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Metric learning pairwise kernel for graph inference

Jean-Philippe Vert , Jian Qiu , William Noble
Preprints, Working Papers, ... hal-00108477v1
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Joseph Boyd , Zelia Gouveia , Franck Perez , Thomas Walter
2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Apr 2020, Iowa City, United States. pp.886-890, ⟨10.1109/ISBI45749.2020.9098696⟩
Conference papers hal-02976141v1
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Statistical methods for deciphering intra-tumor hereterogeneity : challenges and opportunities for cancer clinical management

Judith Abecassis
Bioinformatics [q-bio.QM]. Université Paris sciences et lettres, 2020. English. ⟨NNT : 2020UPSLM065⟩
Theses tel-03228677v1
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Bioimage Informatics for Phenomics

Thomas Walter
Bioinformatics [q-bio.QM]. Sorbonne Université, 2020
Habilitation à diriger des recherches tel-02981391v1

Stability-based comparison of class discovery methods for DNA copy number profiles.

Isabel Brito , Philippe Hupé , Pierre Neuvial , Emmanuel Barillot
PLoS ONE, 2012, 8 (12), pp.e81458
Journal articles hal-01201580v1
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SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

Bruno Zeitouni , Valentina Boeva , Isabelle Janoueix-Lerosey , Sophie Loeillet , Patricia Legoix-Né , et al.
Bioinformatics Application note, 2010, 26 (15), pp.1895-1896. ⟨10.1093/bioinformatics/btq293⟩
Journal articles inserm-00508372v1

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⟩
Journal articles hal-00433573v1

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⟩
Journal articles 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⟩
Journal articles hal-00433577v1

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⟩
Journal articles hal-00433579v1
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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⟩
Journal articles 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
Preprints, Working Papers, ... hal-00594774v1
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RNF: a general framework to evaluate NGS read mappers

Karel Brinda , Valentina Boeva , Gregory Kucherov
Bioinformatics, 2016, 32 (1), pp.136-139. ⟨10.1093/bioinformatics/btv524⟩
Journal articles hal-01220199v2

Proceedings of the 7th European Conference on Python in Science (EuroSciPy 2014)

Pierre de Buyl , Nelle Varoquaux
Books hal-01584599v1
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Qualitative dynamics semantics for SBGN process description

Adrien Rougny , Christine Froidevaux , Laurence Calzone , Loïc Paulevé
BMC Systems Biology, 2016, ⟨10.1186/s12918-016-0285-0⟩
Journal articles hal-01332679v1
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi , Céline Hernandez , Nicolas Levy , Gautier Stoll , Pedro Monteiro , et al.
Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩
Journal articles hal-01794294v2
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Tight convex relaxations for sparse matrix factorization

Emile Richard , Guillaume Obozinski , Jean-Philippe Vert
Preprints, Working Papers, ... hal-01025959v3

Learning with Minimal Effort: Leveraging in Silico Labeling for Cell and Nucleus Segmentation

Thomas Bonte , Maxence Philbert , Emeline Coleno , Edouard Bertrand , Arthur Imbert , et al.
ECCV 2022 Workshops. Lecture Notes in Computer Science, 13804, Springer Nature Switzerland, pp.423-436, 2023, Lecture Notes in Computer Science, 978-3-031-25068-2. ⟨10.1007/978-3-031-25069-9_28⟩
Proceedings hal-04029154v1
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Scaling ResNets in the Large-depth Regime

Pierre Marion , Adeline Fermanian , Gérard Biau , Jean-Philippe Vert
Preprints, Working Papers, ... hal-03697725v1
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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⟩
Journal articles inserm-00663528v1
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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
Conference papers hal-02441304v1

Comparing phylogenetic and statistical classification methods for DNA barcoding

Frédéric Austerlitz , Olivier David , Brigitte Schaeffer , Kevin Bleakley , Madalina Olteanu , et al.
In Second International Barcode of Life Conference. Consortium for the Barcode of Life, Sep 2007, Taipei, Taiwan
Conference papers hal-02757822v1

Efficient multi-task chemogenomics for drug specificity prediction

Benoit Playe , Chloé-Agathe Azencott , Véronique Stoven
PLoS ONE, 2018, 13 (10), pp.e0204999. ⟨10.1371/journal.pone.0204999⟩
Journal articles hal-01984828v1

Segmentation of Nuclei in Histopathology Images by deep regression of the distance map

Peter Naylor , Marick Lae , Fabien Reyal , Thomas Walter
IEEE Transactions on Medical Imaging, 2018, pp.1-12
Journal articles hal-01984033v1

Protein-ligand interaction prediction: an improved chemogenomics approach.

Laurent Jacob , Jean-Philippe Vert
Bioinformatics, 2008, 24 (19), pp.2149-56. ⟨10.1093/bioinformatics/btn409⟩
Journal articles hal-00433572v1
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Near neighbor search in nonmetric space

Joannès Vermorel
Preprints, Working Papers, ... hal-00004887v2
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Multiresolution Kernels

Marco Cuturi , Kenji Fukumizu
Preprints, Working Papers, ... hal-00007489v2

Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data

Héctor Climente-González , Chloé-Agathe Azencott , Samuel Kaski , Makoto Yamada
Bioinformatics, 2019, 35 (14), ⟨10.1093/bioinformatics/btz333⟩
Journal articles hal-02072349v1
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Asymptotic Results on Adaptive False Discovery Rate Controlling Procedures Based on Kernel Estimators

Pierre Neuvial
Journal of Machine Learning Research, 2013, 14, pp.1423-1459
Journal articles hal-00460677v2

Spatial transcriptomics for respiratory research and medicine

Sandra Curras-Alonso , Juliette Soulier , Thomas Walter , Florian Mueller , Arturo Londoño-Vallejo , et al.
European Respiratory Journal, 2021, 58 (1), pp.2004314. ⟨10.1183/13993003.04314-2020⟩
Journal articles hal-03633353v1