Search results for "data structure"
showing 10 items of 441 documents
Measuring the clustering effect of BWT via RLE
2017
Abstract The Burrows–Wheeler Transform (BWT) is a reversible transformation on which are based several text compressors and many other tools used in Bioinformatics and Computational Biology. The BWT is not actually a compressor, but a transformation that performs a context-dependent permutation of the letters of the input text that often create runs of equal letters (clusters) longer than the ones in the original text, usually referred to as the “clustering effect” of BWT. In particular, from a combinatorial point of view, great attention has been given to the case in which the BWT produces the fewest number of clusters (cf. [5] , [16] , [21] , [23] ). In this paper we are concerned about t…
Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties.
2016
Interest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g., the European Union's Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine str…
Block Sorting-Based Transformations on Words: Beyond the Magic BWT
2018
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression and later results have contributed to make it a fundamental tool for the design of self-indexing compressed data structures. The Alternating Burrows-Wheeler Transform (ABWT) is a more recent transformation, studied in the context of Combinatorics on Words, that works in a similar way, using an alternating lexicographical order instead of the usual one. In this paper we study a more general class of block sorting-based transformations. The transformations in this new class prove to be interesting combinatorial tools that offer new research perspectives. In particular, we show that all the tra…
Reactome diagram viewer: data structures and strategies to boost performance
2017
Abstract Motivation Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. Results The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partit…
2020
Abstract. The new PAGES2k global compilation of temperature-sensitive proxies offers an unprecedented opportunity to study regional to global trends associated with orbitally driven changes in solar irradiance over the past 2 millennia. Here, we analyze pre-industrial long-term trends from 1 to 1800 CE across the PAGES2k dataset and find that, in contrast to the gradual cooling apparent in ice core, marine, and lake sediment data, tree rings do not exhibit the same decline. To understand why tree-ring proxies lack any evidence of a significant pre-industrial cooling, we divide those data by location (high Northern Hemisphere latitudes vs. midlatitudes), seasonal response (annual vs. summer)…
Hyperion
2019
Indexes are essential in data management systems to increase the speed of data retrievals. Widespread data structures to provide fast and memory-efficient indexes are prefix tries. Implementations like Judy, ART, or HOT optimize their internal alignments for cache and vector unit efficiency. While these measures usually improve the performance substantially, they can have a negative impact on memory efficiency. In this paper we present Hyperion, a trie-based main-memory key-value store achieving extreme space efficiency. In contrast to other data structures, Hyperion does not depend on CPU vector units, but scans the data structure linearly. Combined with a custom memory allocator, Hyperion…
Reverse-safe data structures for text indexing
2021
We introduce the notion of reverse-safe data structures. These are data structures that prevent the reconstruction of the data they encode (i.e., they cannot be easily reversed). A data structure D is called z-reverse-safe when there exist at least z datasets with the same set of answers as the ones stored by D. The main challenge is to ensure that D stores as many answers to useful queries as possible, is constructed efficiently, and has size close to the size of the original dataset it encodes. Given a text of length n and an integer z, we propose an algorithm which constructs a z-reverse-safe data structure that has size O(n) and answers pattern matching queries of length at most d optim…
Impact of decision horizon on post-prognostics maintenance and missions scheduling: a railways case study
2021
International audience; In this paper, we propose a study of the decision horizon duration for rolling stock mission assignment and maintenance planning in a prognostics and health management (PHM) context. The aim is to determine the best decision horizon duration that allows the con- struction of a suitable schedule that assigns railway vehicles to missions and integrates required maintenance operations accord- ing to the current and future health of the vehicles. A genetic algorithm is used to minimize the overall cost of the joint schedule as a function of the decision horizon. The results are compared to three proposed heuristics to study the influence of the resolution method on the d…
"Exclusion contour(obs.) 9 : Meff" of "Search for squarks and gluinos in final states with jets and missing transverse momentum using 36 fb$^{-1}$ of…
2018
Observed 95% CL exclusion contours from Meff-based searches on the gluino mass and the mass gap ratio x in a SUSY scenario where gluinos are produced in pairs and decay via an intermediate lightest chargino or second lightest neutralino to the lightest neutralino, $\tilde{g} \rightarrow qq \tilde{\chi}_{1}^{\pm} \rightarrow qq W^{\pm} \tilde{\chi}_{1}^{0}$, or $\tilde{g} \rightarrow qq \tilde{\chi}_{2}^{0} \rightarrow qq Z/h \tilde{\chi}_{1}^{0}$.
"Exclusion contour(exp.) 9 : Meff" of "Search for squarks and gluinos in final states with jets and missing transverse momentum using 36 fb$^{-1}$ of…
2018
Expected 95% CL exclusion contours from Meff-based searches on the gluino mass and the mass gap ratio x in a SUSY scenario where gluinos are produced in pairs and decay via an intermediate lightest chargino or second lightest neutralino to the lightest neutralino, $\tilde{g} \rightarrow qq \tilde{\chi}_{1}^{\pm} \rightarrow qq W^{\pm} \tilde{\chi}_{1}^{0}$, or $\tilde{g} \rightarrow qq \tilde{\chi}_{2}^{0} \rightarrow qq Z/h \tilde{\chi}_{1}^{0}$.