Related papers: Improved Approximation Ratios for the Shortest Com…
We examine the minimum entropy coupling problem, where one must find the minimum entropy variable that has a given set of distributions $S = \{p_1, \dots, p_m \}$ as its marginals. Although this problem is NP-Hard, previous works have…
In the longest common substring problem, we are given two strings of length $n$ and must find a substring of maximal length that occurs in both strings. It is well known that the problem can be solved in linear time, but the solution is not…
We study the optimization problem of choosing strings of finite length to maximize string submodular functions on string matroids, which is a broader class of problems than maximizing set submodular functions on set matroids. We provide a…
The randomized coordinate descent (RCD) method is a classical algorithm with simple, lightweight iterations that is widely used for various optimization problems, including the solution of positive semidefinite linear systems. As a linear…
Let s be a string whose symbols are solely available through access(i), a read-only operation that probes s and returns the symbol at position i in s. Many compressed data structures for strings, trees, and graphs, require two kinds of…
Palindromes are popular and important objects in textual data processing, bioinformatics, and combinatorics on words. Let $S = XaY$ be a string where $X$ and $Y$ are of the same length, and $a$ is either a single character or the empty…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
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…
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…
Measuring Sentence Textual Similarity (STS) is a classic task that can be applied to many downstream NLP applications such as text generation and retrieval. In this paper, we focus on unsupervised STS that works on various domains but only…
In the Minimum k-Union problem (MkU) we are given a set system with n sets and are asked to select k sets in order to minimize the size of their union. Despite being a very natural problem, it has received surprisingly little attention: the…
Consider a graph with n nodes and m edges, independent edge weights and lengths, and arbitrary distance demands for node pairs. The spanner problem asks for a minimum-weight subgraph that satisfies these demands via sufficiently short paths…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
The 2-Edge-Connected Spanning Subgraph Problem (2ECSS) is a fundamental problem in survivable network design. Given an undirected $2$-edge-connected graph, the goal is to find a $2$-edge-connected spanning subgraph with the minimum number…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…
Coordinate-type subgradient methods for addressing nonsmooth optimization problems are relatively underexplored due to the set-valued nature of the subdifferential. In this work, our study focuses on nonsmooth composite optimization…
The problem of objectively choosing a string of actions to optimize an objective function that is string submodular has been considered in [1]. There it is shown that the greedy strategy, consisting of a string of actions that only locally…
This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including…
In the minimum $k$-edge-connected spanning subgraph ($k$-ECSS) problem the goal is to find the minimum weight subgraph resistant to up to $k-1$ edge failures. This is a central problem in network design, and a natural generalization of the…