Thick lens

F. Altarelli, A. Braunstein, A. Ramezanpour, and R. Zecchina, Stochastic matching problem, Phys. Rev. Lett. 106, 190601 (2011).

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)

Lens equation

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

“Statistical physics approach to the prediction of native contacts in proteins from sequence variability” Conference: Systems Biology and New Sequencing Techniques, ICTP, November 2011

LensesPhysics

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)

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)

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)

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.

Lens system

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.

Lensesin series

“Triggering cascade processes in biological networks”, Statistical Mechanics in Systems Biology: Regulation, Inference, Optimization, Villa Orlandi, Anacapri, Italy, May 29 – June 1, 2012

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).

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)

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

Lens combination calculator

A. Braunstein, F. Kahyan, R. Zecchina, Efficient data compression from statistical physics of codes over finite fields, Phys. Rev. E 84, 051111  (2011)

Combination oflensesexamples

Algorithms for optimization and statistical inference, with applications in systems biology and protein structure prediction. Control of cascade processes over large scale networks.

From stochastic optimization to inverse dynamical problems”, Granada, workshop on “Statistical physics of control theory and inference”, September 2012

A. Braunstein, A. Ramezanpour, R. Zecchina, and P. Zhang. Inference and learning in sparse systems with multiple states, Phys.  Rev. E 83, 056114  (2011)