Search results for "complex"
showing 10 items of 5889 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…
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…
Learning to Rank Images for Complex Queries in Concept-based Search
2018
Concept-based image search is an emerging search paradigm that utilizes a set of concepts as intermediate semantic descriptors of images to bridge the semantic gap. Typically, a user query is rather complex and cannot be well described using a single concept. However, it is less effective to tackle such complex queries by simply aggregating the individual search results for the constituent concepts. In this paper, we propose to introduce the learning to rank techniques to concept-based image search for complex queries. With freely available social tagged images, we first build concept detectors by jointly leveraging the heterogeneous visual features. Then, to formulate the image relevance, …
Two-way quantum and classical machines with small memory for online minimization problems
2019
We consider online algorithms. Typically the model is investigated with respect to competitive ratio. In this paper, we explore algorithms with small memory. We investigate two-way automata as a model for online algorithms with restricted memory. We focus on quantum and classical online algorithms. We show that there are problems that can be better solved by two-way automata with quantum and classical states than classical two-way automata in the case of sublogarithmic memory (sublinear size).
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 …
An improved quantum query algorithm for computing AND Boolean function
2010
We consider the quantum query model for computing Boolean functions. The definition of the function is known, but a black box contains the input X = (x 1 , x 2 , …, x n ). Black box can be accessed by querying x i values. The goal is to develop an algorithm, which would compute the function value for arbitrary input using as few queries to the black box as possible. We present two different quantum query algorithms for computing the basic Boolean function — logical AND of two bits. Both algorithms use only one query to determine the function value. Correct answer probability for the first algorithm is 80%, but for the second algorithm it is 90%. To compute this function with the same probab…
k-Truss Decomposition for Modular Centrality
2018
There is currently much interest in identifying influential spreaders in complex networks due to many applications concerned, such as controlling the outbreak of epidemics and conducting advertisements for commercial products, and so on. A plethora of centrality measures have been proposed over the years based on the topological properties of networks. However, most of these classical centrality measures fail to select the most influential nodes in networks with a modular structure despite that it is an omnipresent property in real-world networks. Few authors have introduced centrality measures tailored to networks with community structure. In a recent work, we have shown that, in this case…
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…
The heterogeneity of inter-domain Internet application flows: entropic analysis and flow graph modelling
2013
The growing popularity of the Internet has triggered the proliferation of various applications, which possess diverse communication patterns and user behaviour. In this paper, the heterogeneous characteristics of Internet applications and traffic are investigated from a complex network and entropic perspective. On the basis of real-life flow data collected from a public network provided by an Internet service provider, flow graphs are constructed for five types of applications as follows: Web, P2P Download, P2P Stream, Video Stream and Instant Messaging. Three types of entropy measures are introduced to the flow graphs, and the heterogeneity of applications within a 24-h period is analysed …
Statistically validated networks in bipartite complex systems.
2011
Many complex systems present an intrinsic bipartite nature and are often described and modeled in terms of networks [1-5]. Examples include movies and actors [1, 2, 4], authors and scientific papers [6-9], email accounts and emails [10], plants and animals that pollinate them [11, 12]. Bipartite networks are often very heterogeneous in the number of relationships that the elements of one set establish with the elements of the other set. When one constructs a projected network with nodes from only one set, the system heterogeneity makes it very difficult to identify preferential links between the elements. Here we introduce an unsupervised method to statistically validate each link of the pr…