Related papers: Finding Diverse Strings and Longest Common Subsequ…
Longest common subsequence (LCS) is one of the most fundamental problems in combinatorial optimization. Apart from theoretical importance, LCS has enormous applications in bioinformatics, revision control systems, and data comparison…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
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,…
Mathematical modeling is a standard approach to solve many real-world problems and {\em diversity} of solutions is an important issue, emerging in applying solutions obtained from mathematical models to real-world problems. Many studies…
We consider two optimization problems related to finding dense subgraphs. The densest at-least-k-subgraph problem (DalkS) is to find an induced subgraph of highest average degree among all subgraphs with at least k vertices, and the densest…
We generalize the polynomial-time solvability of $k$-\textsc{Diverse Minimum s-t Cuts} (De Berg et al., ISAAC'23) to a wider class of combinatorial problems whose solution sets have a distributive lattice structure. We identify three…
For graph learning tasks, many existing methods utilize a message-passing mechanism where vertex features are updated iteratively by aggregation of neighbor information. This strategy provides an efficient means for graph features…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
The subset sum problem is one of the simplest and most fundamental NP-hard problems in combinatorial optimization. We consider two extensions of this problem: The subset sum problem with digraph constraint (SSG) and subset sum problem with…
Given two equally long, uniformly random binary strings, the expected length of their longest common subsequence (LCS) is asymptotically proportional to the strings' length. Finding the proportionality coefficient $\gamma$, i.e. the limit…
Studying the computational complexity of problems is one of the - if not the - fundamental questions in computer science. Yet, surprisingly little is known about the computational complexity of many central problems in data mining. In this…
A heapable sequence is a sequence of numbers that can be arranged in a "min-heap data structure". Finding a longest heapable subsequence of a given sequence was proposed by Byers, Heeringa, Mitzenmacher, and Zervas (ANALCO 2011) as a…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
Longest common subsequence ($\mathsf{LCS}$) is a classic and central problem in combinatorial optimization. While $\mathsf{LCS}$ admits a quadratic time solution, recent evidence suggests that solving the problem may be impossible in truly…
Adaptations of features commonly applied in the field of visual computing, co-occurrence matrix (COM) and run-length matrix (RLM), are proposed for the similarity computation of strings in general (words, phrases, codes and texts). The…
Consider two random strings having the same length and generated by an iid sequence taking its values uniformly in a fixed finite alphabet. Artificially place a long constant block into one of the strings, where a constant block is a…
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…
Given two sequences $A[1..n]$ and $B[1..m]$ over a totally ordered alphabet, the \emph{Longest Common Bitonic Subsequence} (LCBS) problem asks for a longest common subsequence that is strictly increasing up to a single peak element and…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…