Related papers: The Complexity of Phylogeny Constraint Satisfactio…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
We reveal a complexity chasm, separating the trinomial and tetranomial cases, for solving univariate sparse polynomial equations over certain local fields. First, for any fixed field $K\in\{\mathbb{Q}_2,\mathbb{Q}_3,\mathbb{Q}_5,\ldots\}$,…
Edge-coloring problems with forbidden patterns are decision problems asking to find an edge-coloring of the input graph which avoids a homomorphism from a fixed forbidden family of edge-colored graphs. In the precolored version of these…
Constraint satisfaction problems (CSPs) for first-order reducts of finitely bounded homogeneous structures form a large class of computational problems that might exhibit a complexity dichotomy, P versus NP-complete. A powerful method to…
The computational complexity of solving random 3-Satisfiability (3-SAT) problems is investigated. 3-SAT is a representative example of hard computational tasks; it consists in knowing whether a set of alpha N randomly drawn logical…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
Satisfiability of Boolean circuits is among the most known and important problems in theoretical computer science. This problem is NP-complete in general but becomes polynomial time when restricted either to monotone gates or linear gates.…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
Constraint Satisfaction Problem on finite sets is known to be NP-complete in general but certain restrictions on the constraint language can ensure tractability. It was proved that if a constraint language has a weak near unanimity…
Approximating the roots of a holomorphic function in an input box is a fundamental problem in many domains. Most algorithms in the literature for solving this problem are conditional, i.e., they make some simplifying assumptions, such as,…
We give a trichotomy theorem for the complexity of approximately counting the number of satisfying assignments of a Boolean CSP instance. Such problems are parameterised by a constraint language specifying the relations that may be used in…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Random instances of Constraint Satisfaction Problems (CSP's) appear to be hard for all known algorithms, when the number of constraints per variable lies in a certain interval. Contributing to the general understanding of the structure of…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
In this paper, we study three algorithmic problems involving computation trees: the optimization, solvability, and satisfiability problems. The solvability problem is concerned with recognizing computation trees that solve problems. The…
We study the data complexity of consistent query answering (CQA) on databases that may violate the primary key constraints. A repair is a maximal subset of the database satisfying the primary key constraints. For a Boolean query q, the…
We study the complexity of the Distributed Constraint Satisfaction Problem (DCSP) on a synchronous, anonymous network from a theoretical standpoint. In this setting, variables and constraints are controlled by agents which communicate with…