Related papers: An Efficient Dynamic Programming Algorithm for the…
The Lempel-Ziv 77 (LZ77) factorization is a fundamental compression scheme widely used in text processing and data compression. In this work, we investigate the time complexity of maintaining the LZ77 factorization of a dynamic string. By…
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…
We consider the problem of storing a dynamic string $S$ over an alphabet $\Sigma=\{\,1,\ldots,\sigma\,\}$ in compressed form. Our representation supports insertions and deletions of symbols and answers three fundamental queries:…
The Longest Common Subsequence (LCS) problem is a fundamental problem of sequence comparison. A natural approximation to this problem is a model in which every pairs of letters of two ``sequences'' are matched independently of the other…
The Shortest Common Supersequence problem (SCS for short) consists in finding a shortest common supersequence of a finite set of words on a fixed alphabet Sigma. It is well-known that its decision version denoted [SR8] in [Garey and…
The normalized substring complexity $\delta$ of a string is defined as $\max_k \{c[k]/k\}$, where $c[k]$ is the number of \textit{distinct} substrings of length $k$. This simply defined measure has recently attracted attention due to its…
Sequence partition problems arise in many fields, such as sequential data analysis, information transmission, and parallel computing. In this paper, we study the following partition problem variant: given a sequence of $n$ items…
Given a sequence of n numbers, the Maximum Consecutive Subsums Problem (MCSP) asks for the maximum consecutive sum of lengths l for each l = 1,...,n. No algorithm is known for this problem which is significantly better than the naive…
Let us consider the Multiple String Matching Problem. In this problem, we consider a long string, denoted by $t$, of length $n$. This string is referred to as a text. We also consider a sequence of $m$ strings, denoted by $S$, which we…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
This article presents a validation of a recently proposed strongly polynomial-time algorithm for the general linear programming problem. The proposed algorithm is an implicit reduction procedure that combines primal and dual linear…
The Chance-Constrained Parallel Machine Scheduling Problem (CC-PMSP) assigns jobs with uncertain processing times to machines, ensuring that each machine's availability constraints are met with a certain probability. We present a…
Partitioning a sequence of length $n$ into $k$ coherent segments (Seg) is one of the classic optimization problems. As long as the optimization criterion is additive, Seg can be solved exactly in $O(n^2k)$ time using a classic dynamic…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
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…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
Non-parametric entropy estimation on sequential data is a fundamental tool in signal processing, capturing information flow within or between processes to measure predictability, redundancy, or similarity. Methods based on longest common…
In the minimum common string partition (MCSP) problem two related input strings are given. "Related" refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings.…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
We give an exact algorithm for the 0-1 Integer Linear Programming problem with a linear number of constraints that improves over exhaustive search by an exponential factor. Specifically, our algorithm runs in time…