Related papers: The Complexity of Phylogeny Constraint Satisfactio…
Constraint Satisfaction Problems (CSPs, for short) make up a class of problems with applications in many areas of computer science. The first classification of these problems was given by Schaeffer who showed that every CSP over the domain…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
We study the problem of finding elements in the intersection of an arbitrary conic variety in $\mathbb{F}^n$ with a given linear subspace (where $\mathbb{F}$ can be the real or complex field). This problem captures a rich family of…
The three-in-a-tree problem asks for an induced tree of the input graph containing three mandatory vertices. In 2006, Chudnovsky and Seymour [Combinatorica, 2010] presented the first polynomial time algorithm for this problem, which has…
In this paper we determine the complexity of a broad class of problems that extends the temporal constraint satisfaction problems. To be more precise we study the problems Poset-SAT($\Phi$), where $\Phi$ is a given set of quantifier-free…
A computational problem exhibits a "gap property" when there is no tractable boundary between two disjoint sets of instances. We establish a Gap Trichotomy Theorem for a family of constraint problem variants, completely classifying the…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…
The CSP (constraint satisfaction problems) is a class of problems deciding whether there exists a homomorphism from an instance relational structure to a target one. The CSP dichotomy is a profound result recently proved by Zhuk (2020, J.…
We extend classical methods of computational complexity to the realm of distributed computing, where they sometimes prove more effective than in their original context. Our focus is on decision problems in the LOCAL model, a setting in…
Trigraph list homomorphism problems (also known as list matrix partition problems) have generated recent interest, partly because there are concrete problems that are not known to be polynomial time solvable or NP-complete. Thus while…
This article presents a general solution to the problem of computational complexity. First, it gives a historical introduction to the problem since the revival of the foundational problems of mathematics at the end of the 19th century.…
For $n\geq 3$, let $(H_n, E)$ denote the $n$-th Henson graph, i.e., the unique countable homogeneous graph with exactly those finite graphs as induced subgraphs that do not embed the complete graph on $n$ vertices. We show that for all…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Constraint satisfaction problems are computational problems that naturally appear in many areas of theoretical computer science. One of the central themes is their computational complexity, and in particular the border between…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
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…
Here we study the computational complexity of the constrained synchronization problem for the class of regular commutative constraint languages. Utilizing a vector representation of regular commutative constraint languages, we give a full…
The constraint satisfaction problem (CSP) involves deciding, given a set of variables and a set of constraints on the variables, whether or not there is an assignment to the variables satisfying all of the constraints. One formulation of…