Search results for "Time complexity"
showing 10 items of 99 documents
Forbidden Factors and Fragment Assembly
2002
In this paper we approach the fragment assembly problem by using the notion of minimal forbidden factors introduced in previous paper. Denoting by M(w) the set of minimal forbidden factors of a word w, we first focus on the evaluation of the size of elements in M(w) and on designing of an algorithm to recover the word w from M(w). Actually we prove that for a word w randomly generated by a memoryless source with identical symbol probabilities, the maximal length m(w) of words in M(w) is logarithmic and that the reconstruction algorithm runs in linear time. These results have an interesting application to the fragment assembly problem, i.e. reconstruct a word w from a given set I of substrin…
Adaptive distributed outlier detection for WSNs.
2014
The paradigm of pervasive computing is gaining more and more attention nowadays, thanks to the possibility of obtaining precise and continuous monitoring. Ease of deployment and adaptivity are typically implemented by adopting autonomous and cooperative sensory devices; however, for such systems to be of any practical use, reliability and fault tolerance must be guaranteed, for instance by detecting corrupted readings amidst the huge amount of gathered sensory data. This paper proposes an adaptive distributed Bayesian approach for detecting outliers in data collected by a wireless sensor network; our algorithm aims at optimizing classification accuracy, time complexity and communication com…
A fast recursive algorithm to compute local axial moments
2001
The paper describes a fast algorithm to compute local axial moments used in the algorithm of discrete symmetry transform (DST). The basic idea is grounded on fast recursive implementation of respective linear filters by using the so-called primitive kernel functions since the moment computation can be performed in the framework of linear filtering. The main result is that the computation of the local axial moments is independent of the kernel size, i.e. of the order O(1) per data point (pixel). This result is of relevance whenever the DST is used to face with real time computer vision problems. The experimental results confirm the time complexity predicted by the theory.
Correlations among Game of Thieves and other centrality measures in complex networks
2021
Social Network Analysis (SNA) is used to study the exchange of resources among individuals, groups, or organizations. The role of individuals or connections in a network is described by a set of centrality metrics which represent one of the most important results of SNA. Degree, closeness, betweenness and clustering coefficient are the most used centrality measures. Their use is, however, severely hampered by their computation cost. This issue can be overcome by an algorithm called Game of Thieves (GoT). Thanks to this new algorithm, we can compute the importance of all elements in a network (i.e. vertices and edges), compared to the total number of vertices. This calculation is done not in…
Routing Algorithm for Maximizing Lifetime of Wireless Sensor Network for Broadcast Transmission
2018
In the article we discuss solutions of the maximum lifetime broadcasting problem in wireless sensor networks. Due to limited energy resources of the network nodes to find an optimal transmission route of the broadcasted data we minimize the maximum energy consumed by the nodes. We give an analytical solution of the problem in one dimensional regular sensor network for the point-to-point and point-to-multipoint data transmission scheme. We show that in such a network, when the cost of data transmission is a polynomial function of distance between transmitter and receiver, there exist solutions with an equal energy, i.e., all nodes of the network consume the same amount of energy. We assume t…
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
2018
Abstract Motivation K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability. Results We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Exper…
A sliding mode approach to robust stabilisation of Markovian jump linear time-delay systems with generally incomplete transition rates
2015
Abstract This paper is devoted to investigating the problem of robust sliding mode control for a class of uncertain Markovian jump linear time-delay systems with generally uncertain transition rates (GUTRs). In this GUTR model, each transition rate can be completely unknown or only its estimate value is known. By making use of linear matrix inequalities technique, sufficient conditions are presented to derive the linear switching surface and guarantee the stochastic stability of sliding mode dynamics. A sliding mode control law is developed to drive the state trajectory of the closed-loop system to the specified linear switching surface in a finite-time interval in spite of the existing unc…
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…
Boosting Textual Compression in Optimal Linear Time
2005
We provide a general boosting technique for Textual Data Compression. Qualitatively, it takes a good compression algorithm and turns it into an algorithm with a better compression performance guarantee. It displays the following remarkable properties: (a) it can turn any memoryless compressor into a compression algorithm that uses the “best possible” contexts; (b) it is very simple and optimal in terms of time; and (c) it admits a decompression algorithm again optimal in time. To the best of our knowledge, this is the first boosting technique displaying these properties.Technically, our boosting technique builds upon three main ingredients: the Burrows--Wheeler Transform, the Suffix Tree d…
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…