285 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Génomique Bioinformatique et ApplicationsFR8 papers
- Centre de Bio-InformatiqueFR6 papers
- École Normale Supérieure - PSLFR5 papers
- Département de mathématiques et applicationsFR4 papers
- Greater Boston Interfaith OrganizationUS4 papers
- École Nationale Supérieure des Mines de ParisFR3 papers
- Université Paris Sciences et LettresFR3 papers
- Hôpital Saint-MichelFR2 papers
- InsermFR2 papers
- Institut CurieFR2 papers
- Institut national de recherche en sciences et technologies du numériqueFR2 papers
- Laboratoire d'Informatique Gaspard-MongeFR2 papers
17 papers
A note on a resampling procedure for estimating the density at a given quantile
Beatriz Farah, Aurélien Latouche, Olivier Bouaziz
In this paper we refine the procedure proposed by Lin et al. (2015) to estimate the density at a given quantile based on a resampling method. The approach consists on generating mu…
MIPHEI-ViT: Multiplex Immunofluorescence Prediction from H&E Images using ViT Foundation Models
Guillaume Balezo, Roger Trullo, Albert Pla Planas +2
Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tis…
Interpretable Embeddings for Segmentation-Free Single-Cell Analysis in Multiplex Imaging
Simon Gutwein, Daria Lazic, Thomas Walter +2
Multiplex Imaging (MI) enables the simultaneous visualization of multiple biological markers in separate imaging channels at subcellular resolution, providing valuable insights int…
Local intrinsic dimensionality estimators based on concentration of measure
Jonathan Bac, Andrei Zinovyev
Intrinsic dimensionality (ID) is one of the most fundamental characteristics of multi-dimensional data point clouds. Knowing ID is crucial to choose the appropriate machine learnin…
Robust Seriation and Applications to Cancer Genomics
Antoine Recanati, Nicolas Servant, Jean-Philippe Vert +1
The seriation problem seeks to reorder a set of elements given pairwise similarity information, so that elements with higher similarity are closer in the resulting sequence. When a…
DropLasso: A robust variant of Lasso for single cell RNA-seq data
Beyrem Khalfaoui, Jean-Philippe Vert
Single-cell RNA sequencing (scRNA-seq) is a fast growing approach to measure the genome-wide transcriptome of many individual cells in parallel, but results in noisy data with many…
WHInter: A Working set algorithm for High-dimensional sparse second order Interaction models
Marine Le Morvan, Jean-Philippe Vert
Learning sparse linear models with two-way interactions is desirable in many application domains such as genomics. l1-regularised linear models are popular to estimate sparse model…
The Weighted Kendall and High-order Kernels for Permutations
Yunlong Jiao, Jean-Philippe Vert
We propose new positive definite kernels for permutations. First we introduce a weighted version of the Kendall kernel, which allows to weight unequally the contributions of differ…
Supervised Quantile Normalisation
Marine Le Morvan, Jean-Philippe Vert
Quantile normalisation is a popular normalisation method for data subject to unwanted variations such as images, speech, or genomic data. It applies a monotonic transformation to t…
Network-Guided Biomarker Discovery
Chloé-Agathe Azencott
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a biological system is a key element of precision medicine. Indeed it allows to tailor diagnost…
Dynamic read mapping and online consensus calling for better variant detection
Karel Břinda, Valentina Boeva, Gregory Kucherov
Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, e…
Tight convex relaxations for sparse matrix factorization
Emile Richard, Guillaume Obozinski, Jean-Philippe Vert
Based on a new atomic norm, we propose a new convex formulation for sparse matrix factorization problems in which the number of nonzero elements of the factors is assumed fixed and…
The group fused Lasso for multiple change-point detection
Kevin Bleakley, Jean-Philippe Vert
We present the group fused Lasso for detection of multiple change-points shared by a set of co-occurring one-dimensional signals. Change-points are detected by approximating the or…
Increasing stability and interpretability of gene expression signatures
Anne-Claire Haury, Laurent Jacob, Jean-Philippe Vert
Motivation : Molecular signatures for diagnosis or prognosis estimated from large-scale gene expression data often lack robustness and stability, rendering their biological interpr…
Joint segmentation of many aCGH profiles using fast group LARS
Kevin Bleakley, Jean-Philippe Vert
Array-Based Comparative Genomic Hybridization (aCGH) is a method used to search for genomic regions with copy numbers variations. For a given aCGH profile, one challenge is to accu…
Clustered Multi-Task Learning: A Convex Formulation
Laurent Jacob, Francis Bach, Jean-Philippe Vert
In multi-task learning several related tasks are considered simultaneously, with the hope that by an appropriate sharing of information across tasks, each task may benefit from the…
The optimal assignment kernel is not positive definite
Jean-Philippe Vert
We prove that the optimal assignment kernel, proposed recently as an attempt to embed labeled graphs and more generally tuples of basic data to a Hilbert space, is in fact not alwa…