Related papers: Faster exon assembly by sparse spliced alignment
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
$\newcommand{\popt}{{\mathcal{p}}} \newcommand{\Re}{\mathbb{R}}\newcommand{\N}{{\mathcal{N}}} \newcommand{\BX}{\mathcal{B}} \newcommand{\bb}{\mathsf{b}} \newcommand{\eps}{\varepsilon} \newcommand{\polylog}{\mathrm{polylog}} $ Let…
We give a 3/2-approximation algorithm for stable matchings that runs in $O(m)$ time. The previously best known algorithm by McDermid has the same approximation ratio but runs in $O(n^{3/2}m)$ time, where $n$ denotes the number of people and…
In Constrained Correlation Clustering, the goal is to cluster a complete signed graph in a way that minimizes the number of negative edges inside clusters plus the number of positive edges between clusters, while respecting hard constraints…
The Permutation Pattern Matching problem asks, given two permutations $\sigma$ on $n$ elements and $\pi$, whether $\sigma$ admits a subsequence with the same relative order as $\pi$ (or, in the counting version, how many such subsequences…
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…
Correlation clustering is perhaps the most natural formulation of clustering. Given $n$ objects and a pairwise similarity measure, the goal is to cluster the objects so that, to the best possible extent, similar objects are put in the same…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Uniform sampling of simple graphs having a given degree sequence is a known problem with exponential complexity in the square of the mean degree. For undirected graphs, randomised approximation algorithms have nonetheless been shown to…
In high-dimensional generalized linear models, it is crucial to identify a sparse model that adequately accounts for response variation. Although the best subset section has been widely regarded as the Holy Grail of problems of this type,…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
Computational approaches in historical linguistics have been increasingly applied during the past decade and many new methods that implement parts of the traditional comparative method have been proposed. Despite these increased efforts,…
Correlation clustering is arguably the most natural formulation of clustering. Given n objects and a pairwise similarity measure, the goal is to cluster the objects so that, to the best possible extent, similar objects are put in the same…
The currently fastest algorithm for regular expression pattern matching and membership improves the classical O(nm) time algorithm by a factor of about log^{3/2}n. Instead of focussing on general patterns we analyse homogeneous patterns of…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…
We consider the \emph{approximate minimum selection} problem in presence of \emph{independent random comparison faults}. This problem asks to select one of the smallest $k$ elements in a linearly-ordered collection of $n$ elements by only…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper,…
We generalize the monotone local search approach of Fomin, Gaspers, Lokshtanov and Saurabh [J. ACM 2019], by establishing a connection between parameterized approximation and exponential-time approximation algorithms for monotone subset…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…