and Jure Leskovec. "Higher-order organization of complex networks." Science 353.6295 (2016): 163-166.
URL: https://snap.stanford.edu/higher-order/
Date: 9-30-2021
Date: 9-30-2021
Slides
Papers
Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science 326.5950 (2009): 289-293.
Misteli, T., 2011. The inner life of the genome. Scientific American, 304(2), p.66.
Date: 9-28-2021
Date: 9-28-2021
Papers
Bapat, R. B. "The Laplacian matrix of a graph." Mathematics Student-India 65, no. 1 (1996): 214-223.
Book (Great book!): Chapter 1
Spielman, Daniel A. "Spectral and Algebraic Graph Theory." (2019)
Date: 9-23-2021
Date: 9-23-2021
Papers
Rajapakse, Indika, and Stephen Smale. "Emergence of function from coordinated cells in a tissue." Proceedings of the National Academy of Sciences 114.7 (2017): 1462-1467.
Date: 9-21-2021
Date: 9-21-2021
Papers
Rajapakse, Indika, and Stephen Smale. "Emergence of function from coordinated cells in a tissue." Proceedings of the National Academy of Sciences 114.7 (2017): 1462-1467.
FUN readings.....
Alon, Uri. "Biological networks: the tinkerer as an engineer." Science 301.5641 (2003): 1866-1867.
Date: 9-16-2021
Date: 9-16-2021
Papers
Watts, Duncan J., and Steven H. Strogatz. "Collective dynamics of ‘small-world’networks." Nature 393.6684 (1998): 440-442.
Date: 9-14-2021
Date: 9-14-2021
Papers
Strogatz SH. "Exploring complex networks." nature. 2001 Mar;410(6825):268-76.
Barabási, Albert-László, and Réka Albert. "Emergence of scaling in random networks." science 286, no. 5439 (1999): 509-512.
Date: 9-09-2021
Date: 9-09-2021
Guest Lecture: Dr. Cleve Moler
Date: 9-07-2021
Date: 9-07-2021
Topics
Review of Eigenvalues and Eigenvectors
Introduction to Singular Value Decomposition (SVD)
Slides
Papers
Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science 326.5950 (2009): 289-293.
Turk, Matthew, and Alex Pentland. "Eigenfaces for recognition." Journal of cognitive neuroscience 3.1 (1991): 71-86.
Date: 9-02-2021
Date: 9-02-2021
Topics
Networks: (1) Random, (2) Small-world, (3) Scale-free, (4) Ramanujan
Review of Adjacency, Degree matrices
Laplacian, Eigenvalues and Eigenvectors
Slides
Date: 8-31-2021
Date: 8-31-2021
Topics
Introduction to course logistics
Nodes and Edges
Introduction to Adjacency and Degree matrices
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