Related papers: Alignment-free sequence comparison using absent wo…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
We have attempted in this paper to reduce the number of checked condition through saving frequency of the tandem replicated words, and also using non-overlapping iterative neighbor intervals on plane sweep algorithm. The essential idea of…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…
In this paper we describe an algorithm for aligning sentences with their translations in a bilingual corpus using lexical information of the languages. Existing efficient algorithms ignore word identities and consider only the sentence…
This article considers algorithmic and statistical aspects of linear regression when the correspondence between the covariates and the responses is unknown. First, a fully polynomial-time approximation scheme is given for the natural least…
Given a set of incomplete observations, we study the nonparametric problem of testing whether data are Missing Completely At Random (MCAR). Our first contribution is to characterise precisely the set of alternatives that can be…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
We consider learning a sequence classifier without labeled data by using sequential output statistics. The problem is highly valuable since obtaining labels in training data is often costly, while the sequential output statistics (e.g.,…
In many applications, it is necessary to determine the string similarity. Edit distance[WF74] approach is a classic method to determine Field Similarity. A well known dynamic programming algorithm [GUS97] is used to calculate edit distance…
Parallel sentence extraction is a task addressing the data sparsity problem found in multilingual natural language processing applications. We propose an end-to-end deep neural network approach to detect translational equivalence between…
This study is to review the approaches used for measuring sentences similarity. Measuring similarity between natural language sentences is a crucial task for many Natural Language Processing applications such as text classification,…
The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…
Wake word detection exists in most intelligent homes and portable devices. It offers these devices the ability to "wake up" when summoned at a low cost of power and computing. This paper focuses on understanding alignment's role in…
Most words have several senses and connotations which evolve in time due to semantic shift, so that closely related words may gain different or even opposite meanings over the years. This evolution is very relevant to the study of language…
Sequence discriminative training is a great tool to improve the performance of an automatic speech recognition system. It does, however, necessitate a sum over all possible word sequences, which is intractable to compute in practice.…