Publications

See also my Google Scholar profile. ^* denotes equal contribution.

2026

Machine learning for RNA-targeting drug design

Wissam Karroucha, Carlos Oliver, Véronique Stoven, Vincent Mallet

Journal of Chemical Information and Modeling

paper preprint

Learning dynamic protein representations at scale with distograms

Nicolas Portal, Wissam Karroucha, Vincent Mallet^*, Massimiliano Bonomi^*

ICLR Workshop on Learning Meaningful Representations of Life (LMRL)

preprint

AlphaSurf: on-the-fly surface computations for protein representation learning

Victor Gertner, Frédéric Cazals, Vincent Mallet

ICLR Workshop on Learning Meaningful Representations of Life (LMRL)

paper

2025

Structure-based RNA drug discovery with deep-learning assisted virtual screening

Juan Guillermo Carvajal Patiño^*, Vincent Mallet^*, David Becerra, Luis Fernando Niño, Carlos Oliver, Jérôme Waldispühl

Nature Communications

paper code

InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep

Fabien Mareuil, Rachel Torchet, Luis Checa Ruano, Vincent Mallet, Michael Nilges, Guillaume Bouvier, Olivier Sperandio

Nucleic Acids Research

paper

Finding antibodies in cryo-EM maps with CrAI

Vincent Mallet, Chiara Rapisarda, Hervé Minoux, Maks Ovsjanikov

Bioinformatics

paper code

AtomSurf: surface representation for learning on protein structures

Vincent Mallet^*, Souhaib Attaiki^*, Yangyang Miao^*, Bruno Correia, Maks Ovsjanikov

International Conference on Learning Representations (ICLR)

paper code

A comprehensive library for RNA structure-function modeling

Luis Wyss^*, Vincent Mallet^*, Wissam Karroucha^*, Karsten Borgwardt, Carlos Oliver

ICLR Workshop on AI for Nucleic Acids (AI4NA)

preprint code

2024

AlignScape, displaying sequence similarity using self-organizing maps

Isaac Filella-Merce, Vincent Mallet, Eric Durand, Michael Nilges, Guillaume Bouvier, Riccardo Pellarin

Frontiers in Bioinformatics

paper code

2022

InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions

Vincent Mallet, Luis Checa Ruano, Alexandra Moine Franel, Michael Nilges, Karen Druart, Guillaume Bouvier, Olivier Sperandio

Bioinformatics

paper code

RNAglib: a Python package for RNA 2.5D graphs

Vincent Mallet, Carlos Oliver, Jonathan Broadbent, William L. Hamilton, Jérôme Waldispühl

Bioinformatics

paper code docs pip

VeRNAl: a tool for mining fuzzy network motifs in RNA

Carlos Oliver^*, Vincent Mallet^*, Pericles Philippopoulos, William L. Hamilton, Jérôme Waldispühl

Bioinformatics

paper code

Approximate network motif mining via graph learning

Carlos Oliver, Dexiong Chen, Vincent Mallet, Pericles Philippopoulos, Karsten Borgwardt

arXiv

preprint

2021

quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories

Vincent Mallet, Michael Nilges, Guillaume Bouvier

Bioinformatics

paper code pip

Reverse-complement equivariant networks for DNA sequences

Vincent Mallet, Jean-Philippe Vert

Advances in Neural Information Processing Systems (NeurIPS)

paper code pip

2020

OptiMol: optimization of binding affinities in chemical space for drug discovery

Jacques Boitreaud^*, Vincent Mallet^*, Carlos Oliver, Jérôme Waldispühl

Journal of Chemical Information and Modeling

paper code

Augmented base pairing networks encode RNA-small molecule binding preferences

Carlos Oliver, Vincent Mallet, Roman Sarrazin Gendron, Vladimir Reinharz, William L. Hamilton, Nicolas Moitessier, Jérôme Waldispühl

Nucleic Acids Research

paper code

2019

Leveraging binding-site structure for drug discovery with point-cloud methods

Vincent Mallet, Carlos G. Oliver, Nicolas Moitessier, Jérôme Waldispühl

arXiv

preprint