Simona Cocco

Orcid: 0000-0002-1852-7789

According to our database1, Simona Cocco authored at least 26 papers between 2001 and 2024.

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Bibliography

2024
Restoring balance: principled under/oversampling of data for optimal classification.
Proceedings of the Forty-first International Conference on Machine Learning, 2024

Accelerated Sampling with Stacked Restricted Boltzmann Machines.
Proceedings of the Twelfth International Conference on Learning Representations, 2024

2023
Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.
PLoS Comput. Biol., November, 2023

Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data.
PLoS Comput. Biol., October, 2023

2022
Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection.
PLoS Comput. Biol., September, 2022

Disentangling representations in Restricted Boltzmann Machines without adversaries.
CoRR, 2022

2021
Improving sequence-based modeling of protein families using secondary-structure quality assessment.
Bioinform., November, 2021

Parameters and determinants of responses to selection in antibody libraries.
PLoS Comput. Biol., 2021

Probing T-cell response by sequence-based probabilistic modeling.
PLoS Comput. Biol., 2021

Optimal regularizations for data generation with probabilistic graphical models.
CoRR, 2021

Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines.
CoRR, 2021

2019
Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins.
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.
CoRR, 2019

2018
Integration and multiplexing of positional and contextual information by the hippocampal network.
PLoS Comput. Biol., 2018

2017
Functional connectivity models for decoding of spatial representations from hippocampal CA1 recordings.
J. Comput. Neurosci., 2017

2016
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.
PLoS Comput. Biol., 2016

Neural assemblies revealed by inferred connectivity-based models of prefrontal cortex recordings.
J. Comput. Neurosci., 2016

ACE: adaptive cluster expansion for maximum entropy graphical model inference.
Bioinform., 2016

2013
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction.
PLoS Comput. Biol., 2013

2011
Fast inference of interactions in assemblies of stochastic integrate-and-fire neurons from spike recordings.
J. Comput. Neurosci., 2011

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data
CoRR, 2011

2006
Analyzing Search Algorithms with Physical Methods.
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.
Ann. Math. Artif. Intell., 2005

2004
Heuristic average-case analysis of the backtrack resolution of random 3-satisfiability instances.
Theor. Comput. Sci., 2004

2003
Approximate analysis of search algorithms with "physical" methods
CoRR, 2003

2001
Statistical physics analysis of the backtrack resolution of random 3-SAT instances.
Electron. Notes Discret. Math., 2001


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