Related papers: The Binary Perfect Phylogeny with Persistent chara…
One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
In the Exact Matching Problem (EM), we are given a graph equipped with a fixed coloring of its edges with two colors (red and blue), as well as a positive integer $k$. The task is then to decide whether the given graph contains a perfect…
We study the perfect matching reconfiguration problem: Given two perfect matchings of a graph, is there a sequence of flip operations that transforms one into the other? Here, a flip operation exchanges the edges in an alternating cycle of…
Given an input graph and weights on its vertices, the maximum co-2-plex problem is to find a subset of vertices maximizing the sum of their weights and inducing a graph of degree at most 1. In this article, we analyze polyhedral aspects of…
We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method…
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…
Deep reinforcement learning approaches have shown impressive results in a variety of different domains, however, more complex heterogeneous architectures such as world models require the different neural components to be trained separately…
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…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
Perfect phylogeny consisting of determining the compatibility of a set of characters is known to be NP-complete. We propose in this article a conjecture on the necessary and sufficient conditions of compatibility: Given a set $\mathcal{C}$…
This paper explores the enhancement of solution diversity in evolutionary algorithms (EAs) for the maximum matching problem, concentrating on complete bipartite graphs and paths. We adopt binary string encoding for matchings and use Hamming…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
Bilinear inverse problems (BIPs), the resolution of two vectors given their image under a bilinear mapping, arise in many applications. Without further constraints, BIPs are usually ill-posed. In practice, properties of natural signals are…
We investigate the parameterized complexity of finding subgraphs with hereditary properties on graphs belonging to a hereditary graph class. Given a graph $G$, a non-trivial hereditary property $\Pi$ and an integer parameter $k$, the…
Traditional Linear Genetic Programming (LGP) algorithms are based only on the selection mechanism to guide the search. Genetic operators combine or mutate random portions of the individuals, without knowing if the result will lead to a…
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…