Simona Cocco

According to our database, Simona Cocco authored at least 24 papers between 2001 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.

Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard

PLoS Comput. Biol., November, 2023

Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data.

Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco

PLoS Comput. Biol., October, 2023

2022

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection.

Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Sulc

PLoS Comput. Biol., September, 2022

Disentangling representations in Restricted Boltzmann Machines without adversaries.

Jorge Fernandez-de-Cossío-Diaz, Simona Cocco, Rémi Monasson

CoRR, 2022

2021

Improving sequence-based modeling of protein families using secondary-structure quality assessment.

Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson

Bioinform., November, 2021

Parameters and determinants of responses to selection in antibody libraries.

Steven Schulz, Sebastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire

PLoS Comput. Biol., 2021

Probing T-cell response by sequence-based probabilistic modeling.

Barbara Bravi, Vinod P. Balachandran, Benjamin D. Greenbaum, Aleksandra M. Walczak, Thierry Mora, Rémi Monasson, Simona Cocco

PLoS Comput. Biol., 2021

Optimal regularizations for data generation with probabilistic graphical models.

Arnaud Fanthomme, Francesca Rizzato, Simona Cocco, Rémi Monasson

CoRR, 2021

Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines.

Clément Roussel, Simona Cocco, Rémi Monasson

CoRR, 2021

2019

Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins.

Jérôme Tubiana, Simona Cocco, Rémi Monasson

Neural Comput., 2019

'Place-cell' emergence and learning of invariant data with restricted Boltzmann machines: breaking and dynamical restoration of continuous symmetries in the weight space.

Moshir Harsh, Jérôme Tubiana, Simona Cocco, Rémi Monasson

CoRR, 2019

2018

Integration and multiplexing of positional and contextual information by the hippocampal network.

Lorenzo Posani, Simona Cocco, Rémi Monasson

PLoS Comput. Biol., 2018

2017

Functional connectivity models for decoding of spatial representations from hippocampal CA1 recordings.

Lorenzo Posani, Simona Cocco, Karel Jezek, Rémi Monasson

J. Comput. Neurosci., 2017

2016

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.

Hugo Jacquin, Amy Gilson, Eugene I. Shakhnovich, Simona Cocco, Rémi Monasson

PLoS Comput. Biol., 2016

Neural assemblies revealed by inferred connectivity-based models of prefrontal cortex recordings.

Gaia Tavoni, Simona Cocco, Rémi Monasson

J. Comput. Neurosci., 2016

ACE: adaptive cluster expansion for maximum entropy graphical model inference.

John P. Barton, Eleonora De Leonardis, Alice Coucke, Simona Cocco

Bioinform., 2016

2013

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction.

Simona Cocco, Rémi Monasson, Martin Weigt

PLoS Comput. Biol., 2013

2011

Fast inference of interactions in assemblies of stochastic integrate-and-fire neurons from spike recordings.

Rémi Monasson, Simona Cocco

J. Comput. Neurosci., 2011

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data

Simona Cocco, Rémi Monasson

CoRR, 2011

2006

Analyzing Search Algorithms with Physical Methods.

Simona Cocco, Rémi Monasson, Andrea Montanari, Guilhem Semerjian

Proceedings of the Computational Complexity and Statistical Physics., 2006

2005

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.

Simona Cocco, Rémi Monasson

Ann. Math. Artif. Intell., 2005

2004

Heuristic average-case analysis of the backtrack resolution of random 3-satisfiability instances.

Simona Cocco, Rémi Monasson

Theor. Comput. Sci., 2004

2003

Approximate analysis of search algorithms with "physical" methods

Simona Cocco, Rémi Monasson, Andrea Montanari, Guilhem Semerjian

CoRR, 2003

2001

Statistical physics analysis of the backtrack resolution of random 3-SAT instances.

Simona Cocco, Rémi Monasson

Electron. Notes Discret. Math., 2001