Séminaire virtuel: vendredi 4 février 2022
Tony Ribeiro (LS2N, Nantes) et Philippe Dague (Univ Paris-Saclay)

Lien Zoom

  • Meeting ID: 867 6409 6440
  • passcode: 149120

13h00 - 13h30 – Tony Ribeiro (LS2N, Nantes)

Learning Dynamical Interactions Within Marine Ecosystems with LFIT

Learning From Interpretation Transition (LFIT) is a framework that aims at learning the dynamics of a system by observing its state transitions. LFIT provides explainable predictions in the form of logical rules. In this work, we introduce a method that allows to extract an influence graph from a LFIT model and illustrate it on a marine dataset. Marine ecology models are used to study and anticipate population variations of plankton and microalgae species. These variations can have an impact on ecological niches, the economy or the climate. Our objective is the automation of the creation of such models.

13h30 - 14h00 – Philippe Dague (Univ Paris-Saclay)

Metabolic Pathway Analysis in the Presence of Biological Constraints

Metabolic pathway analysis is a key method to study a metabolism in its steady state, and the concept of elementary fluxes (EFs) plays a major role in the analysis of a network in terms of non-decomposable pathways. The supports of the EFs contain in particular those of the elementary flux modes (EFMs), which are the support-minimal pathways, and EFs coincide with EFMs when the only flux constraints are given by the irreversibility of certain reactions. Practical use of both EFMs and EFs has been hampered by the combinatorial explosion of their number in large, genome-scale systems. The EFs give the possible pathways in a steady state but the real pathways are limited by biological constraints, such as thermodynamic or, more generally, kinetic constraints and regulatory constraints from the genetic network. We provide results on the mathematical structure and geometrical characterization of the solution space in the presence of such biological constraints (which is no longer a convex polyhedral cone or a convex polyhedron) and revisit the concept of EFMs and EFs in this framework. We show that most of the results depend only on very general properties of compatibility of constraints with vector signs: either sign-invariance, satisfied by regulatory constraints, or sign-monotonicity (a stronger property), satisfied by thermodynamic and kinetic constraints. We show in particular that the solution space for sign-monotone constraints is a union of particular faces of the original polyhedral cone or polyhedron and that EFs still coincide with EFMs and are just those of the original EFs that satisfy the constraint, and we show how to integrate their computation efficiently in the double description method, the most widely used method in the tools dedicated to EFs computation. We show that, for sign-invariant constraints, the situation is more complex: the solution space is a disjoint union of particular semi-open faces (i.e., without some of their own faces of lesser dimension) of the original polyhedral cone or polyhedron and, if EFs are still those of the original EFs that satisfy the constraint, their computation cannot be incrementally integrated into the double description method, and the result is not true for EFMs, that are in general strictly more numerous than those of the original EFMs that satisfy the constraint.

Dernière modification le 04/02/2022