Related papers: A Comparative Study on String Matching Algorithm o…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
This study focuses on an alignment-free sequence comparison method: the number of words of length k shared between two sequences, also known as the D_2 statistic. The advantages of the use of this statistic over alignment-based methods are…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We introduce the natural notion of a matching frame in a $2$-dimensional string. A matching frame in a $2$-dimensional $n\times m$ string $M$, is a rectangle such that the strings written on the horizontal sides of the rectangle are…
Peptide strings have been developed as a concept for the past fourteen years. They are proposed to basically entail various quantum states engendered by the physical interactions of proteins containing peptide portions that are similar to…
The study of strings is an important combinatorial field that precedes the digital computer. Strings can be very long, trillions of letters, so it is important to find compact representations. Here we first survey various forms of one…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
Feature selection plays an important role in the data mining process. It is needed to deal with the excessive number of features, which can become a computational burden on the learning algorithms. It is also necessary, even when…
The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
Measuring similarities between strings is central for many established and fast growing research areas including information retrieval, biology, and natural language processing. The traditional approach for string similarity measurements is…
In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…
Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…
High school and college graduates seemingly are often battling for the courses they should major in order to achieve their target career. In this paper, we worked on suggesting a career path to a graduate to reach his/her dream career given…
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…
Research at the intersection of machine learning, programming languages, and software engineering has recently taken important steps in proposing learnable probabilistic models of source code that exploit code's abundance of patterns. In…
String processing, which mainly involves the analysis and manipulation of strings, is a fundamental component of modern computing. Despite the significant advancements of large language models (LLMs) in various natural language processing…
Matching pursuits are a class of greedy algorithms commonly used in signal processing, for solving the sparse approximation problem. They rely on an atom selection step that requires the calculation of numerous projections, which can be…