Search results for "Data structure"
showing 10 items of 441 documents
TREEZZY2, a Fuzzy Logic Computer Code for Fault Tree and Event Tree Analyses
2004
In conventional approach to reliability analysis using logical trees methodologies, uncertainties in system components or basic events failure probabilities are approached by assuming probability distribution functions. However, data are often insufficient for statistical estimation, and therefore it is required to resort to approximate estimations. Moreover, complicate calculations are needed to propagate uncertainties up to the final results. In our work, in order to take account of the uncertainties in system failure probabilities, the methodology based on fuzzy sets theory is used both in fault tree and event tree analyses. This paper just presents our work in this issue, which resulted…
GekkoFS - A Temporary Distributed File System for HPC Applications
2018
We present GekkoFS, a temporary, highly-scalable burst buffer file system which has been specifically optimized for new access patterns of data-intensive High-Performance Computing (HPC) applications. The file system provides relaxed POSIX semantics, only offering features which are actually required by most (not all) applications. It is able to provide scalable I/O performance and reaches millions of metadata operations already for a small number of nodes, significantly outperforming the capabilities of general-purpose parallel file systems. The work has been funded by the German Research Foundation (DFG) through the ADA-FS project as part of the Priority Programme 1648. It is also support…
On Applying Adaptive Data Structures to Multi-Player Game Playing
2013
In the field of game playing, the focus has been on two-player games, such as Chess and Go, rather than on multi-player games, with dominant multi-player techniques largely being an extension of two-player techniques to an \(N\)-player environment. To address the problem of multiple opponents, we propose the merging of two previously unrelated fields, namely those of multi-player game playing and Adaptive Data Structures (ADS). We present here a novel move-ordering heuristic for a dominant multi-player game playing algorithm, namely the Best-Reply Search (BRS). Our enhancement uses an ADS to rank the opponents in terms of their respective threat levels to the player modeled by the AI algori…
Word assembly through minimal forbidden words
2006
AbstractWe give a linear-time algorithm to reconstruct a finite word w over a finite alphabet A of constant size starting from a finite set of factors of w verifying a suitable hypothesis. We use combinatorics techniques based on the minimal forbidden words, which have been introduced in previous papers. This improves a previous algorithm which worked under the assumption of stronger hypothesis.
From Nerode's congruence to Suffix Automata with mismatches
2009
AbstractIn this paper we focus on the minimal deterministic finite automaton Sk that recognizes the set of suffixes of a word w up to k errors. As first result we give a characterization of the Nerode’s right-invariant congruence that is associated with Sk. This result generalizes the classical characterization described in [A. Blumer, J. Blumer, D. Haussler, A. Ehrenfeucht, M. Chen, J. Seiferas, The smallest automaton recognizing the subwords of a text, Theoretical Computer Science, 40, 1985, 31–55]. As second result we present an algorithm that makes use of Sk to accept in an efficient way the language of all suffixes of w up to k errors in every window of size r of a text, where r is the…
Minimal forbidden patterns of multi-dimensional shifts
2005
We study whether the entropy (or growth rate) of minimal forbidden patterns of symbolic dynamical shifts of dimension 2 or more, is a conjugacy invariant. We prove that the entropy of minimal forbidden patterns is a conjugacy invariant for uniformly semi-strongly irreducible shifts. We prove a weaker invariant in the general case.
MetaCache-GPU: Ultra-Fast Metagenomic Classification
2021
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is commonly facilitated by constructing index data structures which allow for efficient querying of substrings. Recent metagenomic classification pipelines annotate reads with taxonomic labels by analyzing their $k$-mer histograms with respect to a reference genome database. CPU-based index construction is often performed in a preprocessing phase due to the relatively high cost of building irregular data structures such as hash maps. However, the rapidly growi…
Comparing DNA sequence collections by direct comparison of compressed text indexes
2012
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the utility of also indexing the query sequences themselves remains relatively unexplored. Here we show that an all-against-all comparison of two sequence collections can be computed from the BWT of each collection with the BWTs held entirely in external memory, i.e. on disk and not in RAM. As an application of this technique, we show that BWTs of transcriptomic and genomic reads can be compared to obtain reference-free predictions of splice junctions that have h…
On the Non-uniform Redundancy of Representations for Grammatical Evolution: The Influence of Grammars
2018
The representation used in grammatical evolution (GE) is non-uniformly redundant as some phenotypes are represented by more genotypes than others. This article studies how the non-uniform redundancy of the GE representation depends on various types of grammars. When constructing the phenotype tree from a genotype, the used grammar determines Bavg, the average branching factor. Bavg measures the expected number of non-terminals chosen when mapping one genotype codon to a phenotype tree node. First, the paper illustrates that the GE representation induces a bias towards small trees. This bias gets stronger with lower Bavg. For example, when using a grammar with Bavg = 0.5, 75% of all genotype…
A survey and comparison of transformation tools based on the transformation tool contest
2014
Model transformation is one of the key tasks in model-driven engineering and relies on the efficient matching and modification of graph-based data structures; its sibling graph rewriting has been used to successfully model problems in a variety of domains. Over the last years, a wide range of graph and model transformation tools have been developed – all of them with their own particular strengths and typical application domains. In this paper, we give a survey and a comparison of the model and graph transformation tools that participated at the Transformation Tool Contest 2011. The reader gains an overview of the field and its tools, based on the illustrative solutions submitted to a Hello…