I am working in CNRS @ Biometry and Evolutionary Biology Lab. With a background in mathematics and computer science, I am involved in projects in ecology, on two main axes :
ecological networks : analysing original datasets, proposing new methodological developments and helping non specialists (see this "quick tips" paper) ;
image, ecology & deep learning : as a leader of the imaginecology initiative (see imaginecology website), developping computer vision pipelines and sharing knowledge with other ecologists.
SELECTED WORK
For a complete list, I am almost 100% degooglized, but you can still have a look at my scholar profile.
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Noa Rigoudy, the DeepFaune consortium, Bruno Spataro, Vincent Miele, Simon Chamaillé-Jammes, The DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images, Preprint bioRxiv (2022)
- Vincent Miele, Stéphane Dray et Olivier Gimenez, Images, écologie et deep learning, Regards sur la biodiversité, Société Française d’Écologie et d’Évolution (2021)
- Vincent Miele, Gaspard Dussert, Bruno Spataro, Simon Chamaillé-Jammes, Dominique Allainé & Christophe Bonenfant, Revisiting giraffe photo-identification using deep learning and network analysis. Methods in Ecology and Evolution (2021) Preprint bioRxiv / Media coverage : France 3, RFI
- Christophe Botella, Stéphane Dray, Catherine Matias, Vincent Miele, Wilfried Thuiller, An appraisal of graph embeddings for comparing trophic network architectures. Methods in Ecology and Evolution (2021)
- Vincent Miele, Catherine Matias, Marc Ohlmann, Giovanni Poggiato, Stéphane Dray, Wilfried Thuiller, Quantifying the overall effect of biotic interactions on species communities along environmental gradients. Preprint HAL (2021)
- Vincent Miele, Catherine Matias, Stéphane Robin & Stéphane Dray, Nine Quick Tips for Analyzing Network Data. PLoS Comp. Biology (2019)
- Catherine Matias & Vincent Miele, Statistical clustering of temporal networks through dynamic a stochastic block model. Journal of the Royal Statistical Society : Series B (2016) Arxiv
Project member :
- ANR FuturePred 2019-2022
- ANR Horizon 2018-2022
- ANR Colib’read 2012-2016
- ANR Ancestrome 2011-2016
- ANR NeMo 2007-2011
Board member
- GdR EcoStat 2019-
- CNRS AISSAI (AI for Science, Science for AI) 2022-
- IXXI 2021-
- Groupe Calcul 2009-2017
- LyonCalcul (co-founder) 2012-2016
- CCIS/COCIN (CNRS) 2012-2015
- SMAI MAIRCI 2013-2015
Reviewer :
- Journal of Statistical Software
- Annals of statistics
- Journal of The Royal Society Interface
- Journal of the American Statistical Association
- PLoS Biology
- PCI Ecology
- The American Naturalist
- Biology Letters
- Scientific Reports
- Science Advances
- IEEE Transactions on Signal and Information Processing over Networks
- Frontiers in Ecology and Evolution
- Biological reviews
- Mammalian Biology
- PLoS ONE
- Bioinformatics
- TCBB
Jury member :
- INRA IRE01, 2022 (président)
- HCERES MISTEA, 2020
- INRA IRE01, 2018 (président)
- UGA IGE, 2017
- CNRS IR43, 2017
- INRA CEI, 2017
- CNRS IE 13INSMI03, 2013
- INRA IRE12, 2012
- INRA IRE05, 2011
- INRA IRE01, 2009
- CNRS IE 155, 2008
Organizing commitee :
- imaginecology workshop, Novembre 2020
- ANF R pour le calcul, Octobre 2015
- Ecole Rhône-Alpes ARC6 Découverte du calcul, Septembre 2013
- Mini-Symposium SMAI 2013 MAT4NET Mathématiques pour l’analyse de grands réseaux, Juin 2013
- ANF Programmation hybride, Octobre 2012
- CEMRACS, Méthodes numériques et algorithmes pour architectures hautes performances, Summer 2012 (le reportage de France3 ici)
- Journées du groupe Calcul , November 2010.
- Le coté Calcul de Jobim , June 2009.
- Mathematics for Biological Networks , December 2007
- European Conference on Computational Biology, September 2003
Here (c) means "co-supervision"
- Elias Chetouane, M2 Informatique et Données, Deep learning for camera traps, 2022
- Marine Desprez (c) , Post Doc, Machine learning in ecology, 2022
- Bastien Payre, M2 Maths en action, Deep learning et séquences d'images, 2021
- Nathan Levray, M2 Maths en action, Higher order networks, 2021
- Noa Rigoudy (c), ENS Lyon, Deep learning for camera traps, 2021
- Julien Bonnier (c), M2 BEE, reconnaissance des pollens, 2021
- Giusseppe Capizzi, M2 Data Science, Machine learning for botanics, 2020-21
- Christophe Botella (c), Post Doc, Graph embeddings, 2020-21
- Thibault Genissel (c), ENS Lyon, Réseaux de contact entre ongulés, 2020
- Gaspard Dussert, ENSTA, imaginecology, 2019
- Claire Gayral, M2 Maths en action, Algorithme EM classifiant dans dynSBM, 2018
- Gonché Danesh (c), M2 Bioinformatique, Simulation de HTT, 2017
- Florent Tessier, M2 Bioinformatique, Génomique comparative du manchot, 2015
- Mamadou Dione, M2 Mathématiques, Etude de la température corporelle des marmottes en lien avec les conditions climatiques, 2014
- Camille Marchet (c), Software Engineer INRIA Bamboo, 2013-2014
- Thomas Bigot (c), Software Engineer ANR Ancestrome, 2013-2015
- Mathilde Boutigny, M1 Ingénieur, Développement du package kissplice2reftranscriptome, 2014
- Alice Julien (c), Software Engineer INRIA Bamboo, 2012-2013
- Patrick Tran Van, L3 UCBL, Intégration de programmes de calcul dédiés aux NGS dans le système GALAXY, 2012
- Vincent Lanore, M1 ENS Info, Hybrid parallel computing applied to DNA processing, 2011
- Aurélie Siberchicot (c), CDD ANR, 2010-11 (C++ development manager)
- Marie Jorandon, M1 INAPG, Etude statistique de données NGS sur l’espacement des nucléosomes, 2009
- Laurent Modolo, L3 UCBL Bio, Packaging d’une application de recherche de motifs, 2008
- econetwork A collection of advanced tools, methods and models for the analysis of ecological networks,
Collaboration with EcoNet group
- queyras A minimal deep learning image classifier, implemented in the french Alps with R and Keras
- dynsbm Dynamic stochastic block models,
Collaboration with C.Matias
- HiFiX + SiLiX Ultra-fast + High Fidelity Clustering of sequences,
efficent parallel algorithms + network science.
Collaboration with L.Duret, D.Kahn, V.Daubin & S.Penel
Ingénieur Mathematics and Modelling - Polytech Clermond-Ferrand
Master Applied Mathematics - University of Clermont Auvergne
Publications
Affichage des publications 1 à 30 sur 46 au total
Core-periphery structure in mutualistic networks: an epitaph for nestedness?
Pré-publication
voir la publicationAn appraisal of graph embeddings for comparing trophic network architectures
Methods in Ecology and Evolution .
Article dans une revue
voir la publicationRevisiting animal photo-identification using deep metric learning and network analysis
Methods in Ecology and Evolution . 12 ( 5 ) : 863-873
Article dans une revue
voir la publicationQuantifying the overall effect of biotic interactions on species communities along environmental gradients
Pré-publication
voir la publicationImages, écologie et deep learning
Regards sur la biodiversité .
Article dans une revue
voir la publicationDeep learning for species identification of modern and fossil rodent molars
Pré-publication
voir la publicationThe diversity of interaction types drives the functioning of ecological communities
DOI: 10.1101/411249
Pré-publication
voir la publicationCore–periphery dynamics in a plant–pollinator network
Journal of Animal Ecology . 89 ( 7 ) : 1670-1677
Article dans une revue
voir la publicationRevisiting giraffe photo-identification using deep learning and network analysis
Pré-publication
voir la publicationNine Quick Tips for Analyzing Network Data
PLoS Computational Biology . 15 ( 12 ) : e1007434
Article dans une revue
voir la publicationNon-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model
PLoS Computational Biology . 15 ( 8 ) : e1007269
Article dans une revue
voir la publicationDiversity indices for ecological networks: a unifying framework using Hill numbers
Ecology Letters . 22 ( 4 ) : 737-747
DOI: 10.1111/ele.13221
Article dans une revue
voir la publicationGlobal survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
PLoS Genetics . 15 ( 2 ) : e1007965
Article dans une revue
voir la publicationStatistical clustering of temporal networks through a dynamic stochastic block model
Journal of the Royal Statistical Society: Series B . 79 ( 4 ) : 1119–1141
DOI: 10.1111/rssb.12200
Article dans une revue
voir la publicationEcological networks to unravel the routes to horizontal transposon transfers
PLoS Biology . 15 ( 2 ) : np
Article dans une revue
voir la publicationRevealing the hidden structure of dynamic ecological networks
Royal Society Open Science . 4 : 170251
DOI: 10.1098/rsos.170251
Article dans une revue
voir la publicationInferring the timing of territoriality and rut in male roe deer from movements? Some preliminary results - and new perspectives
6. EURODEER meeting .
Acte de congrès
voir la publicationRéseaux et connectivité
Prospectives de l’Institut Écologie et environnement du CNRS . : 187-193
Chapitre d'ouvrage
voir la publicationPlaying hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
Algorithms for Molecular Biology . 12 ( 1 ) : 2
Article dans une revue
voir la publicationFruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies
American Naturalist . 188 ( 1 ) : 66-75
DOI: 10.1086/686684
Article dans une revue
voir la publicationInferring the timing of territoriality and rut in male roe deer from movements?
8. EURODEER meeting .
Acte de congrès
voir la publicationHow Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience
PLoS Biology . 14 ( 8 ) : e1002527
Article dans une revue
voir la publicationColib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
GigaScience . 5 ( 1 )
Article dans une revue
voir la publicationDNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity
PLoS ONE . 10 : e0129427
Article dans une revue
voir la publicationFast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles
Lecture Notes in Computer Science . 8452 : 248-258
Article dans une revue
voir la publicationSpatially constrained clustering of ecological networks
Methods in Ecology and Evolution . 5 ( 8 ) : 771-779
Article dans une revue
voir la publicationNavigating in a Sea of Repeats in RNA-seq without Drowning
WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96
Acte de congrès
voir la publicationNew developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) .
Acte de congrès
voir la publicationFast and parallel algorithm for population-based segmentation of copy-number profiles
10. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) . 8452 : 275 p.
Acte de congrès
voir la publication