相关论文: Empirical distribution of k-word matches in biolog…
Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between…
Given two sequences over a finite alphabet $\mathcal{L}$, the $D_2$ statistic is the number of $m$-letter word matches between the two sequences. This statistic is used in bioinformatics for expressed sequence tag database searches. Here we…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Given a random text over a finite alphabet, we study the frequencies at which fixed-length words occur as subsequences. As the data size grows, the joint distribution of word counts exhibits a rich asymptotic structure. We investigate all…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
The problem addressed concerns the determination of the average number of successive attempts of guessing a word of a certain length consisting of letters with given probabilities of occurrence. Both first- and second-order approximations…
In the Dictionary-based String Matching (DSM) problem, a retrieval system has access to a source sequence and stores the position of a certain number of strings in a posting table. When a user inquires the position of a string, the…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
We present DUAL-LOCO, a communication-efficient algorithm for distributed statistical estimation. DUAL-LOCO assumes that the data is distributed according to the features rather than the samples. It requires only a single round of…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
We consider the classical problem of discrete distribution estimation using i.i.d. samples in a novel scenario where additional side information is available on the distribution. In large alphabet datasets such as text corpora, such side…
Statistical matching methods are widely used in the social and health sciences to estimate causal effects using observational data. Often the objective is to find comparable groups with similar covariate distributions in a dataset, with the…
Co-occurrences between two words provide useful insights into the semantics of those words. Consequently, numerous prior work on word embedding learning have used co-occurrences between two words as the training signal for learning word…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
The analysis of strings of $n$ random variables with geometric distribution has recently attracted renewed interest: Archibald et al. consider the number of distinct adjacent pairs in geometrically distributed words. They obtain the…
We describe and experimentally evaluate a method for automatically clustering words according to their distribution in particular syntactic contexts. Deterministic annealing is used to find lowest distortion sets of clusters. As the…