Publications

Note: The list of publications below may not be updated regularly. See Girvan's Google Scholar Profile for up-to-date info.


Submitted articles:

  • A. Wikner, J. Pathak, B. Hunt, M. Girvan, T. Arcomano, I. Szunyogh, A. Pomerance, and E. Ott. "Combining Machine Learning with Knowledge-Based Modeling for Scalable Forecasting and Subgrid-Scale Closure of Large, Complex, Spatiotemporal Systems." arXiv preprint arXiv:2002.05514 (2020).

  • S. Krishnagopal†, R. Von Coelln, L.M. Shulman, and M. Girvan. "Identifying and Predicting Parkinson's Disease Subtypes through Trajectory Clustering via Bipartite Networks." arXiv preprint arXiv:1906.05338 (2019).

  • S. Chandra†, E. Ott, and M. Girvan. "Critical Network Cascades with Re-excitable nodes: Why tree-like approximations usually work, when they breakdown, and how to correct them." arXiv preprint arXiv:1905.07433 (2019).


Articles in refereed journals:

  • P.R. Vlachas, J. Pathak, B. R. Hunt, T. P. Sapsis, M. Girvan, E. Ott, and P. Koumoutsakos. "Backpropagation algorithms and Reservoir Computing in Recurrent Neural Networks for the forecasting of complex spatiotemporal dynamics." Neural Networks (2020).

  • S. Krishnagopal†, M. Girvan, E. Ott, and B.R. Hunt. "Separation of chaotic signals by reservoir computing." Chaos: An Interdisciplinary Journal of Nonlinear Science 30, no. 2 (2020): 023123.S.

  • S. Chandra†, M. Girvan, and E. Ott. "Complexity reduction ansatz for systems of interacting orientable agents: Beyond the Kuramoto model." Chaos: An Interdisciplinary Journal of Nonlinear Science 29, no. 5 (2019): 053107.

  • S. Patange†, M. Girvan, D. Levens, and D.R. Larson. "A Living, Single Cell View of Myc's Effects on Transcription." Biophysical Journal 116, no. 3 (2019): 306a-307a.

  • K. Burghardt†, W. Rand, and M. Girvan. "Inferring models of opinion dynamics from aggregated jury data." PloS one 14, no. 7 (2019).

  • A. Peshkov, M. Girvan, D.C. Richardson, and W. Losert. "Reversibility of granular rotations and translations." Physical Review E 100, no. 4 (2019): 042905.

  • S. Chandra†, M. Girvan, and E. Ott. "Continuous versus Discontinuous Transitions in the D-Dimensional Generalized Kuramoto Model: Odd D is Different." Physical Review X 9, no. 1 (2019): 011002.

  • S. Krishnagopal†, Y. Aloimonos, and M. Girvan. "Similarity Learning and Generalization with Limited Data: A Reservoir Computing Approach." Complexity 2018 (2018).

  • J. Pathak†, B. Hunt, M. Girvan, Z. Lu†, and E. Ott. "Model-free prediction of large spatiotemporally chaotic systems from data: A reservoir computing approach." Physical review letters 120, no. 2 (2018): 024102.

  • S. Patange†, M. Girvan, and D.R. Larson. "Single-cell systems biology: probing the basic unit of information flow." Current opinion in systems biology 8 (2018): 7-15.

  • J. Pathak†, A. Wikner‡, R. Fussell‡, S. Chandra†, B.R. Hunt, M. Girvan, and E. Ott. "Hybrid forecasting of chaotic processes: Using machine learning in conjunction with a knowledge-based model." Chaos: An Interdisciplinary Journal of Nonlinear Science 28, no. 4 (2018): 041101.

  • D. Darmon†,W. Rand, and M. Girvan. "Computational landscape of user behavior on social media." Physical Review E 98, no. 6 (2018): 062306. J. Pathak†, B. Hunt, M. Girvan, Z. Lu†, and E. Ott. "Model-Free Prediction of Large Spatiotemporally Chaotic Systems from Data: A Reservoir Computing Approach." Physical Review Letters 120, no. 2 (2018): 024102.

  • J. Pathak†, A. Wikner‡, R. Fussell‡, S. Chandra†, B.R. Hunt, M. Girvan, and E. Ott. "Hybrid forecasting of chaotic processes: Using machine learning in conjunction with a knowledge-based model." Chaos: An Interdisciplinary Journal of Nonlinear Science 28, no. 4 (2018): 041101.

  • J. Pathak†, B. Hunt, M. Girvan, Z. Lu, and Edward Ott. "Model-Free Prediction of Large Spatiotemporally Chaotic Systems from Data: A Reservoir Computing Approach." Physical Review Letters (2018): 024102.

  • J. Pathak†, Z. Lu†, B.R. Hunt, M. Girvan, and E. Ott. "Using machine learning to replicate chaotic attractors and calculate Lyapunov exponents from data." Chaos: An Interdisciplinary Journal of Nonlinear Science (2017): 121102.

  • J Harada, D Darmon†, M Girvan*, W Rand* . Prediction of Elevated Activity in Online Social Media Using Aggregated and Individualized Models. In Trends in Social Network Analysis 2017 (pp. 169-187). Springer International Publishing.

  • Z. Lu†, J. Pathak, B. Hunt, M. Girvan, R. Brockett, and E. Ott, "Reservoir observers: Model-free inference of unmeasured variables in chaotic systems." Chaos 27, 041102 (2017).

  • K. Burghardt†, E.F. Alsina, M. Girvan, W.M. Rand, and K. Lerman. "The myopia of crowds: A study of collective evaluation on stack exchange,” PLoS One, e0173610 (2017).

  • S. Chandra†, D. Hathcock‡, K. Crain‡, T. M. Antonsen, M. Girvan, and Edward Ott, “Modeling the Network Dynamics of Pulse-Coupled Neurons,” Chaos 27, 033102 (2017).

  • K. Burghardt†, W. Rand, and M. Girvan. “Competing opinions and stubbornness: connecting models to data,” Physical Review E 93 (3), 032305, (2016).

  • Z. Lu†, S. Squires†, E. Ott, and M. Girvan, “Inhibitory neurons promote robust critical firing dynamics in networks of integrate-and-fire neurons,” Physical Review E, 94(6), 062309 (2016).

  • H. Karathia, C. Kingsford, M. Girvan, and S. Hannenhalli, ”A pathway-centric view of spatial proximity in the 3D nucleome across cell lines,” Scientific Reports 6 (2016).

  • Z. Lu†, K. Klein-Cardeña‡, S. Lee‡, T.M. Antonsen, M. Girvan, and E. Ott, "Resynchronization of circadian oscillators and the east-west asymmetry of jet-lag,” Chaos 094811 (2016).

  • K. Glass and M. Girvan, “Finding New Order in Biological Functions from the Network Structure of Gene Annotations,” PLoS Computational Biology 11.11 (2015).

  • W.L. Ku†, M. Girvan, and E. Ott. "Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states." Chaos, 25 (12) 123122 (2015).

  • A. Melchionna‡, J. Caloca‡, S. Squires†, T.M. Antonsen, E. Ott and M. Girvan, "Impact of imperfect information on network attack." Physical Review E 91, no. 3 (2015).

  • J. Harada, D. Darmon†, M. Girvan and W. Rand. "Forecasting High Tide: Predicting Times of Elevated Activity in Online Social Media." In Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining 2015, pp. 504-507. ACM (2015).

  • A. Zitin‡, A. Gorowara‡, S. Squires†, M. Herrera†, T.M. Antonsen, M. Girvan and E. Ott, “Spatially embedded growing small world networks,” Scientific Reports 4, 7047 (2014).

  • K. Glass† and M. Girvan, “Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets,” Scientific Reports 4, 4191 (2014).

  • S. Squires†, A. Pomerance, M. Girvan, and E. Ott, “Stability of Boolean networks: The joint effects of topology and update rules,” Physical Review E 90 (2), 022814 (2014).

  • M. Mailman, M. Harrington, M. Girvan and W. Losert, “Consequences of Anomalous Diffusion in Disordered Systems under Cyclic Forcing,” Physical Review Letters 112 (22), 228001 (2014).

  • T.R. Kießling, M. Herrera†, K.D Nnetu, E.M. Balzer, M. Girvan, A.W. Fritsch, S.S. Martin, J.A. Käs, and W. Losert, "Network Based Biomechanical Phenotyping of Circulating Tumor Cells," European Biophysics Journal 42 (5), 383-394 (2013).

  • D. Darmon†, J. Sylvester, M. Girvan and W. Rand, “Understanding the Predictive Power of Computational Mechanics and Echo State Networks in Social Media.” ASE Human Journal, vol. 2(2), pp. 13–24 (2013).

  • J. Platig†, E. Ott and M. Girvan, "Robustness of network measures to link errors" Physical Review E 88 (6), 062812 (2013).

  • W.L. Ku†, M. Girvan, G.C. Yuan, F. Sorrentino and E. Ott, "Modeling the dynamics of bivalent histone modifications," PLoS ONE 8 (11), e77944 (2013).

  • S. Squires†, K. Sytwu‡, D. Alcala‡, T.M. Antonsen, E. Ott and M. Girvan, "Weakly explosive percolation in directed networks," Physical Review E 87 (5), 052127 (2013).

  • S. Squires†, E. Ott and M. Girvan, “Dynamical Instability in Boolean Networks as a Percolation Problem,” Phys. Rev. Lett. 109, 085701 (2012).

  • S. Chauhan†, M. Girvan and E. Ott, “A network function-based definition of communities in complex networks,” Chaos 22, 033129 (2012).

  • K. Glass†, E. Ott, W. Losert and M. Girvan, “Implications of functional similarity for gene regulatory interactions,” J. R. Soc. Interface, rsif20110585 (2012).

  • W. L. Ku†, G. Duggal†, Y. Li, M. Girvan, and E. Ott, “Interpreting patterns of gene expression: signatures of coregulation, the data processing inequality, and triplet motifs,” PLoS ONE 7(2), e31969 (2012).

  • A. Pomerance†, M. Girvan, and E. Ott, “Stability of Boolean networks with generalized canalizing rules,” Phys. Rev. E 85, 046106 (2012).

  • D. Anderson‡, A. Tenzer‡, G. Barlev, M. Girvan, T.M. Antonsen and E. Ott, “Multiscale dynamics in communities of phase oscillators,” Chaos 22, 013102 (2012).

  • S. Slotterback, M. Mailman, K. Ronaszegi, M. van Hecke, M. Girvan and W. Losert, “Onset of irreversibility in cyclic shear of granular packings,” Phys. Rev. E 85, 021309 (2012).

  • M. Herrera†, S. McCarthy, S. Slotterback, E. Cephas, W. Losert and M. Girvan, “Path to fracture in granular flows: Dynamics of contact networks,” Phys. Rev. E 83, 061303 (2011).

  • C.P. Kempes‡, G.B. West, K. Crowell and M. Girvan, “Predicting maximum tree heights and other traits from allometric scaling and resource limitations,” PLoS ONE 6(6), e20551 (2011).

  • J. Stout‡, M. Whiteway‡, E. Ott, M. Girvan and T.M. Antonsen, “Local synchronization in complex networks of coupled oscillators,” Chaos 21, 025109 (2011).

  • O. Peters and M. Girvan, “Universality under conditions of self-organization,” J. Stat Phys. 141, 53-59 (2010).

  • G. Barlev‡, M. Girvan and E. Ott, “Map model for synchronization of systems of many coupled oscillators,” Chaos 20, 023109 (2010).

  • A. Pomerance†, E. Ott, M. Girvan and W. Losert, “The effect of network topology on the stability of discrete state models of genetic control,” Proc. Natl. Acad. Sci. USA 106, 8209-8214 (2009).

  • S. Chauhan†, M. Girvan, and E. Ott, “Spectral properties of networks with community structure,” Phys. Rev. E 80, 056114 (2009).

  • T. M. Antonsen, R. Faghih, M. Girvan, E. Ott and J. Platig, “External periodic driving of large systems of globally coupled phase oscillators,” Chaos 18, 037112 (2008).

  • E. Ott, J. Platig, T.M. Antonsen Jr. and M. Girvan, “Echo phenomena in large systems of coupled oscillators,” Chaos 18, 037115 (2008).

  • J.C. Flack, M. Girvan, F.B.M. de Waal and D.C. Krakauer, “Policing stabilizes construction social niches in primates.” Nature 439, 426-429 (2006).

  • D. Wiley, S.H. Strogatz and M. Girvan, “The size of the sync basin,” Chaos 16, 015103 (2006).

  • M.E.J. Newman and M. Girvan, “Finding and evaluating community structure in networks,” Phys. Rev. E 69, 026113 (2004).

  • M. Girvan and M.E.J. Newman, “Community structure in social and biological networks,” Proc. Natl. Acad. Sci. USA 99, 8271-8276 (2002).

  • M. Girvan, D.S. Callaway, M.E.J. Newman and S.H. Strogatz, “A simple model of epidemics with pathogen mutation,” Phys Rev. E 65, 031915 (2002).

  • M.E.J. Newman, M. Girvan, and J.D. Farmer, “Optimal Design, robustness, and risk aversion,” Phys. Rev. Lett. 89 028301 (2002).

  • E.M. Jin, M. Girvan and M.E.J. Newman, “The structure of growing social networks,” Phys. Rev. E 64, 046132 (2001).


Refereed proceedings:

  • S. Krishnagopal, G. Katz, M. Girvan, and J. Reggia. "Encoding of a Chaotic Attractor in a Reservoir Computer: A Directional Fiber Investigation." In 2019 International Joint Conference on Neural Networks (IJCNN), pp. 1-8. IEEE, 2019.

  • J. Harada, D. Darmon, M. Girvan, and W. Rand, "Prediction of Elevated Activity in Online Social Media Using Aggregated and Individualized Models." In Trends in Social Network Analysis, pp. 169-187. Springer International Publishing (2017).

  • J. Harada, D. Darmon†, M. Girvan and W. Rand, "Forecasting High Tide: Predicting Times of Elevated Activity in Online Social Media." In Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining 2015, pp. 504-507. ACM (2015).

  • H. Wang, G. Duggal†, R. Patro, M. Girvan, S. Hannenhalli, C. Kingsford, "Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin," Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM (2013).

  • D. Darmon†, J. Sylvester, M. Girvan, and W. Rand, “Predictability of User Behavior in Social Media: Bottom-Up v. Top-Down Modeling,” International Conference on Social Computing (SocialCom), 102-107 (2013).

  • G. Duggal, S. Navlakah, M. Girvan, and C. Kingsford, “Uncovering many views of biological networks using ensembles of near-optimal partitions,” MultiClust: 1st International Workshop on Discovering, Summarizing and Using Multiple Clusterings at KDD (2010).


†graduate student advised by M. Girvan

‡ undergraduate student advised by M. Girvan