Related papers: The Exact Closest String Problem as a Constraint S…
We study the optimization version of constraint satisfaction problems (Max-CSPs) in the framework of parameterized complexity; the goal is to compute the maximum fraction of constraints that can be satisfied simultaneously. In standard…
Sparse and convolutional constraints form a natural prior for many optimization problems that arise from physical processes. Detecting motifs in speech and musical passages, super-resolving images, compressing videos, and reconstructing…
The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
In his 1987 paper entitled "Generalized String Matching", Abrahamson introduced {\em pattern matching with character classes} and provided the first efficient algorithm to solve it. The best known solution to date is due to Linhart and…
The problem of sparse approximation and the closely related compressed sensing have received tremendous attention in the past decade. Primarily studied from the viewpoint of applied harmonic analysis and signal processing, there have been…
Constraint satisfaction problem (CSP) is a well-studied combinatorial search problem, in which we are asked to find an assignment of values to given variables so as to satisfy all of given constraints. We study a reconfiguration variant of…
A constraint satisfaction problem (CSP), $\textsf{Max-CSP}(\mathcal{F})$, is specified by a finite set of constraints $\mathcal{F} \subseteq \{[q]^k \to \{0,1\}\}$ for positive integers $q$ and $k$. An instance of the problem on $n$…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
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…
Biclustering, also known as co-clustering or two-way clustering, simultaneously partitions the rows and columns of a data matrix to reveal submatrices with coherent patterns. Incorporating background knowledge into clustering to enhance…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
Given $k$ collections of 2SAT clauses on the same set of variables $V$, can we find one assignment that satisfies a large fraction of clauses from each collection? We consider such simultaneous constraint satisfaction problems, and design…
We address the separability problem for straight-line string constraints. The separability problem for languages of a class C by a class S asks: given two languages A and B in C, does there exist a language I in S separating A and B (i.e.,…
We initiate a systematic study of utilizing predictions to improve over approximation guarantees of classic algorithms, without increasing the running time. We propose a systematic method for a wide class of optimization problems that ask…
The minimum common string partition problem is an NP-hard combinatorial optimization problem with applications in computational biology. In this work we propose the first integer linear programming model for solving this problem. Moreover,…
A superstring of a set of strings correspond to a string which contains all the other strings as substrings. The problem of finding the Shortest Linear Superstring is a well-know and well-studied problem in stringology. We present here a…
In the maximum constraint satisfaction problem (MAX CSP), one is given a finite collection of (possibly weighted) constraints on overlapping sets of variables, and the goal is to assign values from a given finite domain to the variables so…
Most natural language processing tasks can be formulated as the approximated nearest neighbor search problem, such as word analogy, document similarity, machine translation. Take the question-answering task as an example, given a question…
The abelian pattern matching problem consists in finding all substrings of a text which are permutations of a given pattern. This problem finds application in many areas and can be solved in linear time by a naive sliding window approach.…