Laboratoire d'Informatique Fondamentale de Lille

About: Laboratoire d'Informatique Fondamentale de Lille is a based out in . It is known for research contribution in the topics: Metaheuristic & Grid. The organization has 466 authors who have published 1037 publications receiving 17119 citations.

SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

Abstract: MOTIVATION: The application of Next-Generation Sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The tasks to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS: We present SortMeRNA, a new software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time. AVAILABILITY: http://bioinfo.lifl.fr/RNA/sortmerna CONTACT: evguenia.kopylova@lifl.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Tree Automata Techniques and Applications

Abstract: CONTENTS 7 Acknowledgments Many people gave substantial suggestions to improve the contents of this book. These are, in alphabetic order, Introduction During the past few years, several of us have been asked many times about references on finite tree automata. On one hand, this is the witness of the liveness of this field. On the other hand, it was difficult to answer. Besides several excellent survey chapters on more specific topics, there is only one monograph devoted to tree automata by Gécseg and Steinby. Unfortunately, it is now impossible to find a copy of it and a lot of work has been done on tree automata since the publication of this book. Actually using tree automata has proved to be a powerful approach to simplify and extend previously known results, and also to find new results. For instance recent works use tree automata for application in abstract interpretation using set constraints, rewriting, automated theorem proving and program verification, databases and XML schema languages. Tree automata have been designed a long time ago in the context of circuit verification. Many famous researchers contributed to this school which was headed by A. Church in the late 50's and the early 60's: B. Trakhtenbrot, Many new ideas came out of this program. For instance the connections between automata and logic. Tree automata also appeared first in this framework, following the work of Doner, Thatcher and Wright. In the 70's many new results were established concerning tree automata, which lose a bit their connections with the applications and were studied for their own. In particular, a problem was the very high complexity of decision procedures for the monadic second order logic. Applications of tree automata to program verification revived in the 80's, after the relative failure of automated deduction in this field. It is possible to verify temporal logic formulas (which are particular Monadic Second Order Formulas) on simpler (small) programs. Automata, and in particular tree automata, also appeared as an approximation of programs on which fully automated tools can be used. New results were obtained connecting properties of programs or type systems or rewrite systems with automata. Our goal is to fill in the existing gap and to provide a textbook which presents the basics of tree automata and several variants of tree automata which have been devised for applications in the aforementioned domains. We shall discuss only finite tree automata, and the …

A Taxonomy of Hybrid Metaheuristics

Abstract: Hybrid metaheuristics have received considerable interest these recent years in the field of combinatorial optimization. A wide variety of hybrid approaches have been proposed in the literature. In this paper, a taxonomy of hybrid metaheuristics is presented in an attempt to provide a common terminology and classification mechanisms. The taxonomy, while presented in terms of metaheuristics, is also applicable to most types of heuristics and exact optimization algorithms. As an illustration of the usefulness of the taxonomy an annoted bibliography is given which classifies a large number of hybrid approaches according to the taxonomy.

ParadisEO: A Framework for the Reusable Design of Parallel and Distributed Metaheuristics

Abstract: In this paper, we present the ParadisEO white-box object-oriented framework dedicated to the reusable design of parallel and distributed metaheuristics (PDM). ParadisEO provides a broad range of features including evolutionary algorithms (EA), local searches (LS), the most common parallel and distributed models and hybridization mechanisms, etc. This high content and utility encourages its use at European level. ParadisEO is based on a clear conceptual separation of the solution methods from the problems they are intended to solve. This separation confers to the user a maximum code and design reuse. Furthermore, the fine-grained nature of the classes provided by the framework allow a higher flexibility compared to other frameworks. ParadisEO is of the rare frameworks that provide the most common parallel and distributed models. Their implementation is portable on distributed-memory machines as well as on shared-memory multiprocessors, as it uses standard libraries such as MPI, PVM and PThreads. The models can be exploited in a transparent way, one has just to instantiate their associated provided classes. Their experimentation on the radio network design real-world application demonstrate their efficiency.