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Glycan classification with tree kernels.

Yoshihiro Yamanishi , Francis Bach , Jean-Philippe Vert
Bioinformatics, 2007, 23 (10), pp.1211-6. ⟨10.1093/bioinformatics/btm090⟩
Article dans une revue hal-00433576v1
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The Kendall and Mallows Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
2016
Pré-publication, Document de travail hal-01279273v2
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WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models.

Marine Le Morvan , Jean-Philippe Vert
35th International Conference on Machine Learning, Jul 2018, Stockholm, Sweden. pp.3635--3644
Communication dans un congrès hal-01711018v1
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Epitope prediction improved by multitask support vector machines

Laurent Jacob , Jean-Philippe Vert
2007
Autre publication scientifique hal-00129062v1
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Relating Leverage Scores and Density using Regularized Christoffel Functions

Edouard Pauwels , Francis Bach , Jean-Philippe Vert
32nd Conference on Neural Information Processing Systems (NIPS 2018), Dec 2018, Montréal, Canada. pp.1-21
Communication dans un congrès hal-01796591v2
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The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures

Anne-Claire Haury , Pierre Gestraud , Jean-Philippe Vert
PLoS ONE, 2011, pp.6(12): e28210. ⟨10.1371/journal.pone.0028210⟩
Article dans une revue hal-00559580v2

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

Ferhat Ay , Evelien M. Bunnik , Nelle Varoquaux , Jean-Philippe Vert , William Stafford Noble , et al.
BioEssays, 2015, 37 (2), pp.182-194. ⟨10.1002/bies.201400145⟩
Article dans une revue hal-01246696v1
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Joint segmentation of many aCGH profiles using fast group LARS

Kevin Bleakley , Jean-Philippe Vert
2009
Pré-publication, Document de travail hal-00422430v1
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Phi-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays

Laurent Guyon , Christian Lajaunie , Frédéric Fer , Ricky Bhajun , Eric Sulpice , et al.
Scientific Reports, 2015, 5 (14221), ⟨10.1038/srep14221⟩
Article dans une revue hal-01246683v1

Changes in gene expression control by DNA methylation in cancer

Matahi Moarii , Valentina Boeva , Jean-Philippe Vert , Fabien Reyal
BMC Genomics, 2015, 16 (873), ⟨10.1186/s12864-015-1994-2⟩
Article dans une revue hal-01246674v1

Tight convex relaxations for sparse matrix factorization

Emile Richard , Guillaume Obozinski , Jean-Philippe Vert
Neural Information Processing Systems, Dec 2014, Montreal, Canada. pp.3284-3292
Communication dans un congrès hal-01101878v1

Inference of genome 3D architecture by modeling overdispersion of Hi-C data

Nelle Varoquaux , William Noble , Jean-Philippe Vert
2021
Pré-publication, Document de travail hal-03375900v1

Reverse-Complement Equivariant Networks for DNA Sequences

Vincent Mallet , Jean-Philippe Vert
2022
Pré-publication, Document de travail hal-03510326v1

The Kendall and Mallows Kernels for Permutations

Yunlong Jiao , Jean-Philippe Vert
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2018, 40 (7), pp.1755-1769. ⟨10.1109/TPAMI.2017.2719680⟩
Article dans une revue hal-01679012v1

Supervised reconstruction of biological networks with local models.

Kevin Bleakley , Gérard Biau , Jean-Philippe Vert
Bioinformatics, 2007, 23 (13), pp.i57-65. ⟨10.1093/bioinformatics/btm204⟩
Article dans une revue hal-00433575v1

Classification of microarray data using gene networks.

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
BMC Bioinformatics, 2007, 8, pp.35. ⟨10.1186/1471-2105-8-35⟩
Article dans une revue hal-00433577v1
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Spectral analysis of gene expression profiles using gene networks

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert
2006
Pré-publication, Document de travail hal-00021785v1
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Classification of arrayCGH data using fused SVM.

Franck Rapaport , Emmanuel Barillot , Jean-Philippe Vert
Bioinformatics, 2008, 24 (13), pp.i375-82. ⟨10.1093/bioinformatics/btn188⟩
Article dans une revue inserm-00293893v1
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ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

Fantine Mordelet , Jean-Philippe Vert
2011
Pré-publication, Document de travail hal-00594774v1

Large-scale machine learning for metagenomics sequence classification

Kevin Vervier , Pierre Mahé , Maud Tourmoud , Jean-Baptiste Veyrieras , Jean-Philippe Vert
Bioinformatics, 2016, 32 (7), pp.1023-32
Article dans une revue hal-01420829v1

Support vector machine prediction of signal peptide cleavage site using a new class of kernels for strings.

Jean-Philippe Vert
Pacific Symposium on Biocomputing, 2002, pp.649-60
Article dans une revue hal-00433593v1
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A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction.

Brice Hoffmann , Mikhail Zaslavskiy , Jean-Philippe Vert , Véronique Stoven
BMC Bioinformatics, 2010, 11 (1), pp.99. ⟨10.1186/1471-2105-11-99⟩
Article dans une revue inserm-00663528v1
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Metric learning pairwise kernel for graph inference

Jean-Philippe Vert , Jian Qiu , William Noble
2006
Pré-publication, Document de travail hal-00108477v1

A new pairwise kernel for biological network inference with support vector machines.

Jean-Philippe Vert , Jian Qiu , William S Noble
BMC Bioinformatics, 2007, 8 Suppl 10, pp.S8. ⟨10.1186/1471-2105-8-S10-S8⟩
Article dans une revue hal-00433573v1
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kernelPSI: a Post-Selection Inference Framework for Nonlinear Variable Selection

Lotfi Slim , Clement Chatelain , Chloé-Agathe Azencott , Jean-Philippe Vert
36th International Conference on Machine Learning (ICML 2019), Jun 2019, Long Beach, CA, United States
Communication dans un congrès hal-02441304v1
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Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis

Felix Raimundo , Celine Vallot , Jean-Philippe Vert
Genome Biology, 2020, 21 (1), pp.212. ⟨10.1186/s13059-020-02128-7⟩
Article dans une revue hal-02945105v1

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

Ferhat Ay , Evelien M. Bunnik , Nelle Varoquaux , Sebastiaan M. Bol , Jacques Prudhomme , et al.
Genome Research, 2014, 24, pp.974-988. ⟨10.1101/gr.169417.113⟩
Article dans une revue hal-01101873v1
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Tight convex relaxations for sparse matrix factorization

Emile Richard , Guillaume Obozinski , Jean-Philippe Vert
2014
Pré-publication, Document de travail hal-01025959v3

An accurate and interpretable model for siRNA efficacy prediction.

Jean-Philippe Vert , Nicolas Foveau , Christian Lajaunie , Yves Vandenbrouck
BMC Bioinformatics, 2006, 7, pp.520. ⟨10.1186/1471-2105-7-520⟩
Article dans une revue hal-00433579v1

A general and flexible method for signal extraction from single-cell RNA-seq data

Davide Risso , Fanny Perraudeau , Svetlana Gribkova , Sandrine Dudoit , Jean-Philippe Vert
Nature Communications, 2018, 9 (1)
Article dans une revue hal-01985432v1