Jean-Philippe Vert

ORCID

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 45

Top Venues

Publications

Nelle Varoquaux, William S. Noble, Jean-Philippe Vert
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. Bioinform. 39 (1) (2023)
Lawrence Stewart, Francis R. Bach, Quentin Berthet, Jean-Philippe Vert
Regression as Classification: Influence of Task Formulation on Neural Network Features. AISTATS (2023)
Mathieu Blondel, Quentin Berthet, Marco Cuturi, Roy Frostig, Stephan Hoyer, Felipe Llinares-López, Fabian Pedregosa, Jean-Philippe Vert
Efficient and Modular Implicit Differentiation. NeurIPS (2022)
Lawrence Stewart, Francis R. Bach, Quentin Berthet, Jean-Philippe Vert
Regression as Classification: Influence of Task Formulation on Neural Network Features. CoRR (2022)
Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble
Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning. J. Comput. Biol. 29 (11) (2022)
Luigi Carratino, Moustapha Cissé, Rodolphe Jenatton, Jean-Philippe Vert
On Mixup Regularization. J. Mach. Learn. Res. 23 (2022)
Pierre Marion, Adeline Fermanian, Gérard Biau, Jean-Philippe Vert
Scaling ResNets in the Large-depth Regime. CoRR (2022)
Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble
Semi-supervised Single-Cell Cross-modality Translation Using Polarbear. RECOMB (2022)
Vincent Mallet, Jean-Philippe Vert
Reverse-Complement Equivariant Networks for DNA Sequences. NeurIPS (2021)
Mathieu Blondel, Arthur Mensch, Jean-Philippe Vert
Differentiable Divergences Between Time Series. AISTATS (2021)
Adeline Fermanian, Pierre Marion, Jean-Philippe Vert, Gérard Biau
Framing RNN as a kernel method: A neural ODE approach. NeurIPS (2021)
Mathieu Blondel, Quentin Berthet, Marco Cuturi, Roy Frostig, Stephan Hoyer, Felipe Llinares-López, Fabian Pedregosa, Jean-Philippe Vert
Efficient and Modular Implicit Differentiation. CoRR (2021)
Adeline Fermanian, Pierre Marion, Jean-Philippe Vert, Gérard Biau
Framing RNN as a kernel method: A neural ODE approach. CoRR (2021)
Marco Cuturi, Olivier Teboul, Jonathan Niles-Weed, Jean-Philippe Vert
Supervised Quantile Normalization for Low-rank Matrix Approximation. CoRR (2020)
Marco Cuturi, Olivier Teboul, Jonathan Niles-Weed, Jean-Philippe Vert
Supervised Quantile Normalization for Low Rank Matrix Factorization. ICML (2020)
Marco Cuturi, Olivier Teboul, Jean-Philippe Vert
Noisy Adaptive Group Testing using Bayesian Sequential Experimental Design. CoRR (2020)
Luigi Carratino, Moustapha Cissé, Rodolphe Jenatton, Jean-Philippe Vert
On Mixup Regularization. CoRR (2020)
Pierre-Cyril Aubin-Frankowski, Jean-Philippe Vert
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference. Bioinform. 36 (18) (2020)
Quentin Berthet, Mathieu Blondel, Olivier Teboul, Marco Cuturi, Jean-Philippe Vert, Francis R. Bach
Learning with Differentiable Perturbed Optimizers. CoRR (2020)
Quentin Berthet, Mathieu Blondel, Olivier Teboul, Marco Cuturi, Jean-Philippe Vert, Francis R. Bach
Learning with Differentiable Pertubed Optimizers. NeurIPS (2020)
Mathieu Blondel, Arthur Mensch, Jean-Philippe Vert
Differentiable Divergences Between Time Series. CoRR (2020)
Imke Mayer, Julie Josse, Félix Raimundo, Jean-Philippe Vert
MissDeepCausal: Causal Inference from Incomplete Data Using Deep Latent Variable Models. CoRR (2020)
Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble
Jointly Embedding Multiple Single-Cell Omics Measurements. WABI (2019)
Olivier Collier, Véronique Stoven, Jean-Philippe Vert
LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes. PLoS Comput. Biol. 15 (9) (2019)
Beyrem Khalfaoui, Joseph Boyd, Jean-Philippe Vert
ASNI: Adaptive Structured Noise Injection for shallow and deep neural networks. CoRR (2019)
Marco Cuturi, Olivier Teboul, Jean-Philippe Vert
Differentiable Ranking and Sorting using Optimal Transport. NeurIPS (2019)
Romain Menegaux, Jean-Philippe Vert
Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics. J. Comput. Biol. 26 (6) (2019)
Marco Cuturi, Olivier Teboul, Jean-Philippe Vert
Differentiable Sorting using Optimal Transport: The Sinkhorn CDF and Quantile Operator. CoRR (2019)
Gabriel Dulac-Arnold, Neil Zeghidour, Marco Cuturi, Lucas Beyer, Jean-Philippe Vert
Deep multi-class learning from label proportions. CoRR (2019)
Alexandra Gesine Cauer, Gürkan Yardimci, Jean-Philippe Vert, Nelle Varoquaux, William Stafford Noble
Inferring Diploid 3D Chromatin Structures from Hi-C Data. WABI (2019)
Lotfi Slim, Clément Chatelain, Chloé-Agathe Azencott, Jean-Philippe Vert
kernelPSI: a Post-Selection Inference Framework for Nonlinear Variable Selection. ICML (2019)
Aude Genevay, Gabriel Dulac-Arnold, Jean-Philippe Vert
Differentiable Deep Clustering with Cluster Size Constraints. CoRR (2019)
Edouard Pauwels, Francis R. Bach, Jean-Philippe Vert
Relating Leverage Scores and Density using Regularized Christoffel Functions. NeurIPS (2018)
Yunlong Jiao, Jean-Philippe Vert
The Kendall and Mallows Kernels for Permutations. IEEE Trans. Pattern Anal. Mach. Intell. 40 (7) (2018)
Marine Le Morvan, Jean-Philippe Vert
WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models. CoRR (2018)
Beyrem Khalfaoui, Jean-Philippe Vert
DropLasso: A robust variant of Lasso for single cell RNA-seq data. CoRR (2018)
Nicolas Servant, Nelle Varoquaux, Edith Heard, Emmanuel Barillot, Jean-Philippe Vert
Effective normalization for copy number variation in Hi-C data. BMC Bioinform. 19 (1) (2018)
Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu, Jean-Philippe Vert
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. BMC Bioinform. (1) (2018)
Marine Le Morvan, Jean-Philippe Vert
WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models. ICML (2018)
Yunlong Jiao, Jean-Philippe Vert
The Weighted Kendall and High-order Kernels for Permutations. ICML (2018)
Edouard Pauwels, Francis R. Bach, Jean-Philippe Vert
Relating Leverage Scores and Density using Regularized Christoffel Functions. CoRR (2018)
Yunlong Jiao, Jean-Philippe Vert
The Weighted Kendall and High-order Kernels for Permutations. CoRR (2018)
Marine Le Morvan, Jean-Philippe Vert
Supervised Quantile Normalisation. CoRR (2017)
Marine Le Morvan, Andrei Yu. Zinovyev, Jean-Philippe Vert
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. PLoS Comput. Biol. 13 (6) (2017)
Kevin Vervier, Pierre Mahé, Maud Tournoud, Jean-Baptiste Veyrieras, Jean-Philippe Vert
Large-scale machine learning for metagenomics sequence classification. Bioinform. 32 (7) (2016)
Alice Schoenauer Sebag, Sandra Plancade, Céline Raulet-Tomkiewicz, Robert Barouki, Jean-Philippe Vert, Thomas Walter
Infering an ontology of single cell motions from high-throughput microscopy data. ISBI (2015)
Kevin Vervier, Pierre Mahé, Maud Tournoud, Jean-Baptiste Veyrieras, Jean-Philippe Vert
Large-scale Machine Learning for Metagenomics Sequence Classification. CoRR (2015)
Yunlong Jiao, Jean-Philippe Vert
The Kendall and Mallows Kernels for Permutations. ICML (2015)
Alice Schoenauer Sebag, Sandra Plancade, Céline Raulet-Tomkiewicz, Robert Barouki, Jean-Philippe Vert, Thomas Walter
A generic methodological framework for studying single cell motility in high-throughput time-lapse data. Bioinform. 31 (12) (2015)
Elsa Bernard, Laurent Jacob, Julien Mairal, Eric Viara, Jean-Philippe Vert
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples. BMC Bioinform. 16 (2015)
Kevin Vervier, Pierre Mahé, Jean-Baptiste Veyrieras, Jean-Philippe Vert
Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data. CoRR (2015)
Emile Richard, Guillaume Obozinski, Jean-Philippe Vert
Tight convex relaxations for sparse matrix factorization. NIPS (2014)
Edouard Pauwels, Christian Lajaunie, Jean-Philippe Vert
A Bayesian active learning strategy for sequential experimental design in systems biology. BMC Syst. Biol. 8 (1) (2014)
Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows. Bioinform. 30 (17) (2014)
Emile Richard, Guillaume Obozinski, Jean-Philippe Vert
Tight convex relaxations for sparse matrix factorization. CoRR (2014)
Toby Dylan Hocking, Valentina Boeva, Guillem Rigaill, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Wilfrid Richer, Franck Bourdeaut, Miyuki Suguro, Masao Seto, Francis R. Bach, Jean-Philippe Vert
SegAnnDB: interactive Web-based genomic segmentation. Bioinform. 30 (11) (2014)
Fantine Mordelet, Jean-Philippe Vert
A bagging SVM to learn from positive and unlabeled examples. Pattern Recognit. Lett. 37 (2014)
Kevin Vervier, Pierre Mahé, Alexandre d'Aspremont, Jean-Baptiste Veyrieras, Jean-Philippe Vert
On Learning Matrices with Orthogonal Columns or Disjoint Supports. ECML/PKDD (3) (2014)
Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert
A statistical approach for inferring the 3D structure of the genome. Bioinform. 30 (12) (2014)
Emile Richard, Francis R. Bach, Jean-Philippe Vert
Intersecting singularities for multi-structured estimation. ICML (3) (2013)
Toby Hocking, Guillem Rigaill, Jean-Philippe Vert, Francis R. Bach
Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression. ICML (3) (2013)
Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu, Jean-Philippe Vert
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Bioinform. 29 (17) (2013)
Toby Dylan Hocking, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Valentina Boeva, Julie Cappo, Olivier Delattre, Francis R. Bach, Jean-Philippe Vert
Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinform. 14 (2013)
Anne-Claire Haury, Fantine Mordelet, Paola Vera-Licona, Jean-Philippe Vert
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. BMC Syst. Biol. 6 (2012)
Guillaume Obozinski, Laurent Jacob, Jean-Philippe Vert
Group Lasso with Overlaps: the Latent Group Lasso approach CoRR (2011)
Fantine Mordelet, Jean-Philippe Vert
ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples. BMC Bioinform. 12 (2011)
Tomoko Matsui, Masataka Goto, Jean-Philippe Vert, Yuji Uchiyama
Gradient-based musical feature extraction based on scale-invariant feature transform. EUSIPCO (2011)
Toby Hocking, Jean-Philippe Vert, Francis R. Bach, Armand Joulin
Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties. ICML (2011)
Valentina Boeva, Andrei Yu. Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinform. 27 (2) (2011)
Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert
Many-to-Many Graph Matching: a Continuous Relaxation Approach CoRR (2010)
Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert
Many-to-Many Graph Matching: A Continuous Relaxation Approach. ECML/PKDD (3) (2010)
Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe Vert, Véronique Stoven
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinform. 11 (2010)
Martial Hue, Jean-Philippe Vert
On learning with kernels for unordered pairs. ICML (2010)
Martial Hue, Michael Riffle, Jean-Philippe Vert, William Stafford Noble
Large-scale prediction of protein-protein interactions from structures. BMC Bioinform. 11 (2010)
Jean-Philippe Vert, Kevin Bleakley
Fast detection of multiple change-points shared by many signals using group LARS. NIPS (2010)
Laurent Jacob, Guillaume Obozinski, Jean-Philippe Vert
Group lasso with overlap and graph lasso. ICML (2009)
Jacob D. Abernethy, Francis R. Bach, Theodoros Evgeniou, Jean-Philippe Vert
A New Approach to Collaborative Filtering: Operator Estimation with Spectral Regularization. J. Mach. Learn. Res. 10 (2009)
Marco Cuturi, Jean-Philippe Vert, Alexandre d'Aspremont
White Functionals for Anomaly Detection in Dynamical Systems. NIPS (2009)
Pierre Mahé, Jean-Philippe Vert
Graph kernels based on tree patterns for molecules. Mach. Learn. 75 (1) (2009)
Jean-Philippe Vert, Tomoko Matsui, Shin'ichi Satoh, Yuji Uchiyama
High-level feature extraction using SVM with walk-based graph kernel. ICASSP (2009)
Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert
Global alignment of protein-protein interaction networks by graph matching methods. Bioinform. 25 (12) (2009)
Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert
A Path Following Algorithm for the Graph Matching Problem. IEEE Trans. Pattern Anal. Mach. Intell. 31 (12) (2009)
Jacob D. Abernethy, Theodoros Evgeniou, Olivier Toubia, Jean-Philippe Vert
Eliciting Consumer Preferences Using Robust Adaptive Choice Questionnaires. IEEE Trans. Knowl. Data Eng. 20 (2) (2008)
Fantine Mordelet, Jean-Philippe Vert
SIRENE: supervised inference of regulatory networks. ECCB (2008)
Laurent Jacob, Francis R. Bach, Jean-Philippe Vert
Clustered Multi-Task Learning: A Convex Formulation CoRR (2008)
Tomoko Matsui, Jean-Philippe Vert, Shin'ichi Satoh, Yuji Uchiyama
ISM TRECVID2008 High-level Feature Extraction. TRECVID (2008)
Jean-Philippe Vert
The optimal assignment kernel is not positive definite CoRR (2008)
Francis R. Bach, Jacob D. Abernethy, Jean-Philippe Vert, Theodoros Evgeniou
A New Approach to Collaborative Filtering: Operator Estimation with Spectral Regularization CoRR (2008)
Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert
Classification of arrayCGH data using fused SVM. ISMB (2008)
Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert
A Path Following Algorithm for Graph Matching. ICISP (2008)
Laurent Jacob, Jean-Philippe Vert
Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinform. 24 (3) (2008)
Laurent Jacob, Francis R. Bach, Jean-Philippe Vert
Clustered Multi-Task Learning: A Convex Formulation. NIPS (2008)
Mikhail Zaslavskiy, Francis R. Bach, Jean-Philippe Vert
Path following algorithm for the graph matching problem CoRR (2008)
Laurent Jacob, Jean-Philippe Vert
Protein-ligand interaction prediction: an improved chemogenomics approach. Bioinform. 24 (19) (2008)
Laurent Jacob, Brice Hoffmann, Véronique Stoven, Jean-Philippe Vert
chemogenomics approach. BMC Bioinform. 9 (2008)
Jean-Philippe Vert, Jian Qiu, William Stafford Noble
A new pairwise kernel for biological network inference with support vector machines. BMC Bioinform. 8 (S-10) (2007)
Yoshihiro Yamanishi, Francis R. Bach, Jean-Philippe Vert
Glycan classification with tree kernels. Bioinform. 23 (10) (2007)
Kevin Bleakley, Gérard Biau, Jean-Philippe Vert
Supervised reconstruction of biological networks with local models. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert, William Stafford Noble
A structural alignment kernel for protein structures. Bioinform. 23 (9) (2007)
Pierre Mahé, Jean-Philippe Vert
Virtual screening with support vector machines and structure kernels CoRR (2007)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jean-Philippe Vert