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The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
We study the problem of scheduling jobs on parallel machines minimizing the total completion time, with each job using exactly one resource. First, we derive fundamental properties of the problem and show that the problem is polynomially…
The Longest Common Subsequence Problem (LCS) deals with finding the longest subsequence among a given set of strings. The LCS problem is an NP-hard problem which makes it a target for lots of effort to find a better solution with heuristics…
We consider the SUBSET SUM problem and its important variants in this paper. In the SUBSET SUM problem, a (multi-)set $X$ of $n$ positive numbers and a target number $t$ are given, and the task is to find a subset of $X$ with the maximal…
We study sketching and streaming algorithms for the Longest Common Subsequence problem (LCS) on strings of small alphabet size $|\Sigma|$. For the problem of deciding whether the LCS of strings $x,y$ has length at least $L$, we obtain a…
Distribution testing is a fundamental statistical task with many applications, but we are interested in a variety of problems where systematic mislabelings of the sample prevent us from applying the existing theory. To apply distribution…
We consider the problem of finding a minimum common partition of two strings (MCSP). The problem has its application in genome comparison. MCSP problem is proved to be NP-hard. In this paper, we develop an Integer Programming (IP)…
The closest string problem is an NP-hard problem, whose task is to find a string that minimizes maximum Hamming distance to a given set of strings. This can be reduced to an integer program (IP). However, to date, there exists no known…
A long-standing open question in Integer Programming is whether integer programs with constraint matrices with bounded subdeterminants are efficiently solvable. An important special case thereof are congruency-constrained integer programs…
In the Minimum Consistent Subset (MCS) problem, we are presented with a connected simple undirected graph $G=(V,E)$, consisting of a vertex set $V$ of size $n$ and an edge set $E$. Each vertex in $V$ is assigned a color from the set…
Given a string $P$ of length $m$, a longer string $T$ of length $n>m$, and two integers $l\geq 0$ and $r\geq 0$, the context of $P$ in $T$ is the set of all string pairs $(L,R)$, with $|L|=l$ and $|R|=r$, such that the string $LPR$ occurs…
This paper describes an extension to the constraint satisfaction problem (CSP) called MUSE CSP (MUltiply SEgmented Constraint Satisfaction Problem). This extension is especially useful for those problems which segment into multiple sets of…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
In the minimum constraint removal ($MCR$), there is no feasible path to move from the starting point towards the goal and, the minimum constraints should be removed in order to find a collision-free path. It has been proved that $MCR$…
The range-minimum query (RMQ) problem is a fundamental data structuring task with numerous applications. Despite the fact that succinct solutions with worst-case optimal $2n+o(n)$ bits of space and constant query time are known, it has 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…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
Given a permutation pi, the application of prefix reversal f^(i) to pi reverses the order of the first i elements of pi. The problem of Sorting By Prefix Reversals (also known as pancake flipping), made famous by Gates and Papadimitriou…