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Christophe Ambroise

75
Documents

Publications

Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations.

Romuald Laso-Jadart , Michael O'Malley , Adam M. Sykulski , Christophe Ambroise , Mohammed-Amin Madoui
BMC Ecology and Evolution, 2023, 23 (1), pp.46. ⟨10.1186/s12862-023-02160-8⟩
Article dans une revue hal-04215576v1
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Hierarchical correction of p-values via an ultrametric tree running Ornstein-Uhlenbeck process

Antoine Bichat , Christophe Ambroise , Mahendra Mariadassou
Computational Statistics, 2022, 37 (3), pp.995-1013. ⟨10.1007/s00180-021-01148-6⟩
Article dans une revue hal-04072108v1
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A Sparse Mixture-of-Experts Model With Screening of Genetic Associations to Guide Disease Subtyping

Marie Courbariaux , Kylliann De Santiago , Cyril Dalmasso , Fabrice Danjou , Samir Bekadar
Frontiers in Genetics, 2022, Statistical Methods, Computing, and Resources for Genome-Wide Association Studies, Volume II, 13, ⟨10.3389/fgene.2022.859462⟩
Article dans une revue hal-01822237v5

AI-based mobile application to fight antibiotic resistance

Marco Pascucci , Guilhem Royer , Jakub Adamek , Mai Al Asmar , David Aristizabal
Nature Communications, 2021, 12 (1), pp.1173. ⟨10.1038/s41467-021-21187-3⟩
Article dans une revue hal-03706771v1

Accounting for Missing Actors in Interaction Network Inference from Abundance Data

Raphaëlle Momal , Stephane S. Robin , Christophe Ambroise
Journal of the Royal Statistical Society: Series C Applied Statistics, 2021, 70 (5), pp.1230-1258. ⟨10.1111/rssc.12509⟩
Article dans une revue hal-04495702v1
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Fast computation of genome-metagenome interaction effects

Florent Guinot , Marie Szafranski , Julien Chiquet , Anouk Zancarini , Christine Le Signor
Algorithms for Molecular Biology, 2020, 15 (1), art.13 (21p.). ⟨10.1186/s13015-020-00173-2⟩
Article dans une revue hal-01906069v3
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Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

Antoine Bichat , Jonathan Plassais , Christophe Ambroise , Mahendra Mariadassou
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.00649⟩
Article dans une revue hal-02635268v1
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Exploring the link between additive heritability and prediction accuracy from a ridge regression perspective

Arthur Frouin , Claire Dandine-Roulland , Morgane Pierre-Jean , Jean-François Deleuze , Christophe Ambroise
Frontiers in Genetics, 2020, 11, pp.581594. ⟨10.3389/fgene.2020.581594⟩
Article dans une revue cea-04419427v1
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Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)

Romuald Laso‐jadart , Kevin Sugier , Emmanuelle Petit , Karine Labadie , Pierre Peterlongo
Ecology and Evolution, 2020, 10 (16), pp.8894-8905. ⟨10.1002/ece3.6588⟩
Article dans une revue hal-02999798v1
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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Guillaume Gautreau , Adelme Bazin , Mathieu Gachet , Rémi Planel , Laura Burlot
PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007732⟩
Article dans une revue hal-03089210v1
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metaVaR: introducing metavariant species models for reference-free metagenomic-based population genomics

Romuald Laso-Jadart , Christophe Ambroise , Pierre Peterlongo , Mohammed-Amin Madoui
Article dans une revue hal-02464983v1

Tree‐based inference of species interaction networks from abundance data

Raphaëlle Momal , Stéphane Robin , Christophe Ambroise
Methods in Ecology and Evolution, 2020, 11 (5), pp.621-632. ⟨10.1111/2041-210X.13380⟩
Article dans une revue hal-02918284v1
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A generalized statistical framework to assess mixing ability from incomplete mixing designs using binary or higher order variety mixtures and application to wheat

Emma Forst , Jerome Enjalbert , Vincent Allard , Christophe Ambroise , Inès Krissaane
Field Crops Research, 2019, 242, pp.107571. ⟨10.1016/j.fcr.2019.107571⟩
Article dans une revue hal-02618625v1
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Incomplete graphical model inference via latent tree aggregation

Geneviève Robin , Christophe Ambroise , Stephane S. Robin
Statistical Modelling, 2019, 19 (5), pp.545-568. ⟨10.1177/1471082X18786289⟩
Article dans une revue hal-01686841v1
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Adjacency-constrained hierarchical clustering of a band similarity matrix with application to Genomics

Christophe Ambroise , Alia Dehman , Pierre Neuvial , Guillem Rigaill , Nathalie Vialaneix
Algorithms for Molecular Biology, 2019, 14, pp.22. ⟨10.1186/s13015-019-0157-4⟩
Article dans une revue hal-02006331v2
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Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples.

Marie-Ange Palomares , Cyril Dalmasso , Eric Bonnet , Céline Derbois , Solène Brohard-Julien
Scientific Reports, 2019, 9, pp.1-12. ⟨10.1038/s41598-019-43983-0⟩
Article dans une revue hal-02270990v1
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Learning the optimal scale for GWAS through hierarchical SNP aggregation

Florent Guinot , Marie Szafranski , Christophe Ambroise , Franck Samson
BMC Bioinformatics, 2018, 19 (1), pp.459
Article dans une revue hal-01597553v3
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Learning the optimal scale for GWAS through hierarchical SNP aggregation

Florent Guinot , Marie Szafranski , Christophe Ambroise , Franck Samson
BMC Bioinformatics, 2018, 19, ⟨10.1186/s12859-018-2475-9⟩
Article dans une revue hal-02623460v1
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Beyond support in two-stage variable selection

Jean-Michel Bécu , Yves Grandvalet , Christophe Ambroise , Cyril Dalmasso
Statistics and Computing, 2017, 27 (1), pp.169--179. ⟨10.1007/s11222-015-9614-1⟩
Article dans une revue hal-01246066v1
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Eigen-Epistasis for detecting Gene-Gene interactions

Virginie Stanislas , Cyril Dalmasso , Christophe Ambroise
BMC Bioinformatics, 2017, 18, pp.54
Article dans une revue hal-01275624v6
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Eigen-Epistasis for detecting gene-gene interactions

Virginie Stanislas , Cyril Dalmasso , Christophe Ambroise
BMC Bioinformatics, 2017, 18, ⟨10.1186/s12859-017-1488-0⟩
Article dans une revue hal-01601001v1
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Performance of a blockwise approach in variable selection using linkage disequilibrium information

Alia Dehman , Christophe Ambroise , Pierre Neuvial
BMC Bioinformatics, 2015, 16, pp.14. ⟨10.1186/s12859-015-0556-6⟩
Article dans une revue hal-01193074v1

Model Selection in Overlapping Stochastic Block Models

Pierre Latouche , Etienne E. Birmelé , Christophe Ambroise
Electronic Journal of Statistics , 2014, 8, pp.762-794. ⟨10.1214/14-EJS903⟩
Article dans une revue hal-00990277v1

New consistent and asymptotically normal parameter estimates for random-graph mixture models

Christophe Ambroise , Catherine Matias
Journal of the Royal Statistical Society: Series B, 2012, 74, ⟨10.1111/j.1467-9868.2011.01009.x⟩
Article dans une revue hal-00647817v1

Variational Bayesian Inference and Complexity Control for Stochastic Block Models

Pierre Latouche , Etienne E. Birmelé , Christophe Ambroise
Statistical Modelling, 2012, 12 (1), pp.93-115. ⟨10.1177/1471082X1001200105⟩
Article dans une revue hal-00624536v1
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SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies

Matthieu Bouaziz , Caroline Paccard , Mickaël Guedj , Christophe Ambroise
PLoS ONE, 2012, 7 (10), ⟨10.1371/journal.pone.0045685⟩
Article dans une revue hal-02644356v1

OVERLAPPING STOCHASTIC BLOCK MODELS WITH APPLICATION TO THE FRENCH POLITICAL BLOGOSPHERE

Pierre Latouche , Etienne Birmelé , Christophe Ambroise
Annals of Applied Statistics, 2011, 5 (1), pp.309 - 336. ⟨10.1214/10-AOAS382⟩
Article dans une revue hal-02652556v1
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Accounting for population stratification in practice: a comparison of the main strategies dedicated to genome-wide association studies

Matthieu Bouaziz , Christophe Ambroise , Mickaël Guedj
PLoS ONE, 2011, 6 (12), ⟨10.1371/journal.pone.0028845⟩
Article dans une revue hal-02649658v1
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Inferring Multiple Graphical Structures

Julien Chiquet , Yves Grandvalet , Christophe Ambroise
Statistics and Computing, 2011, 21 (4), pp.537-553. ⟨10.1007/s11222-010-9191-2⟩
Article dans une revue hal-00660169v1

Clustering based on random graph model embedding vertex features

Hugo Zanghi , Stevenn Volant , Christophe Ambroise
Pattern Recognition Letters, 2010, 31 (9), pp.830-836. ⟨10.1016/j.patrec.2010.01.026⟩
Article dans une revue pasteur-02612862v1
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Weighted-LASSO for Structured Network Inference from Time Course Data

Camille Charbonnier , Julien Chiquet , Christophe Ambroise
Statistical Applications in Genetics and Molecular Biology, 2010, 9 (1), pp.15. ⟨10.2202/1544-6115.1519⟩
Article dans une revue hal-01597614v1
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Inferring sparse Gaussian graphical models with latent structure

Christophe Ambroise , Julien Chiquet , Catherine Matias
Electronic Journal of Statistics , 2009, 3, pp.205-238. ⟨10.1214/08-EJS314⟩
Article dans une revue hal-00592201v1
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Inferring sparse Gaussian graphical models with latent structure

Christophe Ambroise , Julien Chiquet , Catherine Matias
Electronic Journal of Statistics , 2009, ⟨10.1214/08-EJS314⟩
Article dans une revue inria-00591491v1
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SIMoNe: Statistical Inference for MOdular NEtworks.

Julien Chiquet , Alexander Smith , Gilles Grasseau , Catherine Matias , Christophe Ambroise
Bioinformatics, 2009, 25 (3), pp.417-418. ⟨10.1093/bioinformatics/btn637⟩
Article dans une revue hal-00592218v1
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Identification of functional modules based on transcriptional regulation structure

Etienne Birmele , Mohamed Elati , Céline Rouveirol , Christophe Ambroise
BMC Proceedings, 2008, 2 (4), pp.S4
Article dans une revue hal-00730904v1
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Parsimonious Additive Models

Marta Avalos , Yves Grandvalet , Christophe Ambroise
Computational Statistics and Data Analysis, 2007, 51 (6), pp.2851-2870. ⟨10.1016/j.csda.2006.10.007⟩
Article dans une revue inserm-00149798v1
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Discrimination par modèles additifs parcimonieux

Marta Avalos , Yves Grandvalet , Christophe Ambroise
Revue dÍntelligence Artificielle, 2005, 19 (4-5), pp.661-682
Article dans une revue inserm-00149790v1
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Hierarchical clustering of self-organizing maps for cloud classification

Christophe Ambroise , Geneviève Sèze , Fouad Badran , Sylvie Thiria
Neurocomputing, 2000, 30 (1-4), pp.47-52. ⟨10.1016/S0925-2312(99)00141-1⟩
Article dans une revue hal-03183040v1

An interdisciplinary approach to increase wheat within-field diversity and promote agro-ecosystem services

Jérôme Enjalbert , Vincent Allard , Christophe Ambroise , Bruno Andrieu , S. Barot
European Conference on Crop Diversification, Sep 2019, Budapest, Hungary
Communication dans un congrès hal-04481348v1
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Quantify Genomic Heritability Through a Prediction Measure

Arthur Frouin , Edith Le Flocch , Christophe Ambroise
46th European Mathematical Genetics Meeting (EMGM), Apr 2018, Cagliari, Italy. pp.2, ⟨10.1159/000488519⟩
Communication dans un congrès hal-02737176v1

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel
JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France
Communication dans un congrès hal-04355945v1

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics

Christophe Ambroise , Alia Dehman , Michel Koskas , Pierre Neuvial , Guillem Rigaill
Journée Régionale de Bioinformatique et Biostatistique, Génopole Toulouse, Dec 2018, Toulouse, France
Communication dans un congrès hal-02788245v1

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel
Genome Informatics 2018, Sep 2018, Hinxton, Cambridge, United Kingdom
Communication dans un congrès hal-04356757v1

Significance testing for variable selection in high-dimension

Jean-Michel Bécu , Yves Grandvalet , Christophe Ambroise , Cyril Dalmasso
Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Aug 2015, Niagara Falls, Canada. pp.1-8, ⟨10.1109/CIBCB.2015.7300313⟩
Communication dans un congrès hal-01313310v1
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A greedy great approach to learn with complementary structured datasets

Christophe Ambroise , Julien Chiquet , Marie Szafranski
Greed Is Great ICML Workshop, Jul 2015, Lille, France
Communication dans un congrès hal-01246419v1

Inférence jointe de la structure de modèles graphiques gaussiens

Julien Chiquet , Yves Grandvalet , Christophe Ambroise
CAp'2010, May 2010, France. pp.217-232
Communication dans un congrès hal-00936741v1
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Modèles de graphe aléatoire à classes chevauchantes pour l'analyse des réseaux

Pierre Latouche , Etienne E. Birmelé , Christophe Ambroise
42èmes Journées de Statistique, 2010, Marseille, France, France
Communication dans un congrès inria-00494820v1
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A latent logistic model to uncover overlapping clusters in networks

Pierre Latouche , Etienne E. Birmelé , Christophe Ambroise
Atelier AGS (Apprentissage et Graphes pour les Systèmes complexes), May 2009, Hammamet, Tunisia. pp.3-8
Communication dans un congrès hal-00629310v1

Les modèles de mélange pour la classification de données massives en temps réel

Allou Samé , Gérard Govaert , Christophe Ambroise
41èmes Journées de Statistique, SFdS, Bordeaux, 2009, Bordeaux, France, France
Communication dans un congrès inria-00386796v1
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Uncovering overlapping clusters in biological networks

Pierre Latouche , Etienne E. Birmelé , Christophe Ambroise
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2009, Nantes, France. pp.28
Communication dans un congrès hal-00629321v1
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Model selection via penalization in the additive Cox model

Marta Avalos , Yves Grandvalet , Christophe Ambroise
The 3rd world conference on Computational Statistics & Data Analysis, 2005, Limassol, Cyprus. pp.45
Communication dans un congrès inserm-00149852v1
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Pénalisation l1 pour les MAG

Marta Avalos , Yves Grandvalet , Christophe Ambroise
2005, pp.25.1
Communication dans un congrès inserm-00149856v1
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Penalized additive logistic regression for cardiovascular risk prediction

Marta Avalos , Yves Grandvalet , Christophe Ambroise
2004, pp.301
Communication dans un congrès inserm-00149854v1
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Généralisation du lasso aux modèles additifs

Marta Avalos , Yves Grandvalet , Christophe Ambroise
2004, pp.83
Communication dans un congrès inserm-00149858v1
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Discriminative Classification vs Modeling Methods in CBIR

Philippe-Henri Gosselin , Micheline Najjar , Matthieu Cord , Christophe Ambroise
IEEE International Conference on Advanced Concepts for Intelligent Vision Systems, Sep 2004, Belgium. pp.1
Communication dans un congrès hal-00520316v1

Mixture model approach for acoustic emission control of pressure equipment

Hani Hamdan , Gérard Govaert , Christophe Ambroise , Catherine Hervé
5th International Conference on Acoustical and Vibratory Surveillance Methods and Diagnostic Techniques, Oct 2004, Senlis, France. pp.1-10
Communication dans un congrès hal-01377401v1
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Regularization methods for additive models

Marta Avalos , Yves Grandvalet , Christophe Ambroise
2003, pp.509-520
Communication dans un congrès inserm-00149855v1

Boosting mixture models for semi-supervised learning task

Yves Grandvalet , Florence d'Alché-Buc , Christophe Ambroise
ICANN 2001 - International Conference on Artificial Neural Networks, Aug 2001, Vienne, Austria. pp.41-48, ⟨10.1007/3-540-44668-0_7⟩
Communication dans un congrès hal-01570826v1

Semi-supervised marginboost

Florence d'Alché-Buc , Yves Grandvalet , Christophe Ambroise
NIPS 2001 - 14th International Conference on Neural Information, Dec 2001, Vancouver, BC, Canada. pp.553-560
Communication dans un congrès hal-01561463v1

PanGBank: depicting microbial species diversity via PPanGGOLiN

Guillaume Gautreau , Adelme Bazin , Rémi Planel , Mathieu Gachet , Mathieu Dubois
JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France
Poster de conférence hal-04358380v1
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Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics

Christophe Ambroise , Alia Dehman , Pierre Neuvial , Guillem Rigaill , Nathalie Vialaneix
Statistical Methods for Post Genomic Data (SMPGD 2019), Jan 2019, Barcelona, Spain. 2019
Poster de conférence hal-02790995v1

A greedy great approach to learn with complementary structured datasets

Julien Chiquet , Marie Szafranski , Christophe Ambroise
ICML 2015 International Conference on Machine Learning, Jul 2015, Lille, France. 2015, Greed Is Great ICML Workshop, Jul 2015, Lille, France
Poster de conférence hal-01608307v1
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Mixture of stochastic block models for multiview clustering

Kylliann De Santiago , Marie Szafranski , Christophe Ambroise
ESANN 2023 - European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, pp.151-156, 2023, ⟨10.14428/esann/2023.ES2023-54⟩
Proceedings/Recueil des communications hal-04363422v1

Compression structurée de l’information génétique et étude d’association pangénomique par modèles additifs

Florent Guinot , Marie Szafranski , Christophe Ambroise
Intégration de données biologiques, ISTE Group, pp.129-163, 2022, ⟨10.51926/ISTE.9030.ch5⟩
Chapitre d'ouvrage hal-04506050v1

Applications in Genomics

Stephane S. Robin , Christophe Ambroise
FruhwirthSchnatter, S; Celeux, G; Robert, CP. HANDBOOK OF MIXTURE ANALYSIS, CRC PRESS-TAYLOR & FRANCIS GROUP, 2019, Chapman & Hall-CRC Handbooks of Modern Statistical Methods, 978-0-429-50824-0; 978-1-4987-6381-3
Chapitre d'ouvrage hal-03111649v1

Epigenetics in Forest Trees: State of the Art and Potential Implications for Breeding and Management in a Context of Climate Change

Mamadou Dia Sow , Isabel Allona , Christophe Ambroise , Daniel Conde , Régis R. Fichot
Plant Epigenetics Coming of Age for Breeding Applications, 88, Academic press, Elsevier, 454 p., 2018, Advances in Botanical Research, 9780128154038. ⟨10.1016/bs.abr.2018.09.003⟩
Chapitre d'ouvrage hal-02791217v1
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Overlapping clustering methods for networks

Pierre Latouche , Etienne E. Birmelé , Christophe Ambroise
Edoardo M. Airoldi, David Blei, Elena A. Erosheva, Stephen E. Fienberg. Chapman and Hall/CRC. Handbook of Mixed Membership Models and Their Applications, Chapman and Hall/CRC, in press, 2014
Chapitre d'ouvrage hal-00984395v1
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Bayesian methods for graph clustering

Pierre Latouche , Etienne E. Birmelé , Christophe Ambroise
Andreas Fink, Berthold Lausen, Wilfried Seidel and Alfred Ultsch. Advances in Data Analysis, Data Handling and Business Intelligence, Springer, pp.229-239, 2009, Studies in Classification, Data Analysis, and Knowledge Organization, 978-3-642-01043-9. ⟨10.1007/978-3-642-01044-6⟩
Chapitre d'ouvrage hal-00629294v1