Julien Chiquet

Total : 96 publications

2026

Article dans une revue

• An integrated method for clustering and association network inference
  Jeanne Tous, Julien Chiquet
  High dimensional Gaussian graphical models provide a rigorous framework to describe a network of statistical dependencies between variables, such as g...
  hal-05625632
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• Overcoming barriers to computational reproducibility
  Roman Hornung, László Németh, Oleksandr Zadorozhnyi, Theresa Ullmann, Michael Kammer, Rebecca Killick, Christopher Paciorek, Julien Chiquet, Moritz Herrmann, Lucija Batinović, Rickard Carlsson, Pierre Neuvial, Boris Hejblum, Julia Wrobel, Anne-Laure Boulesteix, Karsten Tabelow
  Computational reproducibility, the possibility for independent researchers to exactly reproduce published empirical results, is fundamental to science...
  hal-05642924 | ⬇️ Télécharger
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• Learning inherent genetic patterns and trait associations with deep generative models for discrete genotype simulation
  Sihan Xie, Thierry Tribout, Didier Boichard, Blaise Hanczar, Julien Chiquet, Eric Barrey
  Abstract Background Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessi...
  hal-05595894
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2025

Article dans une revue

• Zero-inflation in the multivariate poisson lognormal family
  Bastien Batardière, Julien Chiquet, François Gindraud, Mahendra Mariadassou
  Analyzing high-dimensional count data is a challenge and statistical model-based approaches provide an adequate and efficient framework that preserves...
  hal-05579456
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• Stability Selection and Consensus Clustering in R : The R Package sharp
  Barbara Bodinier, Sabrina Rodrigues, Maryam Karimi, Sarah Filippi, Julien Chiquet, Marc Chadeau-Hyam
  <div><p>The R package sharp (Stability-enHanced Approaches using Resampling Procedures) provides an integrated framework for stability-enhanced variab...
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• Importance sampling-based gradient method for dimension reduction in Poisson log-normal model
  Bastien Batardière, Julien Chiquet, Joon Kwon, Julien Stoehr
  High-dimensional count data poses significant challenges for statistical analysis, necessitating effective methods that also preserve explainability. ...
  hal-04712554 | ⬇️ Télécharger
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Pré-publication, Document de travail

• Deep Generative Models for Discrete Genotype Simulation
  Sihan Xie, Thierry Tribout, Didier Boichard, Blaise Hanczar, Julien Chiquet, Eric Barrey
  Deep generative models for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous st...
  hal-05203813 | ⬇️ Télécharger
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• pyPLNmodels: A Python package to analyze multivariate high-dimensional count data
  Bastien Batardiere, Joon Kwon, Julien Chiquet
  High dimensional count data are complex to analyze as is, and normalization must be performed, but standard normalization does not fit the characteris...
  hal-04738542 | ⬇️ Télécharger
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2024

Pré-publication, Document de travail

• Evaluating Parameter Uncertainty in the Poisson Lognormal Model with Corrected Variational Estimators
  Bastien Batardière, Julien Chiquet, Mahendra Mariadassou
  Count data analysis is essential across diverse fields, from ecology and accident analysis to single-cell RNA sequencing (scRNA-seq) and metagenomics....
  hal-04781942
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• Zero-inflation in the Multivariate Poisson Lognormal Family
  Bastien Batardière, Julien Chiquet, François Gindraud, Mahendra Mariadassou
  Analyzing high-dimensional count data is a challenge and statistical model-based approaches provide an adequate and efficient framework that preserves...
  hal-04586927 | ⬇️ Télécharger
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Logiciel

• pyPLNmodels
  Bastien Batardière, Joon Kwon, Julien Chiquet
  High dimensional count data are complex to analyze as is, and normalization mustbe performed, but standard normalization does not fit the characterist...
  hal-04738553
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Communication dans un congrès

• Zero-inflation in the MPLN Family
  Bastien Batardière, Julien Chiquet, François Gindraud, Mahendra Mariadassou
  Les données de comptage en haute dimension sont difficiles à analyser telles quelles, et les approches basées sur des modèles statistiques restent...
  hal-04738587 | ⬇️ Télécharger
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• A gradient approximation with importance sampling for dimension reduction in natural exponential families
  Bastien Batardière, Julien Chiquet, Joon Kwon, Julien Stoehr
  High-dimensional counting data is challenging to analyze as is, and approaches based on latent variable statistical models remain effective and approp...
  hal-04738600 | ⬇️ Télécharger
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• Benchmarking predictive models: evaluating parametric, ensemble, and deep learning approaches for animal phenotype prediction from genotypes.
  Eric Barrey, Blaise Hanczar, Julien Chiquet, Didier Boichard, Jocelyn de Goër de Herve, Anne Ricard, Thierry Tribout, Joon Kwon, Jean-Benoist Leger, Tristan Mary-Huard, Beatriz Castro Dias Castro Dias Cuyabano, Pascal Croiseau
  Over the past two decades, advancements in DNA genotyping have revolutionized the acquisition of extensive genomic data, essential for enhancing genom...
  hal-04510253 | ⬇️ Télécharger
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2023

Pré-publication, Document de travail

• Finite-sum optimization: Adaptivity to smoothness and loopless variance reduction
  Bastien Batardière, Julien Chiquet, Joon Kwon
  For finite-sum optimization, variance-reduced gradient methods (VR) compute at each iteration the gradient of a single function (or of a mini-batch), ...
  hal-04217357
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• Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq
  Etienne Delannoy, Bastien Batardiere, Stéphanie Pateyron, Ludivine Soubigou-Taconnat, Julien Chiquet, Jean Colcombet, Julien Lang
  Summary Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different proces...
  hal-04186457
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Article dans une revue

• Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq.
  Etienne Delannoy, Bastien Batardiere, Stéphanie Pateyron, Ludivine Soubigou-Taconnat, Julien Chiquet, Jean Colcombet, Julien Lang
  Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different processes are ...
  hal-04194719 | ⬇️ Télécharger
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• Automated calibration for stability selection in penalised regression and graphical models
  Barbara Bodinier, Sarah Filippi, Therese Haugdahl Nøst, Julien Chiquet, Marc Chadeau-Hyam
  Stability selection represents an attractive approach to identify sparse sets of features jointly associated with an outcome in high-dimensional conte...
  hal-04162993 | ⬇️ Télécharger
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• Automated calibration of consensus weighted distance-based clustering approaches using sharp
  Barbara Bodinier, Dragana Vuckovic, Sabrina Rodrigues, Sarah Filippi, Julien Chiquet, Marc Chadeau-Hyam
  Motivation: In consensus clustering, a clustering algorithm is used in combination with a subsampling procedure to detect stable clusters. Previous st...
  hal-04440490 | ⬇️ Télécharger
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2022

Communication dans un congrès

• A Probabilistic Graph Coupling View of Dimension Reduction
  Hugues van Assel, Thibault Espinasse, Julien Chiquet, Franck Picard
  Most popular dimension reduction (DR) methods like t-SNE and UMAP are based on minimizing a cost between input and latent pairwise similarities. Thoug...
  hal-03548776 | ⬇️ Télécharger
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• Multivariate Poisson Lognormal model: optimisation, inference and application to high dimensional data
  Bastien Batardière, Joon Kwon, Laure Sansonnet, Julien Chiquet
  En analyse unicellulaire, il est habituel de traiter des observations non gaussiennes de grande dimension. Un exemple typique est la distribution de c...
  hal-04738628 | ⬇️ Télécharger
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Chapitre d'ouvrage

• Le modèle Poisson log-normal pour l’analyse de distributions jointes d’abondance
  Julien Chiquet, Marie-Josée Cros, Mahendra Mariadassou, Nathalie Peyrard, Stéphane Robin
  Le fonctionnement d’un écosystème dépend essentiellement des interactions des espèces qui le composent avec leur environnement (interactions abi...
  hal-04033421 | ⬇️ Télécharger
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• The Poisson Log-Normal Model: A Generic Framework for Analyzing Joint Abundance Distributions
  Julien Chiquet, Marie-Josée Cros, Mahendra Mariadassou, Nathalie Peyrard, Stéphane Robin
  
  hal-04688958
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Article dans une revue

• Adjusting the adjusted Rand Index A multinomial story
  Martina Sundqvist, Julien Chiquet, Guillem Rigaill
  The Adjusted Rand Index (ARI) is arguably one of the most popular measures for cluster comparison. The adjustment of the ARI is based on a hypergeomet...
  hal-03696588 | ⬇️ Télécharger
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• missSBM: An R Package for Handling Missing Values in the Stochastic Block Model
  Pierre M Barbillon, Julien Chiquet, Timothée Tabouy
  The Stochastic Block Model (SBM) is a popular probabilistic model for random graphs. It is commonly used for clustering network data by aggregating no...
  hal-03481162 | ⬇️ Télécharger
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2021

Article dans une revue

• Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions
  E. Lejal, J. Chiquet, J. Aubert, S. Robin, A. Estrada-Peña, O. Rue, C. Midoux, M. Mariadassou, Xavier Bailly, A. Cougoul, Patrick Gasqui, J. Cosson, Karine Chalvet-Monfray, Muriel Vayssier Taussat, Thomas Pollet
  Background Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease ri...
  hal-03287263 | ⬇️ Télécharger
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• Coupling ecological network analysis with high-throughput sequencing-based surveys: Lessons from the next-generation biomonitoring project
  Maxime Dubart, Pascal Alonso, Didac Barroso-Bergadà, N. Becker, Kévin Béthune, David Bohan, Christophe Boury, Marine Cambon, Elsa Canard, Emilie Chancerel, Julien Chiquet, Patrice David, Natasha de Manincor, Sophie Donnet, Anne Duputié, Benoit Facon, Erwan Guichoux, Tâm Le Minh, Sebastián Ortiz-Martínez, Lucie Piouceau, Ambre Sacco--Martret de Préville, Manuel Plantegenest, Céline Poux, Virginie Ravigné, Stephane S. Robin, Marine Trillat, Corinne Vacher, Christian Vernière, François Massol
  Biomonitoring ecosystems is necessary in order to evaluate risks and to efficiently manage ecosystems and their associated services. Agrosystems are t...
  hal-03634351 | ⬇️ Télécharger
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• Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine
  Charlotte Brault, Agnes Doligez, Loïc Le Cunff, Aude Coupel-Ledru, Thierry Simonneau, Julien Chiquet, Patrice This, Timothée Flutre
  Viticulture has to cope with climate change and to decrease pesticide inputs, while maintaining yield and wine quality. Breeding is a key lever to mee...
  hal-03342409 | ⬇️ Télécharger
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• Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies
  Benoit Facon, Abir Hafsi, Maud Charlery de La Masselière, Stéphane Robin, François Massol, Maxime Dubart, Julien Chiquet, Enric Frago, Frédéric Chiroleu, Pierre François Duyck, Virginie Ravigné
  The relative importance of ecological factors and species interactions for shaping species distributions is still debated. The realised niches of eigh...
  hal-03287942 | ⬇️ Télécharger
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• The Poisson-Lognormal Model as a Versatile Framework for the Joint Analysis of Species Abundances
  Julien Chiquet, Mahendra Mariadassou, Stéphane Robin
  Joint Species Distribution Models (JSDM) provide a general multivariate framework to study the joint abundances of all species from a community. JSDM ...
  hal-03215628 | ⬇️ Télécharger
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• Identification of Deregulated Mechanisms Specific to Bladder Cancer Subtypes
  Magali Champion, Julien Chiquet, Pierre Neuvial, Mohamed Elati, François Radvanyi, Etienne E. Birmelé
  In many cancers, mechanisms of gene regulation can be severely altered. Identification of deregulated genes, which do not follow the regulation proces...
  hal-03079966 | ⬇️ Télécharger
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Pré-publication, Document de travail

• Microbial association networks give relevant insights into plant pathobiomes
  Charlie Pauvert, Tania Fort, Agnes Calonnec, Julie Faivre D’arcier, Emilie Chancerel, Marie Massot, Julien Chiquet, Stéphane Robin, David Bohan, Jessica Vallance, Corinne Vacher
  Interactions between plant pathogens and other plant-associated microorganisms regulate disease. Deciphering the networks formed by these interactions...
  hal-03218256
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2020

Article dans une revue

• Fast tree aggregation for consensus hierarchical clustering
  Audrey Hulot, Julien Chiquet, Florence Jaffrezic, Guillem Rigaill
  Background In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several res...
  hal-02961035 | ⬇️ Télécharger
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• Fast computation of genome-metagenome interaction effects
  Florent Guinot, Marie Szafranski, Julien Chiquet, Anouk Zancarini, Christine Le Signor, Christophe Mougel, Christophe Ambroise
  Motivation Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. Ho...
  hal-01906069 | ⬇️ Télécharger
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• Variational Inference for Stochastic Block Models From Sampled Data
  Timothée Tabouy, Pierre Barbillon, Julien Chiquet
  This article deals with nonobserved dyads during the sampling of a network and consecutive issues in the inference of the stochastic block model (SBM)...
  hal-02316509 | ⬇️ Télécharger
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Poster de conférence

• Comparison of univariate and multivariate models for marker selection and genomic prediction
  Charlotte Brault, Agnes Doligez, Julien Chiquet, Loic Le Cunff, Patrice This, Timothée Flutre
  
  hal-02972998
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Logiciel

• sbm: Stochastic Blockmodels
  Julien Chiquet, Pierre Barbillon, Sophie Donnet
  A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM). Supports at the moment Simple, Bipartite, 'Multipartite' and ...
  hal-04440688 | ⬇️ Télécharger
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• aricode: Efficient Computations of Standard Clustering Comparison Measures
  Julien Chiquet, Guillem Rigaill, Martina Sundqvist
  Implements an efficient O(n) algorithm based on bucket-sorting for fast computation of standard clustering comparison measures. Available measures inc...
  hal-04479410 | ⬇️ Télécharger
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Communication dans un congrès

• Identification of deregulated transcription factors involved in subtypes of cancers
  Magali Champion, Julien Chiquet, Pierre Neuvial, Mohamed Elati, François Radvanyi, Etienne E. Birmelé
  We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is base...
  hal-01516892 | ⬇️ Télécharger
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2019

Chapitre d'ouvrage

• A Multiattribute Gaussian Graphical Model for Inferring Multiscale Regulatory Networks: An Application in Breast Cancer
  Julien Chiquet, Guillem Rigaill, Martina Sundqvist
  
  hal-02961121
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Article dans une revue

• A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication
  Maximilien Grandclaudon, Marie Perrot-Dockes, Coline Trichot, Léa Karpf, Omar Abouzid, Camille Chauvin, Philemon Sirven, Wassim Abou-Jaoudé, Frederique Berger, Philippe Hupé, Denis Thieffry, Laure Sansonnet, Julien Chiquet, Céline Lévy-Leduc, Vassili Soumelis
  Cell-cell communication involves a large number of molecular signals that function as words of a complex language whose grammar remains mostly unknown...
  hal-02316607 | ⬇️ Télécharger
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Logiciel

• mergeTrees: Aggregating Trees
  Julien Chiquet, Guillem Rigaill, Audrey Hulot
  Aggregates a set of trees with the same leaves to create a consensus tree. The trees are typically obtained via hierarchical clustering, hence the hcl...
  hal-04500072 | ⬇️ Télécharger
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• missSBM: Handling missing data in Stochastic Block Models
  Julien Chiquet, Pierre Barbillon, Timothée Tabouy
  When a network is partially observed (here, NAs in the adjacency matrix rather than 1 or 0 due to missing information between node pairs), it is possi...
  hal-04440731 | ⬇️ Télécharger
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• PLNmodels: Poisson lognormal models
  Julien Chiquet, Mahendra Mariadassou, Stephane S. Robin, François Gindraud
  The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be used for a variety of multivaria...
  hal-04440660
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Communication dans un congrès

• Variational Inference for sparse network reconstruction from count data
  Julien Chiquet, Mahendra Mariadassou, Stephane Robin
  The problem of network reconstruction from continuous data has been extensively studied and most state of the art methods rely on variants of Gaussian...
  hal-02735800
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• Fast tree aggregation for consensus hierarchical clustering: application to multi-omics data analysis
  Audrey Hulot, Julien Chiquet, Florence Jaffrezic, Guillem Rigaill
  
  hal-02483674
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2018

Communication dans un congrès

• A Walk Along Models for Count Data in Microbial Ecology
  Mahendra Mariadassou, Julien Chiquet, Stéphane Robin
  
  hal-04382269
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• Multivariate statistical modelling for QTL detection and marker selection in a bi-parental grapevine population
  Charlotte Brault, Marie Perrot-Dockès, Agnes Doligez, Julien Chiquet, Loic Le Cunff, Timothée Flutre
  Genetic selection in grapevine and many similar species is a challenge due to their perennial status and outbred nature. Marker-assisted selection and...
  hal-01868802 | ⬇️ Télécharger
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• Fused-ANOVA : une méthode de clustering en grande dimension
  Audrey Hulot, Julien Chiquet, Florence Jaffrezic, Guillem Rigaill
  Dans le domaine de la génomique, une première approche pour analyser les données est de réaliser un clustering pour identifier des structures dans...
  hal-02483532 | ⬇️ Télécharger
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Logiciel

• blockseg: Two Dimensional Change-Points Detection
  Vincent Brault, Julien Chiquet
  This package is designed to segment a matrix in blocks with constant values....
  hal-02011057
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Poster de conférence

• PO-435 Proteomic classification of triple negative breast cancer
  Martina Sundqvist, Leanne de Koning, Guillem Rigaill, Tristan Dubois, Julien Chiquet
  
  hal-04440537 | ⬇️ Télécharger
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Article dans une revue

• Variable selection in multivariate linear models with high-dimensional covariance matrix estimation
  Marie Perrot-Dockès, Celine Levy Leduc, Laure Sansonnet, Julien Chiquet
  In this paper, we propose a novel variable selection approach in the framework of multivariate linear models taking into account the dependence that m...
  hal-02621107 | ⬇️ Télécharger
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• A variable selection approach in the multivariate linear model: an application to LC-MS metabolomics data
  Marie Perrot-Dockes, Celine Levy Leduc, Julien Chiquet, Laure Sansonnet, Margaux Brégère, Marie-Pierre Etienne, Stephane Robin, Grégory Genta-Jouve
  Omic data are characterized by the presence of strong dependence structures that result either from data acquisition or from some underlying biologica...
  hal-01896164 | ⬇️ Télécharger
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• Variational inference for probabilistic Poisson PCA
  Julien Chiquet, Mahendra Mariadassou, Stephane Robin
  Many application domains such as ecology or genomics have to deal with multivariate non Gaussian observations. A typical example is the joint observat...
  hal-01941270 | ⬇️ Télécharger
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2017

Pré-publication, Document de travail

• Variational Inference for Stochastic Block Models from Sampled Data
  Timothée Tabouy, Pierre Barbillon, Julien Chiquet
  This paper deals with non-observed dyads during the sampling of a network and consecutive issues in the Stochastic Block Model (SBM) inference. We rev...
  hal-01593183
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Communication dans un congrès

• Méthode conjointe de segmentation-classification pour des modèles d'écologie du déplacement
  Sophie Donnet, Julien Chiquet, Marie Pierre Etienne, Adeline Samson
  
  hal-01565530
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• Inférence du Modèle à Blocs Stochastiques en présence de données manquantes.
  Timothée Tabouy, Pierre Barbillon, Julien Chiquet
  Le modèle à blocs stochastiques ou Stochastic Block Model (SBM) [8] est un modèle de graphe aléatoire généralisant le modèle d’Erdős-Reyni [...
  hal-01565531
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Article dans une revue

• Efficient block boundaries estimation in block-wise constant matrices: An Application to HiC data
  Vincent Brault, Julien Chiquet, Céline Lévy-Leduc
  In this paper, we propose a novel modeling and a new methodology for estimating the location of block boundaries in a random matrix consisting of a bl...
  hal-01455732 | ⬇️ Télécharger
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• Fast Tree Inference With Weighted Fusion Penalties
  Julien Chiquet, Pierre Gutierrez, Guillem Rigaill
  Given a data set with many features observed in a large number of conditions, it is desirable to fuse and aggregate conditions which are similar to ea...
  hal-01597604 | ⬇️ Télécharger
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Rapport

• Variational inference for probabilistic Poisson PCA
  Julien Chiquet, Mahendra Mariadassou, Stephane Robin
  Many application domains such as ecology or genomics have to deal with multivariate non Gaussian observations. A typical example is the joint observat...
  hal-01608912 | ⬇️ Télécharger
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2016

Communication dans un congrès

• Fast Detection of Block Boundaries in Block-Wise Constant Matrices
  Vincent Brault, Julien Chiquet, Céline Lévy-Leduc
  We propose a novel approach for estimating the location of block boundaries (change-points) in a random matrix consisting of a block wise constant mat...
  hal-01574362 | ⬇️ Télécharger
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Article dans une revue

• On coding effects in regularized categorical regression
  Julien Chiquet, Yves Grandvalet, Guillem Rigaill
  This discussion is a continuation of Tutz and Gertheiss (2016)’s paper, where we focus on the importance of the coding of effects in regularized cat...
  hal-01338164
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• Structured regularization for conditional Gaussian graphical models
  Julien Chiquet, Tristan Mary-Huard, Stephane Robin
  Conditional Gaussian graphical models are a reparametrization of the multivariate linear regression model which explicitly exhibits (i) the partial co...
  hal-01531660 | ⬇️ Télécharger
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Autre publication scientifique

• Package 'blockseg
  Julien Chiquet, Vincent Brault
  This package is designed to segment a matrix in blocks with constant values....
  hal-01455720 | ⬇️ Télécharger
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Chapitre d'ouvrage

• Learning ecological networks from next-generation sequencing data
  Corinne Vacher, Alireza Tamaddoni-Nezhad, Stefaniya Kamenova, Nathalie Dubois Peyrard, Yann Moalic, Régis Sabbadin, Loïc Schwaller, Julien Chiquet, M. Alex Smith, Jessica Vallance, Virgil Fievet, Boris Jakuschkin, David Bohan
  Species diversity, and the various interactions that occur between species, supports ecosystems functioning and benefit human societies. Monitoring th...
  hal-01533861
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2015

Article dans une revue

• A model for gene deregulation detection using expression data
  Thomas Picchetti, Julien Chiquet, Mohamed Elati, Pierre Neuvial, Rémy Nicolle, Etienne E. Birmelé
  In tumoral cells, gene regulation mechanisms are severely altered, and these modifications in the regulations may be characteristic of different subty...
  hal-01154154 | ⬇️ Télécharger
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• Combining a Relaxed EM Algorithm with Occam's Razor for Bayesian Variable Selection in High-Dimensional Regression
  Pierre Latouche, Pierre-Alexandre Mattei, Charles Bouveyron, Julien Chiquet
  We address the problem of Bayesian variable selection for high-dimensional lin-ear regression. We consider a generative model that uses a spike-and-sl...
  hal-01003395 | ⬇️ Télécharger
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HDR

• Contributions to Sparse Methods for Complex Data Analysis
  Julien Chiquet
  This document is organized around three chapters.that summarize my research activity since 2008, that is, after my PhD thesis. The first chapter provi...
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Communication dans un congrès

• A greedy great approach to learn with complementary structured datasets
  Christophe Ambroise, Julien Chiquet, Marie Szafranski
  We are interested in problems where two hierarchically structured datasets may be complementary for a learning process. This case may arise in biologi...
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• Fast tree inference with weighted fusion penalties
  Julien Chiquet
  Fast tree inference with weighted fusion penalties. 10. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatisti...
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Poster de conférence

• A greedy great approach to learn with complementary structured datasets
  Julien Chiquet, Marie Szafranski, Christophe Ambroise
  We are interested in problems where two hierarchically structured datasets may be complementary for a learning process. This case may arise in biologi...
  hal-01608307
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2014

Communication dans un congrès

• Weighted fusion penalties for tree inference and its oracle properties
  Julien Chiquet, Pierre Gutierrez, Guillem Rigaill
  Weighted fusion penalties for tree inference and its oracle properties. Workshop MLCB NIPS 2014...
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• FLPCA: A Fused Lasso PCA-based approach to identify influential markers in differentiated populations from dense SNP data
  Denis Laloë, Julien Chiquet, Florence Jaffrezic, Mathieu M. Gautier
  Detection of footprints of selection has been a great research interest in population genetics over the past few years, both in Human and Animal popul...
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• FLPCA: A Fused-Lasso based approach to identify footprints of selection in differentiated populations from dense SNP data: applications to human and cattle data
  Denis Laloë, Julien Chiquet, Florence Jaffrezic, Mathieu Gautier
  absent...
  hal-01193942
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Article dans une revue

• Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
  Boulos Chalhoub, France Denoeud, Shengyi Liu, Isobel A. P. Parkin, Haibao Tang, Xiyin Wang, Julien Chiquet, Harry Belcram, Chaobo Tong, Birgit Samans, Margot Corréa, Corinne da Silva, Jérémy Just, Cyril Falentin, Chu Shin Koh, Isabelle Le Clainche, Maria Bernard, Pascal Bento, Benjamin Noel, Karine Labadie, Adriana A. Alberti, Mathieu Charles, Dominique Arnaud, Hui Guo, Christian Daviaud, Salman Alamery, Kamel Jabbari, Meixia Zhao, Patrick P. Edger, Houda Chelaifa-Ammari, David Tack, Gilles Lassalle, Imen Mestiri, Nicolas Schnel, Marie-Christine Le Paslier, Chuchuan Fan, Guangyi Fan, Victor Renault, Philippe E. Bayer, Agnieszka A. Golicz, Sahana Manoli, Tae-Ho Lee, Vinh Ha Dinh Thi, Smahane Chalabi, Qiong Hu, Reece Tollenaere, Yunhai Lu, Christophe Battail, Jinxiong Shen, Christine H. D. Sidebottom, Xinfa Wang, Aurelie Canaguier, Aurelie Chauveau, Aurélie Berard, Gwenaëlle Deniot, Mei Guan, Zhongsong Liu, Fengming Sun, Yong Pyo Lim, Eric Lyons, Christopher D. Town, Ian Bancroft, Xiaowu Wang, Jinling Meng, Jianxin Ma, J. Chris Pires, Graham J. King, Dominique Brunel, Régine Delourme, Michel Renard, Jean-Marc Aury, Keith L. Adams, Patrick Wincker, Jacqueline Batley, Rod J. Snowdon, Jörg Tost, David Edwards, Yongming Zhou, Wei Hua, Andrew G. Sharpe, Andrew H. Paterson, Chunyun Guan
  Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a proce...
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Chapitre d'ouvrage

• Network inference in breast cancer with Gaussian graphical models and extensions
  Julien Chiquet, Marine Jeanmougin, Camille Charbonnier
  Clustering genes with high correlations will group genes with close expression profiles, defining clusters of co-expressed genes. However, such correl...
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2013

Poster de conférence

• Multi-trait genomic selection via multivariate regression with structured regularization
  Julien Chiquet, Tristan Mary, Stephane Robin
  Multi-trait genomic selection via multivariate regression with structured regularization. MLCB NIPS 2013...
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• A fast homotopy algorithm for a large class of weighted classification problems
  Pierre Gutierrez, Guillem Rigaill, Julien Chiquet
  We propose a penalized method to solve the one-way ANOVA problem by collapsing the coefficients of K conditions. We introduce a large class of weights...
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• Sparse Gaussian graphical models for biological network inference
  Julien Chiquet
  Sparse Gaussian graphical models for biological network inference. ISI 59. World Statistics Congress 2013...
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Chapitre d'ouvrage

• Dynamical systems with semi-Markovian perturbations and their use in structural reliability
  Julien Chiquet, Nikolaos Limnios
  The aim of this chapter is to present dynamical systems evolving in continuous-time and perturbed by semi-Markov processes (SMP). We investigate both ...
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2012

Article dans une revue

• Prevalence of gene expression additivity in genetically stable wheat allohexaploids
  Houda Chelaifa-Ammari, Veronique Chague, Smahane Chalabi, Imen Mestiri, Dominique Arnaud, Denise Deffains, Yunhai Lu, Harry Belcram, Virginie Huteau, Julien Chiquet, Olivier Coriton, Jérémy Just, Joseph Jahier, Paul Chalhoub
  The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of...
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• Sparsity with sign-coherent groups of variables via the cooperative-lasso
  Julien Chiquet, Yves Grandvalet, Camille Charbonnier
  We consider the problems of estimation and selection of parameters endowed with a known group structure, when the groups are assumed to be sign-cohere...
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2011

Article dans une revue

• Inferring Multiple Graphical Structures
  Julien Chiquet, Yves Grandvalet, Christophe Ambroise
  Gaussian Graphical Models provide a convenient framework for representing dependencies between variables. Recently, this tool has received a high inte...
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• Statistiques et Génome
  Franck Picard, S. Schbath, E. Lebarbier, Pierre Neuvial, J. Chiquet
  
  hal-00698143
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• Statistique et génome : réseaux biologiques
  Julien Chiquet
  Statistique et génome : réseaux biologiques...
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2010

Communication dans un congrès

• Inférence jointe de la structure de modèles graphiques gaussiens
  Julien Chiquet, Yves Grandvalet, Christophe Ambroise
  Le modèle graphique gaussien est un formalisme de travail bien adapté à la représentation de dépendances entre variables. Récemment, ce modèle ...
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Article dans une revue

• A method to compute the transition function of a piecewise deterministic Markov process with application to reliability
  Julien Chiquet, Nikolaos Limnios
  
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• Weighted-LASSO for Structured Network Inference from Time Course Data
  Camille Charbonnier, Julien Chiquet, Christophe Ambroise
  We present a weighted-LASSO method to infer the parameters of a first-order vector auto-regressive model that describes time course expression data ge...
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2009

Article dans une revue

• Inferring sparse Gaussian graphical models with latent structure
  Christophe Ambroise, Julien Chiquet, Catherine Matias
  Our concern is selecting the concentration matrix's nonzero coefficients for a sparse Gaussian graphical model in a high-dimensional setting. This cor...
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• Piecewise deterministic Markov processes applied to fatigue crack growth modelling
  Julien Chiquet, Nikolaos Limnios, Mohamed Eid
  In this paper, we use a particular piecewise deterministic Markov process (PDMP) to model the evolution of a degradation mechanism that may arise in v...
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• SIMoNe: Statistical Inference for MOdular NEtworks.
  Julien Chiquet, Alexander Smith, Gilles Grasseau, Catherine Matias, Christophe Ambroise
  The R package SIMoNe (Statistical Inference for MOdular NEtworks) enables inference of gene-regulatory networks based on partial correlation coefficie...
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2008

Chapitre d'ouvrage

• Reliability of stochastic dynamical systems applied to fatigue crack growth modeling
  Julien Chiquet, Nikolaos Limnios
  
  hal-00260748
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Article dans une revue

• Modelling and estimating the reliability of stochastic dynamical systems with Markovian switching
  Julien Chiquet, Mohamed Eid, Nikolaos Limnios
  In this paper, a general framework for the modelling of physical phenomena with stochastic dynamical systems switched by jump Markov processes is give...
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2007

Thèse

• Modélisation et estimation des processus de dégradation avec application en fiabilité des structures
  Julien Chiquet
  Nous décrivons le niveau de dégradation caractéristique d'une structure à l'aide d'un processus stochastique appelé processus de dégradation. La...
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Article dans une revue

• A method to compute the transition function of a piecewise deterministic Markov process with application to reliability
  Julien Chiquet, Nikolaos Limnios
  We study the time evolution of an increasing stochastic process governed by a first-order stochastic differential system. This defines a particular pi...
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2006

Article dans une revue

• Estimating Stochastic Dynamical Systems Driven by a Continuous-Time Jump Markov Process
  Julien Chiquet, Nikolaos Limnios
  We discuss the use of a continuous-time jump Markov process as the driving process in stochastic differential systems. Results are given on the estima...
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