Related papers: A Family of Approximation Algorithms for the Maxim…
An instance $I$ of the Stable Matching Problem (SMP) is given by a bipartite graph with a preference list of neighbors for every vertex. A swap in $I$ is the exchange of two consecutive vertices in a preference list. A swap can be viewed as…
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…
In the Demand Strip Packing problem (DSP), we are given a time interval and a collection of tasks, each characterized by a processing time and a demand for a given resource (such as electricity, computational power, etc.). A feasible…
Despite significant research efforts, the state-of-the-art algorithm for maintaining an approximate matching in fully dynamic graphs has a polynomial {worst-case} update time, even for very poor approximation guarantees. In a recent…
Consider two parties who want to compare their strings, e.g., genomes, but do not want to reveal them to each other. We present a system for privacy-preserving matching of strings, which differs from existing systems by providing a…
We propose a new modified primal-dual proximal best approximation method for solving convex not necessarily differentiable optimization problems. The novelty of the method relies on introducing memory by taking into account iterates…
This paper considers pairs of optimization problems that are defined from a single input and for which it is desired to find a good approximation to either one of the problems. In many instances, it is possible to efficiently find an…
The edit distance between two strings is defined as the smallest number of insertions, deletions, and substitutions that need to be made to transform one of the strings to another one. Approximating edit distance in subquadratic time is…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
The problem of finding longest common subsequence (LCS) is one of the fundamental problems in computer science, which finds application in fields such as computational biology, text processing, information retrieval, data compression etc.…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
We study the problem of finding solutions to the stable matching problem that are robust to errors in the input and we obtain a polynomial time algorithm for a special class of errors. In the process, we also initiate work on a new…
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…