Description
Date depot: 28 octobre 2022
Titre: Causal inference for live-cell time-lapse imaging data
Directeur de thèse:
Hervé ISAMBERT (PC_Curie)
Encadrant :
Pascal HERSEN (PC_Curie (ED515))
Domaine scientifique: Sciences et technologies de l'information et de la communication
Thématique CNRS : Sciences de l’information et sciences du vivant
Resumé: Live cell imaging microscopy, now routinely used in cell biology labs, produce massive amounts of time-lapse images at single cell resolution. However, this wealth of state-of-the-art biological data remain largely under-explored due to the lack of unsupervised methods and tools to analyze them without preconceived hypothesis. This highlights the need to develop new Machine Learning and Artificial Intelligence strategies to better exploit the richness and complexity of the information contained in time-resolved cell biology data.
The Isambert lab recently developed novel causal inference methods and tools (https://miic.curie.fr) to learn cause-effect relationships in a variety of biological or clinical datasets, from single-cell transcriptomic and genomic alteration data (Verny et al 2017, Sella et al 2018) to medical records of patients (Cabeli et al 2020). These machine learning methods combine multivariate information analysis with interpretable graphical models (Li et al 2019, Cabeli et al 2021) and outperform other methods on a broad range of benchmarks, achieving better results with only ten to hundred times fewer samples.
The objective of the present PhD project is to extend these causal inference methods to analyze time-resolved cell biology data, for which the information about cellular dynamics can facilitate the discovery of novel cause-effect functional processes. These novel causal inference methods for time series data will then be applied to time-lapse images of cellular systems (Marinkovic et al 2019) from the Hersen lab (Institut Curie) to analyze cell cycle progression and apoptosis in tumor-on-chip devices, in collaboration with the Martinelli lab (University of Rome Tor Vergata, Italy).
Doctorant.e: Tocci Tiziana