| 2023 | AISTATS | Regression as Classification: Influence of Task Formulation on Neural Network Features. | Lawrence Stewart, Francis R. Bach, Quentin Berthet, Jean-Philippe Vert |
| 2022 | RECOMB | Semi-supervised Single-Cell Cross-modality Translation Using Polarbear. | Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble |
| 2021 | AISTATS | Differentiable Divergences Between Time Series. | Mathieu Blondel, Arthur Mensch, Jean-Philippe Vert |
| 2020 | ICML | Supervised Quantile Normalization for Low Rank Matrix Factorization. | Marco Cuturi, Olivier Teboul, Jonathan Niles-Weed, Jean-Philippe Vert |
| 2019 | ICML | kernelPSI: a Post-Selection Inference Framework for Nonlinear Variable Selection. | Lotfi Slim, Clment Chatelain, Chlo-Agathe Azencott, Jean-Philippe Vert |
| 2019 | WABI | Inferring Diploid 3D Chromatin Structures from Hi-C Data. | Alexandra Gesine Cauer, Grkan Yardimci, Jean-Philippe Vert, Nelle Varoquaux, William Stafford Noble |
| 2019 | WABI | Jointly Embedding Multiple Single-Cell Omics Measurements. | Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble |
| 2018 | ICML | The Weighted Kendall and High-order Kernels for Permutations. | Yunlong Jiao, Jean-Philippe Vert |
| 2018 | ICML | WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models. | Marine Le Morvan, Jean-Philippe Vert |
| 2015 | ICML | The Kendall and Mallows Kernels for Permutations. | Yunlong Jiao, Jean-Philippe Vert |
| 2013 | ICML | Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression. | Toby Hocking, Guillem Rigaill, Jean-Philippe Vert, Francis R. Bach |
| 2013 | ICML | Intersecting singularities for multi-structured estimation. | Emile Richard, Francis R. Bach, Jean-Philippe Vert |
| 2011 | ICML | Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties. | Toby Hocking, Jean-Philippe Vert, Francis R. Bach, Armand Joulin |
| 2010 | ICML | On learning with kernels for unordered pairs. | Martial Hue, Jean-Philippe Vert |
| 2009 | ICASSP | High-level feature extraction using SVM with walk-based graph kernel. | Jean-Philippe Vert, Tomoko Matsui, Shin'ichi Satoh, Yuji Uchiyama |
| 2009 | ICML | Group lasso with overlap and graph lasso. | Laurent Jacob, Guillaume Obozinski, Jean-Philippe Vert |
| 2008 | ECCB | SIRENE: supervised inference of regulatory networks. | Fantine Mordelet, Jean-Philippe Vert |
| 2008 | ICISP | A Path Following Algorithm for Graph Matching. | Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert |
| 2008 | ISMB | Classification of arrayCGH data using fused SVM. | Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert |
| 2007 | ICASSP | A Kernel for Time Series Based on Global Alignments. | Marco Cuturi, Jean-Philippe Vert, ystein Birkenes, Tomoko Matsui |
| 2007 | ISMB | Supervised reconstruction of biological networks with local models. | Kevin Bleakley, Grard Biau, Jean-Philippe Vert |
| 2005 | ISMB | Supervised enzyme network inference from the integration of genomic data and chemical information. | Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa |
| 2004 | ICML | Extensions of marginalized graph kernels. | Pierre Mah, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert |
| 2004 | IJCNN | A mutual information kernel for sequences. | Marco Cuturi, Jean-Philippe Vert |
| 2004 | ISMB | Protein network inference from multiple genomic data: a supervised approach. | Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa |
| 2003 | ECCB | Extracting active pathways from gene expression data. | Jean-Philippe Vert, Minoru Kanehisa |
| 2003 | ISMB | Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. | Yoshihiro Yamanishi, Jean-Philippe Vert, Akihiro Nakaya, Minoru Kanehisa |
| 2002 | ISMB | A tree kernel to analyse phylogenetic profiles. | Jean-Philippe Vert |
| 2002 | PSB | Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings. | Jean-Philippe Vert |
| 2001 | CICLING | Text Categorization Using Adaptive Context Trees. | Jean-Philippe Vert |