Jean-Philippe Vert

According to our database1, Jean-Philippe Vert authored at least 79 papers between 2001 and 2019.

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Bibliography

2019
Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.
Journal of Computational Biology, 2019

kernelPSI: a Post-Selection Inference Framework for Nonlinear Variable Selection.
Proceedings of the 36th International Conference on Machine Learning, 2019

2018
Effective normalization for copy number variation in Hi-C data.
BMC Bioinformatics, 2018

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.
BMC Bioinformatics, 2018

Relating Leverage Scores and Density using Regularized Christoffel Functions.
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models.
Proceedings of the 35th International Conference on Machine Learning, 2018

The Weighted Kendall and High-order Kernels for Permutations.
Proceedings of the 35th International Conference on Machine Learning, 2018

2017
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis.
PLoS Computational Biology, 2017

2016
Large-scale machine learning for metagenomics sequence classification.
Bioinformatics, 2016

2015
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples.
BMC Bioinformatics, 2015

A generic methodological framework for studying single cell motility in high-throughput time-lapse data.
Bioinformatics, 2015

Infering an ontology of single cell motions from high-throughput microscopy data.
Proceedings of the 12th IEEE International Symposium on Biomedical Imaging, 2015

The Kendall and Mallows Kernels for Permutations.
Proceedings of the 32nd International Conference on Machine Learning, 2015

2014
A bagging SVM to learn from positive and unlabeled examples.
Pattern Recognition Letters, 2014

A Bayesian active learning strategy for sequential experimental design in systems biology.
BMC Systems Biology, 2014

A statistical approach for inferring the 3D structure of the genome.
Bioinformatics, 2014

SegAnnDB: interactive Web-based genomic segmentation.
Bioinformatics, 2014

Efficient RNA isoform identification and quantification from RNA-Seq data with network flows.
Bioinformatics, 2014

On Learning Matrices with Orthogonal Columns or Disjoint Supports.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2014

Tight convex relaxations for sparse matrix factorization.
Proceedings of the Advances in Neural Information Processing Systems 27: Annual Conference on Neural Information Processing Systems 2014, 2014

2013
Learning smoothing models of copy number profiles using breakpoint annotations.
BMC Bioinformatics, 2013

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks.
Bioinformatics, 2013

Intersecting singularities for multi-structured estimation.
Proceedings of the 30th International Conference on Machine Learning, 2013

Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression.
Proceedings of the 30th International Conference on Machine Learning, 2013

2012
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.
BMC Systems Biology, 2012

2011
ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples.
BMC Bioinformatics, 2011

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
Bioinformatics, 2011

Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties.
Proceedings of the 28th International Conference on Machine Learning, 2011

Gradient-based musical feature extraction based on scale-invariant feature transform.
Proceedings of the 19th European Signal Processing Conference, 2011

2010
Large-scale prediction of protein-protein interactions from structures.
BMC Bioinformatics, 2010

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction.
BMC Bioinformatics, 2010

Many-to-Many Graph Matching: A Continuous Relaxation Approach.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2010

Fast detection of multiple change-points shared by many signals using group LARS.
Proceedings of the Advances in Neural Information Processing Systems 23: 24th Annual Conference on Neural Information Processing Systems 2010. Proceedings of a meeting held 6-9 December 2010, 2010

On learning with kernels for unordered pairs.
Proceedings of the 27th International Conference on Machine Learning (ICML-10), 2010

2009
A Path Following Algorithm for the Graph Matching Problem.
IEEE Trans. Pattern Anal. Mach. Intell., 2009

Graph kernels based on tree patterns for molecules.
Machine Learning, 2009

A New Approach to Collaborative Filtering: Operator Estimation with Spectral Regularization.
J. Mach. Learn. Res., 2009

Global alignment of protein-protein interaction networks by graph matching methods.
Bioinformatics, 2009

White Functionals for Anomaly Detection in Dynamical Systems.
Proceedings of the Advances in Neural Information Processing Systems 22: 23rd Annual Conference on Neural Information Processing Systems 2009. Proceedings of a meeting held 7-10 December 2009, 2009

Group lasso with overlap and graph lasso.
Proceedings of the 26th Annual International Conference on Machine Learning, 2009

High-level feature extraction using SVM with walk-based graph kernel.
Proceedings of the IEEE International Conference on Acoustics, 2009

2008
Eliciting Consumer Preferences Using Robust Adaptive Choice Questionnaires.
IEEE Trans. Knowl. Data Eng., 2008

Virtual screening of GPCRs: An in silico chemogenomics approach.
BMC Bioinformatics, 2008

Protein-ligand interaction prediction: an improved chemogenomics approach.
Bioinformatics, 2008

Efficient peptide-MHC-I binding prediction for alleles with few known binders.
Bioinformatics, 2008

ISM TRECVID2008 High-level Feature Extraction.
Proceedings of the TRECVID 2008 workshop participants notebook papers, 2008

Clustered Multi-Task Learning: A Convex Formulation.
Proceedings of the Advances in Neural Information Processing Systems 21, 2008

Classification of arrayCGH data using fused SVM.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

A Path Following Algorithm for Graph Matching.
Proceedings of the Image and Signal Processing - 3rd International Conference, 2008

SIRENE: supervised inference of regulatory networks.
Proceedings of the ECCB'08 Proceedings, 2008

2007
A new pairwise kernel for biological network inference with support vector machines.
BMC Bioinformatics, 2007

Classification of microarray data using gene networks.
BMC Bioinformatics, 2007

Glycan classification with tree kernels.
Bioinformatics, 2007

A structural alignment kernel for protein structures.
Bioinformatics, 2007

Supervised reconstruction of biological networks with local models.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

A Kernel for Time Series Based on Global Alignments.
Proceedings of the IEEE International Conference on Acoustics, 2007

2006
Consistency and Convergence Rates of One-Class SVMs and Related Algorithms.
J. Mach. Learn. Res., 2006

The Pharmacophore Kernel for Virtual Screening with Support Vector Machines.
Journal of Chemical Information and Modeling, 2006

An accurate and interpretable model for siRNA efficacy prediction.
BMC Bioinformatics, 2006

Optimizing amino acid substitution matrices with a local alignment kernel.
BMC Bioinformatics, 2006

Classification of Biological Sequences with Kernel Methods.
Proceedings of the Grammatical Inference: Algorithms and Applications, 2006

2005
The context-tree kernel for strings.
Neural Networks, 2005

Semigroup Kernels on Measures.
J. Mach. Learn. Res., 2005

Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines.
Journal of Chemical Information and Modeling, 2005

Consistency of one-class SVM and related algorithms.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005

Kernels for gene regulatory regions.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005

Supervised enzyme network inference from the integration of genomic data and chemical information.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004
Protein homology detection using string alignment kernels.
Bioinformatics, 2004

Supervised Graph Inference.
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004

Semigroup Kernels on Finite Sets.
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004

Protein network inference from multiple genomic data: a supervised approach.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Extensions of marginalized graph kernels.
Proceedings of the Machine Learning, 2004

2003
Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

Extracting active pathways from gene expression data.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002
Support Vector Machine Prediction of Signal Peptide Cleavage Site Using a New Class of Kernels for Strings.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Graph-Driven Feature Extraction From Microarray Data Using Diffusion Kernels and Kernel CCA.
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002

A tree kernel to analyse phylogenetic profiles.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001
Adaptive context trees and text clustering.
IEEE Trans. Information Theory, 2001

Text Categorization Using Adaptive Context Trees.
Proceedings of the Computational Linguistics and Intelligent Text Processing, 2001


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