Search results for "data structure"
showing 10 items of 441 documents
Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform
2012
Unprecedented production of short reads from the new high-throughput sequencers has posed challenges to align short reads to reference genomes with high sensitivity and high speed. Many CPU-based short read aligners have been developed to address this challenge. Among them, one popular approach is the seed-and-extend heuristic. For this heuristic, the first and foremost step is to generate seeds between the input reads and the reference genome, where hash tables are the most frequently used data structure. However, hash tables are memory-consuming, making it not well-suited to memory-stringent many-core architectures, like GPUs, even though they usually have a nearly constant query time com…
Work Partitioning on Parallel and Distributed Agent-Based Simulation
2017
Work partitioning is a key challenge with ap- plications in many scientific and technological fields. The problem is very well studied with a rich literature on both distributed and parallel computing architectures. In this paper we deal with the work partitioning problem for parallel and distributed agent-based simulations which aims at (i) balancing the overall load distribution, (ii) minimizing, at the same time, the communication overhead due to agents' inter-dependencies. We introduce a classification taxonomy of work partitioning strategies and present a space-based work partitioning ap- proach, based on a Quad-tree data structure, which enables to: identify a good space partitioning …
OpenCMISS: A multi-physics & multi-scale computational infrastructure for the VPH/Physiome project
2011
The VPH/Physiome Project is developing the model encoding standards CellML (cellml.org) and FieldML (fieldml.org) as well as web-accessible model repositories based on these standards (models.physiome.org). Freely available open source computational modelling software is also being developed to solve the partial differential equations described by the models and to visualise results. The OpenCMISS code (opencmiss.org), described here, has been developed by the authors over the last six years to replace the CMISS code that has supported a number of organ system Physiome projects. OpenCMISS is designed to encompass multiple sets of physical equations and to link subcellular and tissue-level b…
On implicit data structures for priority queues
1985
Comparaison avec une structure liee simple et implementation de certaines structures de donnees implicites pour les files d'attente de priorite. Le minutage des experiences montre que les structures implicites sont plutot lentes
Dictionary-symbolwise flexible parsing
2012
AbstractLinear-time optimal parsing algorithms are rare in the dictionary-based branch of the data compression theory. A recent result is the Flexible Parsing algorithm of Matias and Sahinalp (1999) that works when the dictionary is prefix closed and the encoding of dictionary pointers has a constant cost. We present the Dictionary-Symbolwise Flexible Parsing algorithm that is optimal for prefix-closed dictionaries and any symbolwise compressor under some natural hypothesis. In the case of LZ78-like algorithms with variable costs and any, linear as usual, symbolwise compressor we show how to implement our parsing algorithm in linear time. In the case of LZ77-like dictionaries and any symbol…
Text Compression Using Antidictionaries
1999
International audience; We give a new text compression scheme based on Forbidden Words ("antidictionary"). We prove that our algorithms attain the entropy for balanced binary sources. They run in linear time. Moreover, one of the main advantages of this approach is that it produces very fast decompressors. A second advantage is a synchronization property that is helpful to search compressed data and allows parallel compression. Our algorithms can also be presented as "compilers" that create compressors dedicated to any previously fixed source. The techniques used in this paper are from Information Theory and Finite Automata.
Representation theory treatment of measurement semantics for ratio, ordinal and nominal scales
1997
Within the scope of the representational theory a formal framework for description of semantic aspects of measurement on different scales is proposed. This is done by means of a first-order formal logical system consisting of a set of empirical predicates which play the part of a data structure in the framework, a set of operations by means of which syntactically correct statements can be formed; a set of axioms being true statements and a set of numerical statements which is an aggregation of potential measurement results carrying a meaningful load. On this basis the notation of semantic information on various scales is introduced and some common claims about the measurement semantic infor…
Automata and forbidden words
1998
Abstract Let L ( M ) be the (factorial) language avoiding a given anti-factorial language M . We design an automaton accepting L ( M ) and built from the language M . The construction is effective if M is finite. If M is the set of minimal forbidden words of a single word ν, the automaton turns out to be the factor automaton of ν (the minimal automaton accepting the set of factors of ν). We also give an algorithm that builds the trie of M from the factor automaton of a single word. It yields a nontrivial upper bound on the number of minimal forbidden words of a word.
Minimal forbidden words and factor automata
1998
International audience; Let L(M) be the (factorial) language avoiding a given antifactorial language M. We design an automaton accepting L(M) and built from the language M. The construction is eff ective if M is finite. If M is the set of minimal forbidden words of a single word v, the automaton turns out to be the factor automaton of v (the minimal automaton accepting the set of factors of v). We also give an algorithm that builds the trie of M from the factor automaton of a single word. It yields a non-trivial upper bound on the number of minimal forbidden words of a word.
LinkedSaeima: A Linked Open Dataset of Latvia’s Parliamentary Debates
2019
This paper describes the LinkedSaeima dataset that contains structured data about Latvia’s parliamentary debates from 1993 until 2017. This information is published at http://dati.saeima.korpuss.lv as Linked Open Data. It is a part of the Corpus of Saeima (the Parliament of Latvia) released as open data for multidisciplinary research. The data model of LinkedSaeima follows the data structure of the LinkedEP dataset with a few modifications. The dataset is augmented with links to the Wikidata knowledge base that provide additional information about the speakers and named entities mentioned in the corpus.