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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…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…
In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…
We demonstrate that the problems of finding stable or metastable vacua in a low energy effective field theory requires solving nested NP-hard and co-NP-hard problems, while the problem of finding near-vacua is in P. Multiple problems…
Gibbons and Korach studied a fundamental problem in 1997: given an observed sequence of reads and writes of a multi-threaded program, does there exist an interleaving which is sequentially consistent? Apart from applications in testing…
Many natural combinatorial problems can be expressed as constraint satisfaction problems. This class of problems is known to be NP-complete in general, but certain restrictions on the form of the constraints can ensure tractability. The…
In this paper we consider the $p$-Norm Hamming Centroid problem which asks to determine whether some given binary strings have a centroid with a bound on the $p$-norm of its Hamming distances to the strings. Specifically, given a set of…
We study optimization problems that are neither approximable in polynomial time (at least with a constant factor) nor fixed parameter tractable, under widely believed complexity assumptions. Specifically, we focus on Maximum Independent…
We consider the problem of optimally compressing and caching data across a communication network. Given the data generated at edge nodes and a routing path, our goal is to determine the optimal data compression ratios and caching decisions…
We address the satisfiability problem for string constraints that combine relational constraints represented by transducers, word equations, and string length constraints. This problem is undecidable in general. Therefore, we propose a new…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
In the Closest String problem one is given a family $\mathcal S$ of equal-length strings over some fixed alphabet, and the task is to find a string $y$ that minimizes the maximum Hamming distance between $y$ and a string from $\mathcal S$.…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…
Performance of optimization on quadratic problems sensitively depends on the low-lying part of the spectrum. For large (effectively infinite-dimensional) problems, this part of the spectrum can often be naturally represented or approximated…
Widespread use of string solvers in formal analysis of string-heavy programs has led to a growing demand for more efficient and reliable techniques which can be applied in this context, especially for real-world cases. Designing an…
This paper presents the following results on sets that are complete for NP. 1. If there is a problem in NP that requires exponential time at almost all lengths, then every many-one NP-complete set is complete under length-increasing…