Vincent MIELE

Publications

Article dans une revue (42)

Paying attention to other animal detections improves camera trap classification models Gaspard Dussert,Stéphane Dray,Simon Chamaillé‐jammes,Vincent Miele Methods in Ecology and Evolution, 2026, 17 (4), pp.1248-1258. ⟨10.1111/2041-210x.70260⟩ Article dans une revue hal-05543064v1
Zero‐shot animal behaviour classification with vision‐language foundation models Gaspard Dussert,Vincent Miele,Colin van Reeth,Anne Delestrade,Stéphane Drayet al. Methods in Ecology and Evolution, 2025, 16 (7), pp.1460-1472. ⟨10.1111/2041-210x.70059⟩ Article dans une revue hal-05093147v1
Multilayer Network Analysis Reveals Connectivity Synergies Between Protected Area Levels Across Various Taxonomic Groups Marie‐caroline Prima,Lucia Oliveira-Cruz,Vincent Miele,Sara Si-Moussi,Paul Rouveyrolet al. Conservation Letters, 2025, 18 (5), pp.e13148. ⟨10.1111/conl.13148⟩ Article dans une revue hal-05308071v1
ORCHAMP: an observation network formonitoring biodiversity and ecosystem functioning across space and time inmountainous regions Wilfried Thuiller,Amélie Saillard,Sylvain Abdulhak,Vincent Augé,Carole Bircket al. Comptes Rendus. Biologies, 2024, 347, pp.223-247. ⟨10.5802/crbiol.165⟩ Article dans une revue hal-04793697v1
Being confident in confidence scores: calibration in deep learning models for camera trap image sequences Gaspard Dussert,Simon Chamaillé-Jammes,Stéphane Dray,Vincent Miele Remote Sensing in Ecology and Conservation, 2024, 11 (1), pp.88-99. ⟨10.1002/rse2.412⟩ Article dans une revue hal-04749328v1
The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images Noa Rigoudy,Gaspard Dussert,Abdelbaki Benyoub,Aurélien Besnard,Carole Bircket al. European Journal of Wildlife Research, 2023, 69 (6), pp.113. ⟨10.1007/s10344-023-01742-7⟩ Article dans une revue hal-04278674v2
Quantifying the overall effect of biotic interactions on species distributions along environmental gradients Marc Ohlmann,Catherine Matias,Giovanni Poggiato,Stéphane Dray,Wilfried Thuilleret al. Ecological Modelling, 2023, 483, pp.110424. ⟨10.1016/j.ecolmodel.2023.110424⟩ Article dans une revue hal-03172480v4
An appraisal of graph embeddings for comparing trophic network architectures Christophe Botella,Stéphane Dray,Catherine Matias,Vincent Miele,Wilfried Thuiller Methods in Ecology and Evolution, 2022, 13 (1), pp.203-216. ⟨10.1111/2041-210X.13738⟩ Article dans une revue hal-03191630v2
Revisiting animal photo-identification using deep metric learning and network analysis Vincent Miele,Gaspard Dussert,Bruno Spataro,Simon Chamaillé-Jammes,Dominique Allainéet al. Methods in Ecology and Evolution, 2021, 12 (5), pp.863-873. ⟨10.1111/2041-210X.13577⟩ Article dans une revue hal-03425925v1
Images, écologie et deep learning Vincent Miele,Stéphane Dray,Olivier Gimenez Regards sur la biodiversité, 2021 Article dans une revue hal-03142486v1
Core–periphery dynamics in a plant–pollinator network Vincent Miele,Rodrigo Ramos-Jiliberto,Diego Vázquez Journal of Animal Ecology, 2020, 89 (7), pp.1670-1677. ⟨10.1111/1365-2656.13217⟩ Article dans une revue hal-03418817v1
The diversity of interaction types drives the functioning of ecological communities Vincent Miele,Christian Guill,Rodrigo Ramos-Jiliberto,Sonia Kéfi PLoS Computational Biology, 2019, 15 (8), pp.e1007269. ⟨10.1101/411249⟩ Article dans une revue hal-03009740v1
Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot Daphné Reiss,Gladys Mialdea,Vincent Miele,Damien M. de Vienne,Jean Peccoudet al. PLoS Genetics, 2019, 15 (2), pp.e1007965. ⟨10.1371/journal.pgen.1007965⟩ Article dans une revue hal-02140494v1
Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model Vincent Miele,Christian Guill,Rodrigo Ramos-Jiliberto,Sonia Kéfi PLoS Computational Biology, 2019, 15 (8), pp.e1007269. ⟨10.1371/journal.pcbi.1007269⟩ Article dans une revue hal-02331446v1
Diversity indices for ecological networks: a unifying framework using Hill numbers Marc Ohlmann,Vincent Miele,Stéphane Dray,Loic Chalmandrier,Louise O’connoret al. Ecology Letters, 2019, 22 (4), pp.737-747. ⟨10.1111/ele.13221⟩ Article dans une revue hal-02078993v1
Nine Quick Tips for Analyzing Network Data Vincent Miele,Stephane S. Robin,Catherine Matias,Stéphane Dray PLoS Computational Biology, 2019, 15 (12), pp.e1007434. ⟨10.1371/journal.pcbi.1007434⟩ Article dans une revue hal-02089501v2
Statistical clustering of temporal networks through a dynamic stochastic block model Catherine Matias,Vincent Miele Journal of the Royal Statistical Society: Series B, 2017, 79 (4), pp.1119-1141. ⟨10.1111/rssb.12200⟩ Article dans une revue hal-01167837v2
Ecological networks to unravel the routes to horizontal transposon transfers Samuel Venner,Vincent Miele,Christophe Terzian,Christian Biemont,Vincent Daubinet al. PLoS Biology, 2017, 15 (2), ⟨10.1371/journal.pbio.2001536⟩ Article dans une revue hal-01608245v1
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads Leandro Lima,Blerina Sinaimeri,Gustavo Sacomoto,Helene Lopez-Maestre,Camille Marchetet al. Algorithms for Molecular Biology, 2017, 12 (1), pp.2. ⟨10.1186/s13015-017-0091-2⟩ Article dans une revue hal-01474524v1
Revealing the hidden structure of dynamic ecological networks Vincent Miele,Catherine Matias Royal Society Open Science, 2017, 4, pp.170251. ⟨10.1098/rsos.170251⟩ Article dans une revue hal-01426652v1
Fruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies Samuel Venner,A. Siberchicot,P.F. Pélisson,E. Schermer,Marie-Claude Bel-Venneret al. The American Naturalist, 2016, 188 (1), pp.66-75. ⟨10.1086/686684⟩ Article dans une revue hal-02049895v1
How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience Sonia Kéfi,Vincent Miele,Evie Wieters,Sergio Navarrete,Eric Berlow PLoS Biology, 2016, 14 (8), pp.e1002527. ⟨10.1371/journal.pbio.1002527⟩ Article dans une revue hal-01938697v1
Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads Yvan Le Bras,Olivier Collin,Cyril Monjeaud,Vincent Lacroix,Eric Rivalset al. GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩ Article dans une revue hal-01280238v1
DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity Monica Naughtin,Zofia Haftek-Terreau,Johan Xavier,Sam Meyer,Maud Silvainet al. PLoS ONE, 2015, 10, pp.e0129427. ⟨10.1371/journal.pone.0129427⟩ Article dans une revue pasteur-01416841v1
Fast and Parallel Algorithm for Population-Based Segmentation of Copy-Number Profiles Guillem Rigaill,Vincent Miele,Franck Picard Lecture Notes in Computer Science, 2014, 8452, pp.248-258 Article dans une revue hal-02045097v1
Spatially constrained clustering of ecological networks Vincent Miele,Franck Picard,S. Dray Methods in Ecology and Evolution, 2014, 5 (8), pp.771-779. ⟨10.1111/2041-210X.12208⟩ Article dans une revue hal-02045124v1
Toward community standards in the quest for orthologs Christophe Dessimoz,Toni Gabaldon,David Roos,Erik L L Sonnhammer,Javier Herreroet al. Bioinformatics, 2012, 28 (6), pp.900-904. ⟨10.1093/bioinformatics/bts050⟩ Article dans une revue hal-01636872v1
High-quality sequence clustering guided by network topology and multiple alignment likelihood. Vincent Miele,Simon Penel,Vincent Daubin,Franck Picard,Daniel Kahnet al. Bioinformatics, 2012, 28 (8), pp.1078-85. ⟨10.1093/bioinformatics/bts098⟩ Article dans une revue hal-00965711v1
Ultra-fast sequence clustering from similarity networks with SiLiX V. Miele,Simon Penel,L. Duret BMC Bioinformatics, 2011, 12(116), pp.1-9. ⟨10.1186/1471-2105-12-116⟩ Article dans une revue hal-00698365v1
Strategies for online inference of model-based clustering in large and growing networks H. Zanghi,Franck Picard,V. Miele,C. Ambroise Annals of Applied Statistics, 2010, 4 (2), pp.687-714. ⟨10.1214/10-AOAS359⟩ Article dans une revue hal-00539318v1
Deciphering the connectivity structure of biological networks using MixNet Franck Picard,V. Miele,L. Cottret,J.J. Daudin,S. Robin BMC Bioinformatics, 2009, in press, pp.1-1 Article dans une revue hal-00391483v1
Deciphering the connectivity structure of biological networks using MixNet Franck Picard,Vincent Miele,Jean-Jacques J.-J. Daudin,Ludovic Cottret,Stephane S. Robin BMC Bioinformatics, 2009, 10, pp.1-11. ⟨10.1186/1471-2105-10-S6-S17⟩ Article dans une revue hal-02658961v1
Deciphering the connectivity structure of biological networks using MixNet Franck Picard,V. Miele,J.J. Daudin,L. Cottret,S. Robin BMC Bioinformatics, 2009, 10, pp.1-11 Article dans une revue hal-00428390v1
DNA physical properties determine nucleosome occupancy from yeast to fly V. Miele,C. Vaillant,Y. d'Aubenton-Carafa,C. Thermes,T. Grange Nucleic Acids Research, 2008, 36, pp.3746-3756 Article dans une revue hal-00428131v1
Fast online graph clustering via Erdos–Rényimixture H. Zanghi,C. Ambroise,V. Miele Pattern Recognition, 2008, 41, pp.3592-3599 Article dans une revue hal-00428182v1
DNA physical properties determine nucleosome occupancy from yeast to fly. Vincent Miele,Cédric Vaillant,Yves d'Aubenton-Carafa,Claude Thermes,Thierry Grange Nucleic Acids Research, 2008, 36 (11), pp.3746-56. ⟨10.1093/nar/gkn262⟩ Article dans une revue hal-00319296v1
Taking into account missing genotypes and errors in Family Based Association Testing using an Expectation-Maximization framework V. Miele,Y. Slaoui,A. Rebai incollection, 2008, --, pp.508-514 Article dans une revue hal-00428088v1
A reversible jump Markov chain Monte Carlo algorithm for bacterial promoter motifs discovery Pierre P. Nicolas,Anne-Sophie Tocquet,Vincent Miele,Florence Muri Journal of Computational Biology, 2006, 13 (3), pp.651-667 Article dans une revue hal-02654141v1
A reversible jump Markov chain Monte Carlo algorithm for bacterial promoter motifs discovery P. Nicolas,A.-S. Tocquet,V. Miele,F. Muri Journal of Computational Biology, 2006, 13, pp.651-667 Article dans une revue hal-00428049v1
DNA sequence drives nucleosome occupancy of yeast promoters V. Miele,C. Vaillant,Y. d'Aubenton,David Robelin,B. Prumet al. incollection, 2006, --, pp.2783-2784 Article dans une revue hal-00427880v1
Uncovering structure in biological networks J.J. Daudin,Vincent Lacroix,M. Mariadassou,V. Miele,Franck Picardet al. incollection, 2006, --, pp.471-483 Article dans une revue hal-00427936v1
seq++: a package for biological sequences analysis with a range of Markov-related models V. Miele,P.Y. Bourguignon,David Robelin,Gregory Nuel,H. Richard Bioinformatics, 2005, 21, pp.2783-2784 Article dans une revue hal-00427832v1

Cours (1)

Using synthetic controls to attribute biodiversity shifts to remotely sensed landscape modifications Joaquim Estopinan,Sara Si‐moussi,Lori Giagnacovo,Vincent Miele,Wilfried Thuiller École thématique. France. 2025, pp.13 Cours hal-04947333v1

Communication dans un congrès (6)

DeepFaune: A journey towards an efficient classifier for the european fauna Vincent Miele LifeCLEF, Alexis Joly; Henning Müller; Hervé Goëau, Sep 2024, Grenoble, France Communication dans un congrès hal-04849520v1
Inferring the timing of territoriality and rut in male roe deer from movements? Nicolas Morellet,Christophe Bonenfant,Vincent Miele,Marco Heurich,Stefano Focardi 8. EURODEER meeting, Jun 2016, Badia di Moscheta, Italy Communication dans un congrès hal-02793574v1
Inferring the timing of territoriality and rut in male roe deer from movements? Some preliminary results - and new perspectives Nicolas Morellet,Vincent Miele,Christophe Bonenfant 6. EURODEER meeting, Jun 2017, Grimsö, Sweden Communication dans un congrès hal-02793581v1
Fast and parallel algorithm for population-based segmentation of copy-number profiles Guillem Rigaill,Vincent Miele,Franck Picard 10. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), Jun 2013, Nice, France. 275 p., ⟨10.1007/978-3-319-09042-9_18⟩ Communication dans un congrès hal-02742012v1
Navigating in a Sea of Repeats in RNA-seq without Drowning Gustavo Sacomoto,Blerina Sinaimeri,Camille Marchet,Vincent Miele,Marie-France Sagotet al. WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics, Sep 2014, Wroclaw, Poland. pp.82-96, ⟨10.1007/978-3-662-44753-6_7⟩ Communication dans un congrès hal-01079947v1
New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data Alice Julien-Laferriere,Gustavo Sacomoto,Rayan Chikhi,Erwan Scaon,David P. Parsonset al. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2013, Toulouse, France Communication dans un congrès hal-02069363v1

Pré-publication, Document de travail (6)

Zero-shot animal behavior classification with vision-language foundation models Gaspard Dussert,Vincent Miele,Colin van Reeth,Anne Delestrade,Stéphane Drayet al. 2024 Pré-publication, Document de travail hal-04779471v1
Beyond accuracy : score calibration in deep learning models for camera trap image sequences Gaspard Dussert,Simon Chamaillé-Jammes,Stéphane Dray,Vincent Miele 2023 Pré-publication, Document de travail hal-04305463v1
Nine tips for ecologists using machine learning Marine Desprez,Vincent Miele,Olivier Gimenez 2023 Pré-publication, Document de travail hal-04168831v1
Core-periphery structure in mutualistic networks: an epitaph for nestedness? Ana Martín González,Diego Vázquez,Rodrigo Ramos-Jiliberto,Sang Hoon Lee,Vincent Miele 2021 Pré-publication, Document de travail hal-03418833v1
Deep learning for species identification of modern and fossil rodent molars Vincent Miele,Gaspard Dussert,Thomas Cucchi,S. Renaud 2020 Pré-publication, Document de travail hal-03024134v1
Revisiting giraffe photo-identification using deep learning and network analysis Vincent Miele,Gaspard Dussert,Bruno Spataro,Simon Chamaillé-Jammes,Dominique Allainéet al. 2020 Pré-publication, Document de travail hal-03029446v1

Chapitre d'ouvrage (2)

Chapter 6: Using Latent Block Models to Detect Structure in Ecological Networks Julie J. Aubert,Pierre M Barbillon,Sophie Donnet,Vincent Miele Statistical Approaches for Hidden Variables in Ecology., Wiley, pp.117-134, 2022, ⟨10.1002/9781119902799.ch6⟩ Chapitre d'ouvrage hal-03811607v1
Réseaux et connectivité Etienne Edouard Cossart,Colin Fontaine,Grégor Marchand,Marie Balasse,Stéphanie Bréhardet al. Stéphanie Thiébault et al. (coord.). Prospectives de l’Institut Écologie et environnement du CNRS, CNRS, pp.187-193, 2017, Les Cahiers Prospectives Chapitre d'ouvrage hal-02473919v1

Rapport (1)

Dynamic of social interactions: analysis and modeling from movement in several large mammal species Thibault Génissel,Vincent Miele,Anne Loison CNRS. 2020 Rapport hal-04934960v1

Ouvrages (1)

Calcul parallèle avec R Vincent Miele,Violaine Louvet EDP sciences, 2016, 978-2-7598-2060-3 Ouvrages hal-02090003v1