Related papers: Modulated String Searching
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
We study the maximum likelihood model in emission tomography and propose a new family of algorithms for its solution, called String-Averaging Expectation-Maximization (SAEM). In the String-Averaging algorithmic regime, the index set of all…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
Learning an appropriate (dis)similarity function from the available data is a central problem in machine learning, since the success of many machine learning algorithms critically depends on the choice of a similarity function to compare…
Bayesian Optimization is ubiquitous in experimental design and black-box optimization for improving search efficiency. However, most existing approaches rely on regression models which are limited to fixed search spaces and structured,…
We investigate the number of nested string replacements required to reduce a string of identical characters to one character.
Beam search is a go-to strategy for decoding neural sequence models. The algorithm can naturally be viewed as a subset optimization problem, albeit one where the corresponding set function does not reflect interactions between candidates.…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
In the Shortest-Superstring problem, we are given a set of strings S and want to find a string that contains all strings in S as substrings and has minimum length. This is a classical problem in approximation and the best known…
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…
The vocabulary mismatch problem is a long-standing problem in information retrieval. Semantic matching holds the promise of solving the problem. Recent advances in language technology have given rise to unsupervised neural models for…
We study the following rearrangement problem: Given $n$ words, rearrange and concatenate them so that the obtained string is lexicographically smallest (or largest, respectively). We show that this problem reduces to sorting the given words…
In the computational-mechanics structural analysis of one-dimensional cellular automata the following automata-theoretic analogue of the \emph{change-point problem} from time series analysis arises: \emph{Given a string $\sigma$ and a…
Parameterized complexity enables the practical solution of generally intractable NP-hard problems when certain parameters are small, making it particularly useful in real-world applications. The study of string problems in this framework…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for…
This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not…
An extended regular expression $R$ specifies a set of strings formed by characters from an alphabet combined with concatenation, union, intersection, complement, and star operators. Given an extended regular expression $R$ and a string $Q$,…