Related papers: The Longest Run Subsequence Problem: Further Compl…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
Pattern matching queries on strings can be solved in linear time by Knuth-Morris-Pratt (KMP) algorithm. In 1973, Weiner introduced the suffix tree of a string [FOCS 1973] and showed that the seemingly more difficult problem of computing…
We study systems of String Equations where block variables need to be assigned strings so that their concatenation gives a specified target string. We investigate this problem under a multivariate complexity framework, searching for…
We study the well-established problem of finding an optimal routing of unsplittable flows in a graph. While by now there is an extensive body of work targeting the problem on graph classes such as paths and trees, we aim at using the…
The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
This paper investigates the complexity of finding secluded paths in graphs. We focus on the \textsc{Short Secluded Path} problem and a natural new variant we introduce, \textsc{Shortest Secluded Path}. Formally, given an undirected graph…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
This paper presents results on maximal runs, order of squares, palindromes, and unbordered factors of members of the family of binary pattern sequences with the all-one pattern. Restricting ourselves to binary pattern sequences with the…
Graph pattern matching is a routine process for a wide variety of applications such as social network analysis. It is typically defined in terms of subgraph isomorphism which is NP-Complete. To lower its complexity, many extensions of graph…
We study the following combinatorial version of the Slepian-Wolf coding scheme. Two isolated Senders are given binary strings $X$ and $Y$ respectively; the length of each string is equal to $n$, and the Hamming distance between the strings…
The problem of maximizing the $p$-th power of a $p$-norm over a halfspace-presented polytope in $\R^d$ is a convex maximization problem which plays a fundamental role in computational convexity. It has been shown in 1986 that this problem…
The Longest Common Subsequence (LCS) Problem asks for the longest sequence of (non-contiguous) matches between two given strings of characters. Using extensive Monte Carlo simulations, we find a finite size scaling law of the form E(L)/N =C…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
A workflow specification defines a set of steps and the order in which those steps must be executed. Security requirements may impose constraints on which groups of users are permitted to perform subsets of those steps. A workflow…
In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…
An st-shortest path, or st-path for short, in a graph G is a shortest (induced) path from s to t in G. Two st-paths are said to be adjacent if they differ on exactly one vertex. A reconfiguration sequence between two st-paths P and Q is a…
In the Selective Coloring problem, we are given an integer $k$, a graph $G$, and a partition of $V(G)$ into $p$ parts, and the goal is to decide whether or not we can pick exactly one vertex of each part and obtain a $k$-colorable induced…
It has been observed in many places that constant-factor approximable problems often admit polynomial or even linear problem kernels for their decision versions, e.g., Vertex Cover, Feedback Vertex Set, and Triangle Packing. While there…
Many machine learning tasks can be expressed as the transformation---or \emph{transduction}---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to…