Outcomes

Outcomes created during the M4DI project

Project HAL link: https://hal.science/search/index/q/*/anrProjectId_i/98247

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26 documents

Journal articles4 document
David P Hirst, Morgane Térézol, Laura Cantini, Paul Villoutreix, Matthieu Vignes, et al.. MOTL: enhancing multi-omics matrix factorization with transfer learning. Genome Biology, 2025, 26 (1), pp.224. ⟨10.1186/s13059-025-03675-7⟩. ⟨hal-05212749v2⟩
Nawel Benarba, Sara Bouchenak. Bias in Federated Learning: A Comprehensive Survey. ACM Computing Surveys, 2025, ⟨10.1145/3735125⟩. ⟨hal-05093158⟩
Amazigh Mokhtari, El Chérif Ibrahim, Arnaud Gloaguen, Claire-Cécile Barrot, David Cohen, et al.. Using multiomic integration to improve blood biomarkers of major depressive disorder: a case-control study. EBioMedicine, 2025, 113, pp.105569. ⟨10.1016/j.ebiom.2025.105569⟩. ⟨hal-04934910⟩
Elise Amblard, Vadim Bertrand, Hugo Barbot, Luis Martin Peña, Slim Karkar, et al.. A robust workflow to benchmark deconvolution of multi-omic data. Genome Biology, 2025, 26 (1), pp.429. ⟨10.1186/s13059-025-03897-9⟩. ⟨hal-05444478⟩

Conference papers9 document
Silvia Grosso, Samuele Fonio, Mirko Polato, Roberto Esposito, Sara Bouchenak. When Curvature Counts: Hyperbolic Geometry in Prototype-Based Image Classification. European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN), Apr 2026, Bruges, Belgium. pp.511-516, ⟨10.14428/esann/2026.ES2026-214⟩. ⟨hal-05538796⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Inferring cellular heterogeneity with mixture models for DNA methylation rates (SMPGD 2026). SMPGD 2026, Jan 2026, Grenoble, France. ⟨hal-05489490⟩
Joanna Pautonnier, David Causeur, Pascal Roy. Améliorer la sélection et la précision des modèles de survie : une approche bayésienne spike and slab.. Journée AppliBUGS, Dec 2025, Lyon, France. ⟨hal-05568489⟩
Samuele Fonio, Silvia Grosso, Sara Bouchenak. Non-Euclidean Geometries for Prototype-Based Image Classification: a Reality Check. Proceedings of the 4th Italian Conference on Big Data and Data Science (ITADATA 2025), Sep 2025, Torino, Italy. ⟨hal-05557672⟩
Margot Derouin, Amazigh Mokhtari, El Chérif Ibrahim, Pierre-Eric Lutz, Raoul Belzeaux, et al.. Leveraging multi-omics integration to uncover childhood traumarelated mechanisms in bipolar disorder. JOBIM 2025, Jul 2025, Bordeaux, France. pp.228-229. ⟨hal-05344676⟩
H Barbot, D Causeur, Y Blum, M Richard. Inferring cellular heterogeneity with mixture models for DNA methylation rates. Journées de Statistique, Jun 2025, Marseille, France. ⟨hal-05489385⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Inferring cellular heterogeneity with mixture models for DNA methylation rates. JdS, Jun 2025, Marseille, France. ⟨hal-05065027⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Multi-omic statistical inference of cellular heterogeneity – JOBIM 2024. JOBIM 2024, Jun 2024, Toulouse, France. ⟨hal-04664788⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Multi-omic statistical inference of cellular heterogeneity – JdS 2024. JdS 2024, May 2024, Bordeaux, France. ⟨hal-04664748⟩

Poster communications6 document
Océane Carpentier, Yann Le Cunff, Emmanuelle Becker, Nicolas Jay, Aurélie Bannay. Definition of an ontology consistent Adjusted Rand Index (ARIoc). MosAIK PhD Day, Dec 2025, Nancy, France. 2025. ⟨hal-05569869⟩
Elouan Deffains, Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Evaluation of linear modeling assumptions in a simulation context for deconvolution of multi-omic data. Journée de Biologie In Silico de Rennes, Nov 2025, Rennes, France. . ⟨hal-05489405⟩
Florence Ghestem, Gaëlle Marenne, Emmanuelle Genin, Anne-Sophie Jannot, Anaïs Baudot, et al.. Knowledge graph to dissect genotype phenotype associations. IGES 2025 – Annual Meeting on International Genetic Epidemiology Society, Aug 2025, Cologne, Germany. 2025. ⟨hal-05333821⟩
Christophe Vroland, Rodrigo Pracana, Alice Lambolez, Pelin Sahlén, Masaki Kato, et al.. DNA replication timing and Copy Number Variations are confounders of ATAC-Seq and RNA-DNA interaction data. ISBM/ECCB 2025 – 33rd Conference on Intelligent Systems for Molecular Biology and 24th European Conference on Computational Biology, Jul 2025, Liverpool, United Kingdom. . ⟨hal-05162278v3⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Simulation of data-driven multi-omic benchmark data for cellular deconvolution methods evaluation. IGDR PhD symposium, Nov 2024, Rennes (Campus de Beaulieu), France. 2024. ⟨hal-04790951⟩
Hugo Barbot, David Causeur, Yuna Blum, Magali Richard. Multi-omic statistical inference of cellular heterogeneity – COBICA 2024. cobica2024 : Computational Biology of Cancer 2024, Mar 2024, Grenoble, France. ⟨hal-04664694⟩

Preprints, Working Papers6 document
Nicolas Homberg, Lucie Lamothe, Elise Amblard, Hugo Barbot, Morgane Térézol, et al.. How to organise a scientific competition to benchmark methods and algorithms in computational biology?. 2026. ⟨hal-05445539v2⟩
Rahaf Ahmad, Michał Denkiewicz, Rishika Gupta, Sachin Gadakh, Jędrzej Kubica, et al.. AI for Computational Biology: Highlights from the first BioAI Hackathon at University of Warsaw. 2025. ⟨hal-05274112⟩
Siddharth Sabata, Jędrzej Kubica, Rishika Gupta, Lars Warren Ericson, Halimat Chisom Atanda, et al.. Addressing Background Genomic and Environmental Effects on Health through Accelerated Computing and Machine Learning: Results from the 2025 Hackathon at Carnegie Mellon University. 2025. ⟨hal-05274100⟩
Silvia Grosso, Nawel Benarba, Sara Bouchenak, Roberto Esposito, Mirko Polato. A Survey on Multimodal Federated Learning. 2025. ⟨hal-05366356v2⟩
Océane Cassan, Julien Raynal, Christophe Vroland, Kayoko Yasuzawa, Tsukasa Kouno, et al.. A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation. 2025. ⟨hal-05069585⟩
Mathys Grapotte, Christophe Vroland, Diego Garrido-Martín, Alessio Vignoli, Lisa Calero, et al.. Evidence of distal regulations orchestrated by RNAs initiating at short tandem repeats. 2025. ⟨hal-05030164⟩

Lectures1 document
Hugo Barbot. Reminder on hypothesis testing. Master. Rennes, France. 2025. ⟨hal-05065036⟩