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Register a new userEfficient Index for Weighted Sequences
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Added by
Jakub Radoszewski
Publication date
2016
fields
Informatics Engineering
and research's language is
English
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The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to support efficient on-line pattern queries. We study this problem in the case where the text is weighted: for every position of the text and every letter of the alphabet a probability of occurrence of this letter at this position is given. Sequences of this type, also called position weight matrices, are commonly used to represent imprecise or uncertain data. A weighted sequence may represent many different strings, each with probability of occurrence equal to the product of probabilities of its letters at subsequent positions. Given a probability threshold $1/z$, we say that a pattern string $P$ matches a weighted text at position $i$ if the product of probabilities of the letters of $P$ at positions $i,ldots,i+|P|-1$ in the text is at least $1/z$. In this article, we present an $O(nz)$-time construction of an $O(nz)$-sized index that can answer pattern matching queries in a weighted text in optimal time improving upon the state of the art by a factor of $z log z$. Other applications of this data structure include an $O(nz)$-time construction of the weighted prefix table and an $O(nz)$-time computation of all covers of a weighted sequence, which improve upon the state of the art by the same factor.
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Weighted Szeged index is a recently introduced extension of the well-known Szeged index. In this paper, we present a new tool to analyze and characterize minimum weighted Szeged index trees. We exhibit the best trees with up to 81 vertices and use this information, together with our results, to propose various conjectures on the structure of minimum weighted Szeged index trees.
Understanding the correlation between two different scores for the same set of items is a common problem in information retrieval, and the most commonly used statistics that quantifies this correlation is Kendalls $tau$. However, the standard definition fails to capture that discordances between items with high rank are more important than those between items with low rank. Recently, a new measure of correlation based on average precision has been proposed to solve this problem, but like many alternative proposals in the literature it assumes that there are no ties in the scores. This is a major deficiency in a number of contexts, and in particular while comparing centrality scores on large graphs, as the obvious baseline, indegree, has a very large number of ties in web and social graphs. We propose to extend Kendalls definition in a natural way to take into account weights in the presence of ties. We prove a number of interesting mathematical properties of our generalization and describe an $O(nlog n)$ algorithm for its computation. We also validate the usefulness of our weighted measure of correlation using experimental data.
We discuss one of the most fundamental scheduling problem of processing jobs on a single machine to minimize the weighted flow time (weighted response time). Our main result is a $O(log P)$-competitive algorithm, where $P$ is the maximum-to-minimum processing time ratio, improving upon the $O(log^{2}P)$-competitive algorithm of Chekuri, Khanna and Zhu (STOC 2001). We also design a $O(log D)$-competitive algorithm, where $D$ is the maximum-to-minimum density ratio of jobs. Finally, we show how to combine these results with the result of Bansal and Dhamdhere (SODA 2003) to achieve a $O(log(min(P,D,W)))$-competitive algorithm (where $W$ is the maximum-to-minimum weight ratio), without knowing $P,D,W$ in advance. As shown by Bansal and Chan (SODA 2009), no constant-competitive algorithm is achievable for this problem.
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Sequences set is a mathematical model used in many applications. As the number of the sequences becomes larger, single sequence set model is not appropriate for the rapidly increasing problem sizes. For example, more and more text processing applications separate a single big text file into multiple files before processing. For these applications, the underline mathematical model is multiple sequences sets (MSS). Though there is increasing use of MSS, there is little research on how to process MSS efficiently. To process multiple sequences sets, sequences are first distributed to different sets, and then sequences for each set are processed. Deriving effective algorithm for MSS processing is both interesting and challenging. In this paper, we have defined the cost functions and performance ratio for analysis of the quality of synthesis sequences. Based on these, the problem of Process of Multiple Sequences Sets (PMSS) is formulated. We have first proposed two greedy algorithms for the PMSS problem, which are based on generalization of algorithms for single sequences set. Then based on the analysis of the characteristics of multiple sequences sets, we have proposed the Distribution and Deposition (DDA) algorithm and DDA* algorithm for PMSS problem. In DDA algorithm, the sequences are first distributed to multiple sets according to their alphabet contents; then sequences in each set are deposited by the deposition algorithm. The DDA* algorithm differs from the DDA algorithm in that the DDA* algorithm distributes sequences by clustering based on sequence profiles. Experiments show that DDA and DDA* always output results with smaller costs than other algorithms, and DDA* outperforms DDA in most instances. The DDA and DDA* algorithms are also efficient both in time and space.
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