Related papers: The Complexity of Phylogeny Constraint Satisfactio…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We analyse how the standard reductions between constraint satisfaction problems affect their proof complexity. We show that, for the most studied propositional, algebraic, and semi-algebraic proof systems, the classical constructions of…
Inferring probabilistic networks from data is a notoriously difficult task. Under various goodness-of-fit measures, finding an optimal network is NP-hard, even if restricted to polytrees of bounded in-degree. Polynomial-time algorithms are…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
This work explores the relationship between solution space and time complexity in the context of the $\textbf{P}$ vs. $\textbf{NP}$ problem, particularly through the lens of the sliding tile puzzle and root finding algorithms. We focus on…
We study here several variants of the covariates fine balance problem where we generalize some of these problems and introduce a number of others. We present here a comprehensive complexity study of the covariates problems providing…
The constraint satisfaction problem (CSP) of a first-order theory T is the computational problem of deciding whether a given conjunction of atomic formulas is satisfiable in some model of T. We study the computational complexity of CSP$(T_1…
The constraint satisfaction problem (CSP) is a computational problem that includes a range of important problems in computer science. We point out that fundamental concepts of the CSP, such as the solution set of an instance and…
Constraint Satisfaction Problems (CSP) constitute a convenient way to capture many combinatorial problems. The general CSP is known to be NP-complete, but its complexity depends on a template, usually a set of relations, upon which they are…
Consider the problem of determining whether there exists a spanning hypertree in a given k-uniform hypergraph. This problem is trivially in P for k=2, and is NP-complete for k>= 4, whereas for k=3, there exists a polynomial-time algorithm…
We propose an exact polynomial algorithm for a resource allocation problem with convex costs and constraints on partial sums of resource consumptions, in the presence of either continuous or integer variables. No assumption of strict…
Several variants of the Constraint Satisfaction Problem have been proposed and investigated in the literature for modelling those scenarios where solutions are associated with some given costs. Within these frameworks computing an optimal…
We present three new complexity results for classes of planning problems with simple causal graphs. First, we describe a polynomial-time algorithm that uses macros to generate plans for the class 3S of planning problems with binary state…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
We consider the general problem of blocking all solutions of some given combinatorial problem with only few elements. For example, the problem of destroying all maximum cliques of a given graph by forbidding only few vertices. Problems of…
Typestate systems ensure many desirable properties of imperative programs, including initialization of object fields and correct use of stateful library interfaces. Abstract sets with cardinality constraints naturally generalize typestate…