Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics

In this study, we address the challenge of using energy-based models to produce high-quality, label-specific data in complex structured datasets, such as population genetics, RNA or protein sequences data. Traditional training methods encounter difficulties due to inefficient Markov chain Monte Carlo mixing, which affects the diversity of synthetic data and increases generation times. To address these issues, we use a novel training algorithm that exploits non-equilibrium effects. This approach, applied to the Restricted Boltzmann Machine, improves the model's ability to correctly classify samples and generate high-quality synthetic data in only a few sampling steps. The effectiveness of this method is demonstrated by its successful application to five different types of data: handwritten digits, mutations of human genomes classified by continental origin, functionally characterized sequences of an enzyme protein family, homologous RNA sequences from specific taxonomies and real classical piano pieces classified by their composer.

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Publication Details

Journal
IEEE Transactions on Pattern Analysis and Machine Intelligence
Published
2024-11-11
DOI
https://doi.org/10.1109/tpami.2024.3495999
Citations
6
Primary Topic
Protein Structure and Dynamics
Type
article
Field-Weighted Citation Impact
1.40

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article

Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics

Beatriz Seoane, Alessandra Carbone, Aurélien Decelle, Lorenzo Rosset
6 citations
IEEE Transactions on Pattern Analysis and Machine Intelligence
Protein Structure and Dynamics
1.40
article

Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics

Beatriz Seoane, Alessandra Carbone, Aurélien Decelle, Lorenzo Rosset
article en
6 citations

Abstract

In this study, we address the challenge of using energy-based models to produce high-quality, label-specific data in complex structured datasets, such as population genetics, RNA or protein sequences data. Traditional training methods encounter difficulties due to inefficient Markov chain Monte Carlo mixing, which affects the diversity of synthetic data and increases generation times. To address these issues, we use a novel training algorithm that exploits non-equilibrium effects. This approach, applied to the Restricted Boltzmann Machine, improves the model's ability to correctly classify samples and generate high-quality synthetic data in only a few sampling steps. The effectiveness of this method is demonstrated by its successful application to five different types of data: handwritten digits, mutations of human genomes classified by continental origin, functionally characterized sequences of an enzyme protein family, homologous RNA sequences from specific taxonomies and real classical piano pieces classified by their composer.

IEEE Transactions on Pattern Analysis and Machine IntelligenceVol. 47(2)
Universidad Complutense de Madrid (ES), Centre National de la Recherche Scientifique (FR), Sorbonne Université (FR), Biologie Computationnelle, Quantitative et Synthétique (FR)
Banco Santander
Openalex Percentile: Top 18%
Protein Structure and Dynamics
1.40
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Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics — Beatriz Seoane, Alessandra Carbone, et al. · IEEE Transactions on Pattern Analysis and Machine Intelligence (2024) | TGRS Research Map | TGRS