Algorithms for optimization and statistical inference, with applications in systems biology and protein structure prediction. Control of cascade processes over large scale networks.
Statistical physics of optimization and inference, static and dynamical inverse problems, maximization of the spread of influence over networks, distributed algorithms for optimization and inference, applications in computational biology
Examples of Outreach
From stochastic optimization to inverse dynamical problems”, Granada, workshop on “Statistical physics of control theory and inference”, September 2012
“Triggering cascade processes in biological networks”, Statistical Mechanics in Systems Biology: Regulation, Inference, Optimization, Villa Orlandi, Anacapri, Italy, May 29 – June 1, 2012
“Statistical physics approach to the prediction of native contacts in proteins from sequence variability” Conference: Systems Biology and New Sequencing Techniques, ICTP, November 2011
F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Onuchic, T. Hwa, M. Weigt, Direct-coupling analysis of residue co-evolution captures native contacts across many protein families, Natl. Acad. Sci. 2011,doi:10.1073/pnas.111147110.
D.S. Marks, L.J. Colwell, R. Sheridan, T.A. Hopf, A. Pagnani, R. Zecchina, C. Sander, Protein 3D Structure from Evolutionary Sequence Variation, Plos-ONE 6(12):e28766 (2011)
A.Braunstein, I. Biazzo, R. Zecchina, Performance of a cavity-method-based algorithm for the prize-collecting Steiner tree problem on graphs, Phys. Rev. E, 86, 026706, (2012).
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, and Ernest Fraenkel, Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem, RECOMB2012.
Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, François JM, R. Zecchina. Finding undetected protein associations in cell signaling by belief propagation. Proc. Natl. Acad. Sci. 108 (2) 882-887 (2011)
M. Bailly-Bechet, A. Benecke, W.D. Hard, V. Lanza, A. Sturm, R. Zecchina, An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium, Journal of Mathematical Biology 63, 637-662 (2011)
F. Altarelli, A. Braunstein, A. Ramezanpour, and R. Zecchina, Stochastic matching problem, Phys. Rev. Lett. 106, 190601 (2011).
A. Ramezanpour, J. Realpe-Gomez, R. Zecchina, Statistical physics approach to graphical games: local and global interactions, Europ. Phys. J. B 81, 327-339 (2011)
A. Braunstein, F. Kahyan, R. Zecchina, Efficient data compression from statistical physics of codes over finite fields, Phys. Rev. E 84, 051111 (2011)
A. Braunstein, A. Ramezanpour, R. Zecchina, and P. Zhang. Inference and learning in sparse systems with multiple states, Phys. Rev. E 83, 056114 (2011)
M. Pagan, A. Alemi-Neissi, C. Baldassi, R. Zecchina, J.J. DiCarlo, D. Zoccolan D, From luminance to semantics: how natural objects are represented in monkey inferotemporal cortex, Computational and System Neuroscience (COSYNE) 2011, Salt Lake City, Utah, USA
M. Bayati, C. Borgs, J. Chaeys, R. Zecchina, Belief Propagation for weighted b-matchings on arbitrary graphs and its relations with linear programs with integer solutions, SIAM Journal on Discrete Mathematics 25, 989-1011 (2011)