Related papers: The Complexity of Phylogeny Constraint Satisfactio…
The purpose of this article is to examine and limit the conditions in which the P complexity class could be equivalent to the NP complexity class. Proof is provided by demonstrating that as the number of clauses in a NP-complete problem…
A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
Robin Hirsch posed in 1996 the 'Really Big Complexity Problem': classify the computational complexity of the network satisfaction problem for all finite relation algebras A. We provide a complete classification for the case that A is…
To any fixed, finite relational structure, $\mathbb{D}$, there is an associated decision problem, CSP$(\mathbb{D})$, which is a restricted version of the constraint satisfaction problem. In [8], the so called "algebraic approach" to the…
The Dichotomy Conjecture for constraint satisfaction problems (CSPs) states that every CSP is in P or is NP-complete (Feder-Vardi, 1993). It has been verified for conservative problems (also known as list homomorphism problems) by A.…
We study a class of functional problems reducible to computing $f^{(n)}(x)$ for inputs $n$ and $x$, where $f$ is a polynomial-time bijection. As we prove, the definition is robust against variations in the type of reduction used in its…
We initiate a systematic study of the computational complexity of the Constraint Satisfaction Problem (CSP) over finite structures that may contain both relations and operations. We show the close connection between this problem and a…
A binary matrix satisfies the consecutive ones property (COP) if its columns can be permuted such that the ones in each row of the resulting matrix are consecutive. Equivalently, a family of sets F = {Q_1,..,Q_m}, where Q_i is subset of R…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view…
For any particular class of graphs, algorithms for computational problems restricted to the class often rely on structural properties that depend on the specific problem at hand. This begs the question if a large set of such results can be…
There exist two conjectures for constraint satisfaction problems (CSPs) of reducts of finitely bounded homogeneous structures: the first one states that tractability of the CSP of such a structure is, when the structure is a model-complete…
We study the computational complexity of fundamental problems over the $p$-adic numbers ${\mathbb Q}_p$ and the $p$-adic integers ${\mathbb Z}_p$. Gu\'epin, Haase, and Worrell proved that checking satisfiability of systems of linear…
The congested clique model of distributed computing has been receiving attention as a model for densely connected distributed systems. While there has been significant progress on the side of upper bounds, we have very little in terms of…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
A Boolean constraint satisfaction instance is a conjunction of constraint applications, where the allowed constraints are drawn from a fixed set B of Boolean functions. We consider the problem of determining whether two given constraint…
Bayesian networks are probabilistic graphical models with a wide range of application areas including gene regulatory networks inference, risk analysis and image processing. Learning the structure of a Bayesian network (BNSL) from discrete…
An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…