Efficient Methods for Finding Optimal Convolutional Self-Doubly Orthogonal Codes

Résumé: Au cours des dernières années, la hausse sans précédent du nombre d'ultrabooks et d'appareils mobiles s'est accompagnée d'un besoin toujours croissant d'accès aux technologies permettant des communications sans-fil fiables et à haut débit. Pour atténuer ou éliminer les erreurs induites par les interférences et le bruit dans les canaux de communication, il est important de développer des systèmes de codage efficaces pour la correction d'erreurs. En effet, lors de communications de données numériques sur un canal ayant un faible rapport signal sur bruit, ces codes permettent de conserver un taux d'erreur faible tout en augmentant le débit des transmissions et/ou en diminuant la puissance d'émission requise. Ceci contribue grandement à améliorer l'efficacité énergétique de ces dispositifs électroniques sans-fil et, ainsi, à prolonger leur autonomie. Dans cette thèse par articles, nous présentons un algorithme de recherche efficace pour trouver deux types de codes correcteurs d'erreur: les codes convolutionnels doublement orthogonaux (CDO) et les codes convolutionnels doublement orthogonaux simplifiés (S-CDO). En effet, ces codes sont utilisés dans un système de contrôle d'erreurs ayant un décodage à seuil itératif différent de la procédure de décodage Turbo classique, puisqu'il ne nécessite aucun entrelaceur, ni à l'encodage, ni aux étapes de décodage. Néanmoins, son processus de décodage à seuil nécessite que ces codes convolutionnels systématiques satisfassent des propriétés dites de « double orthogonalité », allant au-delà des conditions requises par les codes « simplement orthogonaux », bien connus et habituellement utilisés lors d'un décodage à seuil non-itératif. Afin de pouvoir construire des codecs à haute performance et à faible latence avec ces codes, il est important de minimiser leur longueur de contrainte ou « span » pour un nombre J de connexions donné. Bien que trouver des codes CDO et S-CDO ne soit pas difficile, déterminer les codes ayant un span minimal (dit optimal) pour un ordre J donné est mathématiquement très complexe. En effet, la construction directe de codes CDO / S-CDO à span court/optimal reste un problème ouvert et qui est soupçonné d'être NP-complet. Cette thèse présente un total de trois articles: deux articles publiés dans IEEE Transactions on Communications et un article soumis au journal IEEE Transactions on Parallel and Distributed Systems . Dans ces articles, nous décrivons un nouvel algorithme de recherche parallèle, efficace et implicitement-exhaustif pour trouver des codes CDO et S-CDO systématiques, à taux R=1/2 et ayant un span plus court, voire minimal, c.à.d. optimal. Comparé à l'algorithme de recherche implicitement-exhaustif de référence, l'algorithme de recherche à haute performance proposé reste exhaustif mais fournit un facteur d'accélération très important, supérieur à 16300 pour les codes CDO (J=7) et supérieur à 6300 pour les codes S-CDO (J=8).----------Abstract: In recent years, the rise of ultrabooks and mobile devices has been accompanied by an ever increasing need for reliable high-bandwidth wireless communications. To mitigate or eliminate the errors that are invariably introduced due to noise and interference in the communication channels, it is important to develop efficient error-correcting coding schemes. Indeed, these codes may be used to preserve the error performance while allowing the data-rate of digital communications to be increased and the transmission power at lower signal-to-noise ratios to be reduced, thereby improving the overall power efficiency of these devices. In this manuscript-based thesis, we present an efficient search algorithm for finding optimal/short-span Convolutional Self-Doubly Orthogonal (CDO) codes and Simplified Convolutional Self-Doubly Orthogonal (S-CDO) codes. These error-correcting codes are employed in an iterative error-control coding scheme that differs from the classical Turbo code procedure, as it does not require any interleaver, neither at the encoding nor at the decoding stages. However, its iterative threshold decoding procedure requires that these systematic convolutional codes satisfy some “double orthogonality properties”, beyond those of the well-known orthogonal codes used in the usual non-iterative threshold decoding. In order to build high-performance, low-latency codecs with these codes, it is important to minimize the constraint length, also called “span”, for a given number J of generator connections. Although finding CDO/S-CDO codes is not difficult, determining the optimal/short-span codes for a given order J is computationally very challenging. The direct construction of optimal or shortest-span CDO and S-CDO codes has so far eluded analysis, and the search for these codes is believed to be an NP-complete problem. The thesis presents a total of three articles: two articles that were published in IEEE Transactions on Communications , and one article that was submitted for publication to IEEE Transactions on Parallel and Distributed Systems . In these articles, we describe a novel efficient and parallel implicitly-exhaustive search algorithm for finding rate R=1/2 systematic optimal/short-span CDO and S-CDO codes. The high-performance search algorithm is still exhaustive in nature, yet it provides an impressive speedup that is larger than 16300 (CDO, J=7) and 6300 (S-CDO, J=8) over the reference implicitly-exhaustive search algorithm, and larger than 2000 (CDO, J=17) over the fastest known CDO validation function used in high-performance pseudo-random search algorithms

Kiel Declarative Programming Days 2013

This report contains the papers presented at the Kiel Declarative Programming Days 2013, held in Kiel (Germany) during September 11-13, 2013. The Kiel Declarative Programming Days 2013 unified the following events: * 20th International Conference on Applications of Declarative Programming and Knowledge Management (INAP 2013) * 22nd International Workshop on Functional and (Constraint) Logic Programming (WFLP 2013) * 27th Workshop on Logic Programming (WLP 2013) All these events are centered around declarative programming, an advanced paradigm for the modeling and solving of complex problems. These specification and implementation methods attracted increasing attention over the last decades, e.g., in the domains of databases and natural language processing, for modeling and processing combinatorial problems, and for high-level programming of complex, in particular, knowledge-based systems

Hardware-software codesign and parallel implementation of a golomb ruler derivation engine

Summarization: A new architecture for Golomb ruler derivation has been developed so that rulers up to 24 marks can be proven on it. In this architecture, 8-mark stubs that are derived on a personal computer are subsequently processed by the FCCM, called GE2, allowing for parallel processing of as many stubs as are the available FPGAs. Actual runs of the new design have been performed on the TOP parallel FPGA machine at Virginia Tech. This paper presents the design improvements over the original architecture, which include single FPGA implementation, hardware/software codesign, FIFO based I/O, design for parallel execution, and performance results from actual runs.Presented on

Novel computational techniques for mapping and classifying Next-Generation Sequencing data

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up