International Conference on Computational Methods in Systems Biology 2025 - Sciencesconf.org

Week Wed. 10 Thu. 11 Fri. 12 List

	Wed. 10	Thu. 11	Fri. 12
08:00 09:00 10:00 11:00 12:00 13:00 14:00 15:00 16:00 17:00 18:00 19:00 20:00 21:00	Opening - François Fages & Sabine Pérès 8:30 - 9:00 (30min) Opening - François Fages & Sabine Pérès Chair: F. Fages, Machine learning session 1 ---- Invited talk: Causal discovery and network inference for biological and biomedical data - Hervé Isambert 9:00 - 10:00 (1h) Chair: F. Fages, Machine learning session 1 ---- Invited talk: Causal discovery and network inference for biological and biomedical data - Hervé Isambert https://cmsb2025.sciencesconf.org/data/program/keynote_isambert.pdf Kolmogorov-Arnold Network for Gene Regulatory Network Inference. 10:00 - 10:30 (30min) Kolmogorov-Arnold Network for Gene Regulatory Network Inference. Tsz Pan Tong, Aoran Wang, George Panagopoulos and Jun Pang Coffee break 10:30 - 11:00 (30min) Coffee break Chair Loïc Paulevé, Boolean network session I ---- Three-State Gene Expression Model Parameterized for Single-Cell Multi-Omics Data. 11:00 - 11:30 (30min) Chair Loïc Paulevé, Boolean network session I ---- Three-State Gene Expression Model Parameterized for Single-Cell Multi-Omics Data. Thibaut Peyric, Thomas Lepoutre, Anton Crombach and Thomas Guyet Computation of immediate neighbours of monotone Boolean functions. 11:30 - 12:00 (30min) Computation of immediate neighbours of monotone Boolean functions. José E.R. Cury, Patrı́cia Roxo, Vasco Manquinho, Claudine Chaouiya and Pedro T. Monteiro. On Model Reductions of Boolean Networks. 12:00 - 12:30 (30min) On Model Reductions of Boolean Networks. Claudine Chaouiya, Jérôme Feret and Patrı́cia T. Roxo AEON 2025: Robust Control of Partially-Specified Boolean Networks (tool paper). 12:30 - 13:00 (30min) AEON 2025: Robust Control of Partially-Specified Boolean Networks (tool paper). Vojtěch Veselý, Eva Šmijáková, Samuel Pastva, Nikola Beneš and David Šafránek Lunch 13:20 - 14:30 (1h10) Lunch Chair Marco Antoniotti, Population model and control session ---- Eukaryotic ancestry in a finite world. 14:30 - 15:00 (30min) Chair Marco Antoniotti, Population model and control session ---- Eukaryotic ancestry in a finite world. Juliette Luiselli and Manuel Lafond Minimal metabolic exchanges for microbial communities in a chemostat at steady state. 15:00 - 15:30 (30min) Minimal metabolic exchanges for microbial communities in a chemostat at steady state. Alix Moawad and Jörg Stelling Seed inference in interacting microbial communities using combinatorial optimization. 15:30 - 16:00 (30min) Seed inference in interacting microbial communities using combinatorial optimization. Chabname Ghassemi Nedjad, Clémence Frioux, Loı̈c Paulevé and Sebastı́an Nelson Mendoza A model-free control strategy for selective disruption of parkinsonian brain oscillations. 16:00 - 16:30 (30min) A model-free control strategy for selective disruption of parkinsonian brain oscillations. Cédric Join, Jakub Orlowski, Antoine Chaillet, Madeleine Lowery, Hugues Mounier and Michel Fliess Poster aperitif: 25 posters exposed for discussion in lunch room 16:30 - 18:30 (2h) Poster aperitif: 25 posters exposed for discussion in lunch room	Chair Jun Pang, Machine learning session 2 ---- Invited talk: Kernel-based perturbation testing for single-cell data - Franck Picard 9:00 - 10:00 (1h) Chair Jun Pang, Machine learning session 2 ---- Invited talk: Kernel-based perturbation testing for single-cell data - Franck Picard https://cmsb2025.sciencesconf.org/data/program/keynote_picard.pdf Optimal input design for model selection in systems with cell-to-cell variability. 10:00 - 10:30 (30min) Optimal input design for model selection in systems with cell-to-cell variability. Andrea Stallvik, Hans-Michael Kaltenbach and Jörg Stelling Coffee break 10:30 - 11:00 (30min) Coffee break Chair Ion Petre, Machine learning session 3 ---- Decoding Gene Regulation in Alzheimer’s disease with Transfer Learning and Explainable Machine Learning. 11:00 - 11:30 (30min) Chair Ion Petre, Machine learning session 3 ---- Decoding Gene Regulation in Alzheimer’s disease with Transfer Learning and Explainable Machine Learning. Sergio Peignier, Amanda Lo Van, Yann Meunier, Elea Pauliat, Matis Zouari and Federica Calevro Interaction Graphs of Phytoplankton Species Interactions using Logical Learning 11:30 - 12:00 (30min) Interaction Graphs of Phytoplankton Species Interactions using Logical Learning Madeleine Eyraud, Maxime Folschette, Katsumi Inoue, Sébastien Lefebvre and Cédric Lhoussaine Evaluating PDE discovery methods for multiscale modeling of biological signals. 12:00 - 12:30 (30min) Evaluating PDE discovery methods for multiscale modeling of biological signals. Andréa Ducos, Audrey Denizot, Thomas Guyet and Hugues Berry Optimizing Feature Extraction Methods using Class Similarity Ratio for EMG-based Hand Gesture Classification. 12:30 - 13:00 (30min) Optimizing Feature Extraction Methods using Class Similarity Ratio for EMG-based Hand Gesture Classification. Felicity Escarzaga, Brian Donnelly and Kyle Winfree Lunch and posters 13:20 - 14:30 (1h10) Lunch and posters Chair Elisabeth Pecou, Invited talk: Reverse Engineering and Optimization of Metabolic Networks - Susana Vinga 14:30 - 15:30 (1h) Chair Elisabeth Pecou, Invited talk: Reverse Engineering and Optimization of Metabolic Networks - Susana Vinga https://cmsb2025.sciencesconf.org/data/program/keynote_vinga.pdf Chair Pedro Monteiro, Boolean network session 2 ---- Continuous Petri Nets Faithfully Fluidify Most Permissive Boolean Networks. 15:30 - 16:00 (30min) Chair Pedro Monteiro, Boolean network session 2 ---- Continuous Petri Nets Faithfully Fluidify Most Permissive Boolean Networks. Stefan Haar and Juri Kolčák Looking for Signs: Reasoning About FOBNNs Using SAT. 16:00 - 16:30 (30min) Looking for Signs: Reasoning About FOBNNs Using SAT. Hans-Jörg Schurr and Athénaı̈s Vaginay Social event 16:30 - 19:00 (2h30) Social event in Lugdunum Dinner 19:00 - 21:00 (2h) Dinner	Chair: Sabine Pérès, Invited talk: Predicting metabolic interactions between multiple species from first principles - Jörg Stellling 9:00 - 10:00 (1h) Chair: Sabine Pérès, Invited talk: Predicting metabolic interactions between multiple species from first principles - Jörg Stellling https://cmsb2025.sciencesconf.org/data/program/keynote_stelling.pdf Chair Stefan Haar, Continuous and hybrid models session ---- Efficient stochastic simulation of gene regulatory networks using hybrid models of transcriptional bursting. 10:00 - 10:30 (30min) Chair Stefan Haar, Continuous and hybrid models session ---- Efficient stochastic simulation of gene regulatory networks using hybrid models of transcriptional bursting. Mathilde Gaillard and Ulysse Herbach Coffee break 10:30 - 11:00 (30min) Coffee break Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN. 11:00 - 11:30 (30min) Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN. Maryam Yousefian, Luca Donati, Alexander Sikorski, Marcus Weber and Susanna Röblitz Chair Linda Brodo, Rule-based models session ---- Reachability Analysis for Parametric Rule-Based Models. 11:30 - 12:00 (30min) Chair Linda Brodo, Rule-based models session ---- Reachability Analysis for Parametric Rule-Based Models. Jerome Feret and Rebecca Ghidini A rule-based modeling approach for studying animal collectives: a case study of juvenile honeybee thermotaxis. 12:00 - 12:30 (30min) A rule-based modeling approach for studying animal collectives: a case study of juvenile honeybee thermotaxis. Matthieu Bouguéon, Tatjana Petrov and Albin Salazar A Formal Approach to Identify Structural Patterns in RNA. 12:30 - 13:00 (30min) A Formal Approach to Identify Structural Patterns in RNA. Michele Loreti, Michela Quadrini, Matteo Scoccia and Luca Tesei Closing session 13:00 - 13:10 (10min) Closing session Lunch 13:20 - 14:30 (1h10) Lunch

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