Soft Pattern Discovery in Pre-Classified Protein Families through Constraint Optimization

International audienc

A Decomposition Approach for Discovering Discriminative Motifs in a Sequence Database

Short paperInternational audienceThis paper addresses the discovery of discriminative nary motifs in databases of labeled sequences. We consider databases made up of positive and negative sequences and define a motif as a set of patterns embedded in all positive sequences and subject to alignment constraints. We formulate constraints to eliminate redundant motifs and present a general constraint optimization framework to compute motifs that are exclusive to the positive sequences. We cast the discovery of closed and replication-free motifs in this framework and propose a two-stage approach whose last stage reduces to a minimum set covering problem. Experiments on protein sequence datasets demonstrate its efficiency

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.

Developing Approaches for Solving a Telecommunications Feature Subscription Problem

Call control features (e.g., call-divert, voice-mail) are primitive options to which users can subscribe off-line to personalise their service. The configuration of a feature subscription involves choosing and sequencing features from a catalogue and is subject to constraints that prevent undesirable feature interactions at run-time. When the subscription requested by a user is inconsistent, one problem is to find an optimal relaxation, which is a generalisation of the feedback vertex set problem on directed graphs, and thus it is an NP-hard task. We present several constraint programming formulations of the problem. We also present formulations using partial weighted maximum Boolean satisfiability and mixed integer linear programming. We study all these formulations by experimentally comparing them on a variety of randomly generated instances of the feature subscription problem

Electrical Network-Based Time-Dependent Model of Electrical Breakdown in Water

A time-dependent, two-dimensional, percolative approach to model dielectric breakdown based on a network of parallel resistor–capacitor elements having random values, has been developed. The breakdown criteria rely on a threshold electric field and on energy dissipation exceeding the heat of vaporization. By carrying out this time-dependent analysis, the development and propagation of streamers and prebreakdown dynamical evolution have been obtained directly. These model simulations also provide the streamer shape, characteristics such as streamer velocity, the prebreakdown delay time, time-dependent current, and relationship between breakdown times, and applied electric fields for a given geometry. The results agree well with experimental data and reports in literature. The time to breakdown (tbr) for a 100 μm water gap has been shown to be strong function of the applied bias, with a 15–185 ns range. It is also shown that the current is fashioned not only by dynamic changes in local resistance, but that capacitive modifications arising from vaporization and streamer development also affect the transient behavior