Leveraging binding-site structure for drug discovery with point-cloud methods. - Vincent Mallet; Carlos G. Oliver; Nicolas Moitessier; Jérôme Waldispühl (CoRR, 2019)

OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery. - Jacques Boitreaud; Vincent Mallet; Carlos G. Oliver; Jérôme Waldispühl (J. Chem. Inf. Model., 2020)

Reverse-Complement Equivariant Networks for DNA Sequences. - Vincent Mallet; Jean-Philippe Vert (NeurIPS, 2021)

Edge-similarity-aware Graph Neural Networks. - Vincent Mallet; Carlos G. Oliver; William L. Hamilton (CoRR, 2021)

RNAglib: a python package for RNA 2.5 D graphs. - Vincent Mallet; Carlos G. Oliver; Jonathan Broadbent; William L. Hamilton; Jérôme Waldispühl (Bioinform., 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 (Bioinform., 2022)

Vernal: a tool for mining fuzzy network motifs in RNA. - Carlos G. Oliver; Vincent Mallet; Pericles Philippopoulos; William L. Hamilton; Jérôme Waldispühl (Bioinform., 2022)

Approximate Network Motif Mining Via Graph Learning. - Carlos G. Oliver; Dexiong Chen; Vincent Mallet; Pericles Philippopoulos; Karsten M. Borgwardt (CoRR, 2022)

Geometric deep learning for structural bioinformatics. (Apprentissage profond géométrique pour la bioinformatique structurale). - Vincent Mallet (2022)

AtomSurf : Surface Representation for Learning on Protein Structures. - Vincent Mallet; Souhaib Attaiki; Maks Ovsjanikov (CoRR, 2023)

3D-based RNA function prediction tools in rnaglib. - Carlos G. Oliver; Vincent Mallet; Jérôme Waldispühl (CoRR, 2024)

AlignScape, displaying sequence similarity using self-organizing maps. - Isaac Filella-Merce; Vincent Mallet; Eric Durand; Michael Nilges; Guillaume Bouvier; Riccardo Pellarin (Frontiers Bioinform., 2024)

AI-Driven Identification of Subclinical Alcohol Use Disorder in Type 2 Diabetes Patients. - Melissa Larbi; Edouard Audit; Joël Chavas; Simplice Donfack; Vincent Mallet (AIME (2), 2025)

AtomSurf: Surface Representation for Learning on Protein Structures. - Vincent Mallet; Yangyang Miao; Souhaib Attaiki; Bruno Correia; Maks Ovsjanikov (ICLR, 2025)

A Comprehensive Benchmark for RNA 3D Structure-Function Modeling. - Luis Wyss; Vincent Mallet; Wissam Karroucha; Karsten M. Borgwardt; Carlos G. Oliver (CoRR, 2025)