
Miele Vincent
Ingénieur de recherche
CNRS
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 (co-leader of the DeepFaune project) and sharing knowledge with ecologists.
I am almost 100% degooglized, but you can still have a look at my scholar profile.
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
- Ecological Informatics
- 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"
- Gaspard Dussert (c), Doc, DeepFaune project, 2022-25
- 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
- deepfaune Automatic identification of the French fauna in camera-trap images
Collaboration with Simon Chamaillé-Jammes et Bruno Spataro - econetwork A collection of advanced tools, methods and models for the analysis of ecological networks,
Collaboration with EcoNet group - 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
- 2023- : Ingenieur de Recherche CNRS hors classe, Laboratory Biometry and Evolutionary Biology (U.Lyon)
- 2017-2022 : Ingenieur de Recherche CNRS 1ère classe, Laboratory Biometry and Evolutionary Biology (U.Lyon)
- 2008-2016 : Ingenieur de Recherche CNRS 2nd classe, Laboratory Biometry and Evolutionary Biology (U.Lyon)
- 2001-2007 : Ingenieur de Recherche CNRS 2nd classe, Laboratory Statistics and Genome (U.Evry)
- 2000 : Ingénieur "Grandes écoles" Mathematics and Modelling - (Polytech Clermond-Ferrand)
- 2000 : Master Applied Mathematics (U.Clermont Auvergne)
Publications
Display of 1 to 30 publications on 48 in total
Quantifying the overall effect of biotic interactions on species distributions along environmental gradients
Preprint
see the publicationThe DeepFaune initiative: a collaborative effort towards the automatic identification of the French fauna in camera-trap images
Preprint
see the publicationChapter 6: Using Latent Block Models to Detect Structure in Ecological Networks
Statistical Approaches for Hidden Variables in Ecology. . : 117-134
Book chapter
see the publicationAn appraisal of graph embeddings for comparing trophic network architectures
Methods in Ecology and Evolution . 13 ( 1 ) : 203-216
Journal article
see the publicationCore-periphery structure in mutualistic networks: an epitaph for nestedness?
Preprint
see the publicationRevisiting animal photo-identification using deep metric learning and network analysis
Methods in Ecology and Evolution . 12 ( 5 ) : 863-873
Journal article
see the publicationRevisiting giraffe photo-identification using deep learning and network analysis
Preprint
see the publicationDeep learning for species identification of modern and fossil rodent molars
Preprint
see the publicationThe diversity of interaction types drives the functioning of ecological communities
DOI: 10.1101/411249
Preprint
see the publicationCore–periphery dynamics in a plant–pollinator network
Journal of Animal Ecology . 89 ( 7 ) : 1670-1677
Journal article
see the publicationGlobal survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot
PLoS Genetics . 15 ( 2 ) : e1007965
Journal article
see the publicationNine Quick Tips for Analyzing Network Data
PLoS Computational Biology . 15 ( 12 ) : e1007434
Journal article
see the publicationNon-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model
PLoS Computational Biology . 15 ( 8 ) : e1007269
Journal article
see the publicationDiversity indices for ecological networks: a unifying framework using Hill numbers
Ecology Letters . 22 ( 4 ) : 737-747
DOI: 10.1111/ele.13221
Journal article
see the publicationInferring the timing of territoriality and rut in male roe deer from movements? Some preliminary results - and new perspectives
6. EURODEER meeting .
Conference paper
see the 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
Journal article
see the 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
Journal article
see the publicationEcological networks to unravel the routes to horizontal transposon transfers
PLoS Biology . 15 ( 2 ) : np
Journal article
see the publicationRevealing the hidden structure of dynamic ecological networks
Royal Society Open Science . 4 : 170251
DOI: 10.1098/rsos.170251
Journal article
see the publicationRéseaux et connectivité
Prospectives de l’Institut Écologie et environnement du CNRS . : 187-193
Book chapter
see the publicationInferring the timing of territoriality and rut in male roe deer from movements?
8. EURODEER meeting .
Conference paper
see the 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
Journal article
see the publicationColib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
GigaScience . 5 ( 1 )
Journal article
see the 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
Journal article
see the publicationDNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity
PLoS ONE . 10 : e0129427
Journal article
see the publicationSpatially constrained clustering of ecological networks
Methods in Ecology and Evolution . 5 ( 8 ) : 771-779
Journal article
see the publicationFast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles
Lecture Notes in Computer Science . 8452 : 248-258
Journal article
see the publicationNavigating in a Sea of Repeats in RNA-seq without Drowning
WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96
Conference paper
see the publication