Related papers: The Longest Run Subsequence Problem: Further Compl…
We are interested in the statistics of the length of the longest increasing subsequence of 2-rowed lexicographically sorted arrays chosen according to distinct families of distributions D = (D_n)_n, and when n goes to infinity. This…
Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is…
The maximum-likelihood decoding problem is known to be NP-hard for general linear and Reed-Solomon codes. In this paper, we introduce the notion of A-covered codes, that is, codes that can be decoded through a polynomial time algorithm A…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
First, we close the multivariate analysis of a canonical problem concerning short reset words (SYN), as it was started by Fernau et al. (2013). Namely, we prove that the problem, parameterized by the number of states, does not admit a…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
A matching is a set of edges in a graph with no common endpoint. A matching M is called acyclic if the induced subgraph on the endpoints of the edges in M is acyclic. Given a graph G and an integer k, Acyclic Matching Problem seeks for an…
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…
We consider the learning and communication complexity of subsequence containment. In the learning problem, we seek to learn a classifier that positively labels a binary string $x$ if it contains a fixed binary string $y$ as a subsequence.…
The complexity of computing the Lempel-Ziv factorization and the set of all runs (= maximal repetitions) is studied in the decision tree model of computation over ordered alphabet. It is known that both these problems can be solved by RAM…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
We continue and extend previous work on the parameterized complexity analysis of the NP-hard Stable Roommates with Ties and Incomplete Lists problem, thereby strengthening earlier results both on the side of parameterized hardness as well…
In the maximum satisfiability problem (MAX-SAT) we are given a propositional formula in conjunctive normal form and have to find an assignment that satisfies as many clauses as possible. We study the parallel parameterized complexity of…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
Given a graph $G$ and a positive integer $k$, the 2-Load coloring problem is to check whether there is a $2$-coloring $f:V(G) \rightarrow \{r,b\}$ of $G$ such that for every $i \in \{r,b\}$, there are at least $k$ edges with both end…
This thesis concerns sequential-access data compression, i.e., by algorithms that read the input one or more times from beginning to end. In one chapter we consider adaptive prefix coding, for which we must read the input character by…
In the Shortest Common Superstring problem, one needs to find the shortest superstring for a set of strings. This problem is APX-hard, and many approximation algorithms were proposed, with the current best approximation factor of 2.466.…
The suffix array, perhaps the most important data structure in modern string processing, is often augmented with the longest common prefix (LCP) array which stores the lengths of the LCPs for lexicographically adjacent suffixes of a string.…
Finding a maximum clique in a given graph is one of the fundamental NP-hard problems. We compare two multi-core thread-parallel adaptations of a state-of-the-art branch and bound algorithm for the maximum clique problem, and provide a novel…
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…