Related papers: Computing alignment plots efficiently
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. A standard approach to speed up this task is to compute "sketches" of the DNA reads (typically via…
The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…
Given a source of iid samples of edges of an input graph $G$ with $n$ vertices and $m$ edges, how many samples does one need to compute a constant factor approximation to the maximum matching size in $G$? Moreover, is it possible to obtain…
In this work, we study the maximum matching problem from the perspective of sensitivity. The sensitivity of an algorithm $A$ on a graph $G$ is defined as the maximum Wasserstein distance between the output distributions of $A$ on $G$ and on…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
For any $T \geq 1$, there are constants $R=R(T) \geq 1$ and $\zeta=\zeta(T)>0$ and a randomized algorithm that takes as input an integer $n$ and two strings $x,y$ of length at most $n$, and runs in time $O(n^{1+\frac{1}{T}})$ and outputs an…
The Universal Similarity Metric (USM) has been demonstrated to give practically useful measures of "similarity" between sequence data. Here we have used the USM as an alternative distance metric in a K-Nearest Neighbours (K-NN) learner to…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
A string $w$ is called a minimal absent word (MAW) for a string $S$ if $w$ does not occur as a substring in $S$ and all proper substrings of $w$ occur in $S$. MAWs are well-studied combinatorial string objects that have potential…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
Many applications generate and consume temporal data and retrieval of time series is a key processing step in many application domains. Dynamic time warping (DTW) distance between time series of size N and M is computed relying on a dynamic…
The decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), asks to list all fragments of $T$ that are at edit distance at…
We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to help deal with errors. Our method receives as input a…
In this paper we consider the fundamental problem of approximating the diameter $D$ of directed or undirected graphs. In a seminal paper, Aingworth, Chekuri, Indyk and Motwani [SIAM J. Comput. 1999] presented an algorithm that computes in…
We study fundamental graph parameters such as the Diameter and Radius in directed graphs, when distances are measured using a somewhat unorthodox but natural measure: the distance between $u$ and $v$ is the minimum of the shortest path…
A skew-symmetric graph $(D=(V,A),\sigma)$ is a directed graph $D$ with an involution $\sigma$ on the set of vertices and arcs. In this paper, we introduce a separation problem, $d$-Skew-Symmetric Multicut, where we are given a…
We propose the neural string edit distance model for string-pair matching and string transduction based on learnable string edit distance. We modify the original expectation-maximization learned edit distance algorithm into a differentiable…
We present a new randomized algorithm for computing the diameter of a weighted directed graph. The algorithm runs in $\Ot(M^{\w/(\w+1)}n^{(\w^2+3)/(\w+1)})$ time, where $\w < 2.376$ is the exponent of fast matrix multiplication, $n$ is the…
It is shown that for finding rational approximates to m'th root of any integer to any accuracy one only needs the ability to count and to distinguish between m different classes of objects. To every integer N can be associated a…
Quantifying the similarity between two graphs is a fundamental algorithmic problem at the heart of many data analysis tasks for graph-based data. In this paper, we study the computational complexity of a family of similarity measures based…