A Bottom-Up Implementation of Path-Relinking for Phylogenetic Reconstruction Applied to Maximum Parsimony

In this article we describe a bottom-up implementation of Path-Relinking for Phylogenetic Trees in the context of the resolution of the Maximum Parsimony problem with Fitch optimality criterion. This bottom-up implementation is compared to two versions of an existing top-down implementation. We show that our implementation is more efficient, more interesting to compare trees and to give an estimation of the distance between two trees in terms of the number of transformation

Model and Combinatorial Optimization Methods for Tactical Planning in Closed-Loop Supply Chains

International audienc

A Metaheuristic for Tactical Inventory Planning in Closed-Loop Supply Chains

International audienc

Strategies for handling uncertainty in tactical distribution planning - an empirical study

International audienc

Une Approche par Décomposition pour la Découverte de Motifs sur Données Séquentielles

National audienc

Calcul par Contraintes de Motifs Ordonnés

Itemset and pattern mining has numerous applications ranging from Marketing to Bioinformatics. We introduce a language, dubbed Maximal Matrix Problem (MMP), to model such problems. An instance of MMP is based on a matrix of finite domain variables and a set of matrix constraints. A solution is a maximal consistent submatrix whose assignment of the variables in its scope satisfies the constraints but cannot be extended over additional lines while preserving consistency. We propose a generic CP model for MMP and present various types of matrix contraints. We then tackle the problem of partially or totally ordering patterns that have been prelocalized over sequences in order to exclude predefined sequences. We present two CP models to solve these MMP together with a genetic algorithm. Experiments on datasets of protein sequences demonstrate the efficiency of the approach.