Related papers: A Dynamic Programming Solution to a Generalized LC…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
In this paper we initiate the study of computing a maximal (not necessarily maximum) repeating pattern in a single input string, where the corresponding problems have been studied (e.g., a maximal common subsequence) only in two or more…
We present the first $\mathrm{o}(n)$-space polynomial-time algorithm for computing the length of a longest common subsequence. Given two strings of length $n$, the algorithm runs in $\mathrm{O}(n^{3})$ time with $\mathrm{O}\left(\frac{n…
The longest induced (or chordless) cycle problem is a graph problem classified as NP-complete and involves the task of determining the largest possible subset of vertices within a graph in such a way that the induced subgraph forms a cycle.…
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton…
The goal of this paper is to set a constraint programming framework to solve lot-sizing problems. More specifically, we consider a single-item lot-sizing problem with time-varying lower and upper bounds for production and inventory. The…
The length-constrained cycle partition problem (LCCP) is a graph optimization problem in which a set of nodes must be partitioned into a minimum number of cycles. Every node is associated with a critical time and the length of every cycle…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
A sparse linear programming (SLP) problem is a linear programming problem equipped with a sparsity (or cardinality) constraint, which is nonconvex and discontinuous theoretically and generally NP-hard computationally due to the…
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements…
We propose an exact algorithm for solving the longest simple path problem between two given vertices in undirected weighted graphs. By using graph partitioning and dynamic programming, we obtain an algorithm that is significantly faster…
The expected length of longest common subsequences is a problem that has been in the literature for at least twenty five years. Determining the limiting constants \gamma_k appears to be quite difficult, and the current best bounds leave…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
The problem of finding network codes for general connections is inherently difficult in capacity constrained networks. Resource minimization for general connections with network coding is further complicated. Existing methods for…
A technique using a systolic array structure is proposed for solving the common approximate substring (CAS) problem. This approach extends the technique introduced in earlier work from the computation of the edit-distance between two…
Sublinear time complexity is required by the massively parallel computation (MPC) model. Breaking dynamic programs into a set of sparse dynamic programs that can be divided, solved, and merged in sublinear time. The rectangle escape problem…
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…
Dynamic programming is a powerful technique that is, unfortunately, often inherently sequential. That is, there exists no unified method to parallelize algorithms that use dynamic programming. In this paper, we attempt to address this issue…
We revisit the longest common extension (LCE) problem, that is, preprocess a string $T$ into a compact data structure that supports fast LCE queries. An LCE query takes a pair $(i,j)$ of indices in $T$ and returns the length of the longest…