Related papers: Approximating LCS and Alignment Distance over Mult…
We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorithm. This procedure provides an efficient and simple method by…
The recently introduced longest common substring with $k$-mismatches ($k$-LCF) problem is to find, given two sequences $S_1$ and $S_2$ of length $n$ each, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance…
One of the most challenging and long-standing problems in computational biology is the prediction of three-dimensional protein structure from amino acid sequence. A promising approach to infer spatial proximity between residues is the study…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
Low-discrepancy points are designed to efficiently fill the space in a uniform manner. This uniformity is highly advantageous in many problems in science and engineering, including in numerical integration, computer vision, machine…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
Linear complementary dual (LCD) maximum distance separable (MDS) codes are constructed to given specifications. For given $n$ and $r<n$, with $n$ or $r$ (or both) odd, MDS LCD $(n,r)$ codes are constructed over finite fields whose…
An algorithm is proposed for solving optimization problems arising in neural network training for supervised learning. The unique feature of the algorithm is the use of an auxiliary loss, in addition to the original loss employed for model…
Time Series Alignment is a critical task in signal processing with numerous real-world applications. In practice, signals often exhibit temporal shifts and scaling, making classification on raw data prone to errors. This paper introduces a…
We present the first near optimal approximation schemes for the maximum weighted (uncapacitated or capacitated) $b$--matching problems for non-bipartite graphs that run in time (near) linear in the number of edges. For any…
Given $x \in (\mathbb{R}_{\geq 0})^{\binom{[n]}{2}}$ recording pairwise distances, the METRIC VIOLATION DISTANCE (MVD) problem asks to compute the $\ell_0$ distance between $x$ and the metric cone; i.e., modify the minimum number of entries…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
We consider approximate circular pattern matching (CPM, in short) under the Hamming and edit distance, in which we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a threshold $k>0$, and we are to report all starting positions…
Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA…
We present a practical algorithm for the cyclic longest common subsequence (CLCS) problem that runs in O(mn) time, where m and n are the lengths of the two input strings. While this is not necessarily an asymptotic improvement over the…
In this paper, we propose a new algorithm for the estimation of multiple time delays (TDs). Since a TD is a fundamental spatial cue for sensor array signal processing techniques, many methods for estimating it have been studied. Most of…
Conformance checking encompasses a body of process mining techniques which aim to find and describe the differences between a process model capturing the expected process behavior and a corresponding event log recording the observed…
The problem of finding \emph{distance} between \emph{pattern} of length $m$ and \emph{text} of length $n$ is a typical way of generalizing pattern matching to incorporate dissimilarity score. For both Hamming and $L_1$ distances only a…
The widespread collection of data from mobile and wearable devices has created unprecedented opportunities to study human behavior in fine temporal resolution. One common structure for such data is categorical sequences: ordered,…
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…