Related papers: Rank and Select on Degenerate Strings
Motivated by the problem of storing coloured de Bruijn graphs, we show how, if we can already support fast select queries on one string, then we can store a little extra information and support fairly fast select queries on a similar…
An enumeration kernel as defined by Creignou et al. [Theory Comput. Syst. 2017] for a parameterized enumeration problem consists of an algorithm that transforms each instance into one whose size is bounded by the parameter plus a…
The sparse regression problem, also known as best subset selection problem, can be cast as follows: Given a set $S$ of $n$ points in $\mathbb{R}^d$, a point $y\in \mathbb{R}^d$, and an integer $2 \leq k \leq d$, find an affine combination…
Recurrent neural network (RNN) and connectionist temporal classification (CTC) have showed successes in many sequence labeling tasks with the strong ability of dealing with the problems where the alignment between the inputs and the target…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
Clustering is a well-known and studied problem, one of its variants, called contiguity-constrained clustering, accepts as a second input a graph used to encode prior information about cluster structure by means of contiguity constraints…
A rank estimator in robust regression is a minimizer of a function which depends (in addition to other factors) on the ordering of residuals but not on their values. Here we focus on the optimization aspects of rank estimators. We…
The importance of a node in a directed graph can be measured by its PageRank. The PageRank of a node is used in a number of application contexts - including ranking websites - and can be interpreted as the average portion of time spent at…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
In this paper, we consider tree decompositions, branch decompositions, and clique decompositions. We improve the running time of dynamic programming algorithms on these graph decompositions for a large number of problems as a function of…
Similar question retrieval is a core task in community-based question answering (CQA) services. To balance the effectiveness and efficiency, the question retrieval system is typically implemented as multi-stage rankers: The first-stage…
Scenario-based optimization problems can be solved via Benders decomposition, which separates first-stage (master problem) decisions from second-stage (subproblem) recourse actions and iteratively refines the master problem with Benders…
A string $S[1,n]$ is a power (or tandem repeat) of order $k$ and period $n/k$ if it can decomposed into $k$ consecutive equal-length blocks of letters. Powers and periods are fundamental to string processing, and algorithms for their…
In the classical linear degeneracy testing problem, we are given $n$ real numbers and a $k$-variate linear polynomial $F$, for some constant $k$, and have to determine whether there exist $k$ numbers $a_1,\ldots,a_k$ from the set such that…
The selection problem, where one wishes to locate the $k^{th}$ smallest element in an unsorted array of size $n$, is one of the basic problems studied in computer science. The main focus of this work is designing algorithms for solving the…
We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…
Finding "densely connected clusters" in a graph is in general an important and well studied problem in the literature \cite{Schaeffer}. It has various applications in pattern recognition, social networking and data mining…
String attractors [STOC 2018] are combinatorial objects recently introduced to unify all known dictionary compression techniques in a single theory. A set $\Gamma\subseteq [1..n]$ is a $k$-attractor for a string $S\in[1..\sigma]^n$ if and…
String analysis is the problem of reasoning about how strings are manipulated by a program. It has numerous applications including automatic detection of cross-site scripting (XSS). A popular string analysis technique includes symbolic…