Simona Cocco

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 19

Top Topics

Probabilistic Graphical Models

Protein Families

Restricted Boltzmann Machine

Quality Assessment

Top Venues

PLoS Comput. Biol.

J. Comput. Neurosci.

Publications

Jorge Fernandez-de-Cossío-Diaz, Clément Roussel, Simona Cocco, Rémi Monasson
Accelerated Sampling with Stacked Restricted Boltzmann Machines. ICLR (2024)
Emanuele Loffredo, Mauro Pastore, Simona Cocco, Rémi Monasson
Restoring balance: principled under/oversampling of data for optimal classification. CoRR (2024)
Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco
Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data. PLoS Comput. Biol. 19 (10) (2023)
Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard
Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment. PLoS Comput. Biol. 19 (11) (2023)
Jorge Fernandez-de-Cossío-Diaz, Simona Cocco, Rémi Monasson
Disentangling representations in Restricted Boltzmann Machines without adversaries. CoRR (2022)
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Sulc
Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection. PLoS Comput. Biol. 18 (9) (2022)
Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson
Improving sequence-based modeling of protein families using secondary-structure quality assessment. Bioinform. 37 (22) (2021)
Steven Schulz, Sebastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
Parameters and determinants of responses to selection in antibody libraries. PLoS Comput. Biol. 17 (3) (2021)
Clément Roussel, Simona Cocco, Rémi Monasson
Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines. CoRR (2021)
Arnaud Fanthomme, F. Rizzato, Simona Cocco, Rémi Monasson
Optimal regularizations for data generation with probabilistic graphical models. CoRR (2021)
Barbara Bravi, Vinod P. Balachandran, Benjamin D. Greenbaum, Aleksandra M. Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
Probing T-cell response by sequence-based probabilistic modeling. PLoS Comput. Biol. 17 (9) (2021)
Moshir Harsh, Jérôme Tubiana, Simona Cocco, Rémi Monasson
'Place-cell' emergence and learning of invariant data with restricted Boltzmann machines: breaking and dynamical restoration of continuous symmetries in the weight space. CoRR (2019)
Jérôme Tubiana, Simona Cocco, Rémi Monasson
Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins. Neural Comput. 31 (8) (2019)
Jérôme Tubiana, Simona Cocco, Rémi Monasson
Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins. CoRR (2019)
Lorenzo Posani, Simona Cocco, Rémi Monasson
Integration and multiplexing of positional and contextual information by the hippocampal network. PLoS Comput. Biol. 14 (8) (2018)
Lorenzo Posani, Simona Cocco, Karel Jezek, Rémi Monasson
Functional connectivity models for decoding of spatial representations from hippocampal CA1 recordings. J. Comput. Neurosci. 43 (1) (2017)
Gaia Tavoni, Simona Cocco, Rémi Monasson
Neural assemblies revealed by inferred connectivity-based models of prefrontal cortex recordings. J. Comput. Neurosci. 41 (3) (2016)
Hugo Jacquin, Amy Gilson, Eugene I. Shakhnovich, Simona Cocco, Rémi Monasson
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models. PLoS Comput. Biol. 12 (5) (2016)
John P. Barton, Eleonora De Leonardis, Alice Coucke, Simona Cocco
ACE: adaptive cluster expansion for maximum entropy graphical model inference. Bioinform. 32 (20) (2016)
Simona Cocco, Rémi Monasson, Martin Weigt
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction. PLoS Comput. Biol. 9 (8) (2013)
Simona Cocco, Rémi Monasson
Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data CoRR (2011)
Rémi Monasson, Simona Cocco
Fast inference of interactions in assemblies of stochastic integrate-and-fire neurons from spike recordings. J. Comput. Neurosci. 31 (2) (2011)
Simona Cocco, Rémi Monasson
Restarts and exponential acceleration of the Davis-Putnam-Loveland-Logemann algorithm: A large deviation analysis of the generalized unit clause heuristic for random 3-SAT. Ann. Math. Artif. Intell. 43 (1) (2005)
Simona Cocco, Rémi Monasson
Heuristic average-case analysis of the backtrack resolution of random 3-Satisfiability instances CoRR (2004)
Simona Cocco, Rémi Monasson
Heuristic average-case analysis of the backtrack resolution of random 3-satisfiability instances. Theor. Comput. Sci. 320 (2-3) (2004)
Simona Cocco, Rémi Monasson, Andrea Montanari, Guilhem Semerjian
Approximate analysis of search algorithms with "physical" methods CoRR (2003)
Simona Cocco, Rémi Monasson
Statistical physics analysis of the backtrack resolution of random 3-SAT instances. Electron. Notes Discret. Math. 9 (2001)