arXiv subjects

Lorenzo Rosset

Publications and source records attributed to Lorenzo Rosset.

5 recordsLinked to original sources

arXiv2026

From Scarce Functional Labels to Label-Aware Generation in Homologous Protein Families

Accurately annotating and controlling protein function from sequence data remains a major challenge in protein engineering, especially when functional labels are scarce within large homologous families. Here, we study a two-stage light-supervision strategy for fine-grained functional annotation and label-aware sequence generation. First, we compare several sequence representations, including one-hot encodings, Restricted Boltzmann Machines (RBMs), and ESM2-based protein language model embeddings, for predicting intra-family specificity labels from limited supervision. By using train/test splits that explicitly reduce phylogenetic leakage, we show that ESM2-based representations do not systematically outperform family-specific RBM embeddings or even simple one-hot baselines in this regime. Second, we use the inferred annotations to train an annotation-aware RBM capable of generating artificial homologs conditioned on prescribed labels. Across several protein families, we quantify how the number and quality of available labels determine the reliability of conditional generation. Our results show that scarce annotations can support label-aware protein design when they are accurately propagated, while also highlighting the importance of phylogeny-aware evaluation for assessing functional annotation methods within homologous families.

q-bio.QM↗

arXiv2025

Fast training and sampling of Restricted Boltzmann Machines

Restricted Boltzmann Machines (RBMs) are powerful tools for modeling complex systems and extracting insights from data, but their training is hindered by the slow mixing of Markov Chain Monte Carlo (MCMC) processes, especially with highly structured datasets. In this study, we build on recent theoretical advances in RBM training and focus on the stepwise encoding of data patterns into singular vectors of the coupling matrix, significantly reducing the cost of generating new samples and evaluating the quality of the model, as well as the training cost in highly clustered datasets. The learning process is analogous to the thermodynamic continuous phase transitions observed in ferromagnetic models, where new modes in the probability measure emerge in a continuous manner. We leverage the continuous transitions in the training process to define a smooth annealing trajectory that enables reliable and computationally efficient log-likelihood estimates. This approach enables online assessment during training and introduces a novel sampling strategy called Parallel Trajectory Tempering (PTT) that outperforms previously optimized MCMC methods. To mitigate the critical slowdown effect in the early stages of training, we propose a pre-training phase. In this phase, the principal components are encoded into a low-rank RBM through a convex optimization process, facilitating efficient static Monte Carlo sampling and accurate computation of the partition function. Our results demonstrate that this pre-training strategy allows RBMs to efficiently handle highly structured datasets where conventional methods fail. Additionally, our log-likelihood estimation outperforms computationally intensive approaches in controlled scenarios, while the PTT algorithm significantly accelerates MCMC processes compared to conventional methods.

cs.LG↗

arXiv2025

adabmDCA 2.0 -- a flexible but easy-to-use package for Direct Coupling Analysis

In this methods article, we provide a flexible but easy-to-use implementation of Direct Coupling Analysis (DCA) based on Boltzmann machine learning, together with a tutorial on how to use it. The package \texttt{adabmDCA 2.0} is available in different programming languages (C++, Julia, Python) usable on different architectures (single-core and multi-core CPU, GPU) using a common front-end interface. In addition to several learning protocols for dense and sparse generative DCA models, it allows to directly address common downstream tasks like residue-residue contact prediction, mutational-effect prediction, scoring of sequence libraries and generation of artificial sequences for sequence design. It is readily applicable to protein and RNA sequence data.

q-bio.QM↗

arXiv2024

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 on 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 four different types of data: handwritten digits, mutations of human genomes classified by continental origin, functionally characterized sequences of an enzyme protein family, and homologous RNA sequences from specific taxonomies.

cs.LG↗

arXiv2023

Unsupervised hierarchical clustering using the learning dynamics of RBMs

Datasets in the real world are often complex and to some degree hierarchical, with groups and sub-groups of data sharing common characteristics at different levels of abstraction. Understanding and uncovering the hidden structure of these datasets is an important task that has many practical applications. To address this challenge, we present a new and general method for building relational data trees by exploiting the learning dynamics of the Restricted Boltzmann Machine (RBM). Our method is based on the mean-field approach, derived from the Plefka expansion, and developed in the context of disordered systems. It is designed to be easily interpretable. We tested our method in an artificially created hierarchical dataset and on three different real-world datasets (images of digits, mutations in the human genome, and a homologous family of proteins). The method is able to automatically identify the hierarchical structure of the data. This could be useful in the study of homologous protein sequences, where the relationships between proteins are critical for understanding their function and evolution.

cs.LG↗