Related papers: The Complexity of Phylogeny Constraint Satisfactio…
Consider a set of labels $L$ and a set of trees ${\mathcal T} = \{{\mathcal T}^{(1), {\mathcal T}^{(2), ..., {\mathcal T}^{(k) \$ where each tree ${\mathcal T}^{(i)$ is distinctly leaf-labeled by some subset of $L$. One fundamental problem…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…
Satisfiability problems play a central role in computer science and engineering as a general framework for studying the complexity of various problems. Schaefer proved in 1978 that truth satisfaction of propositional formulas given a…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
The question of whether the complexity class P is equal to the complexity class NP has been a seemingly intractable problem for over 4 decades. It has been clear that if an algorithm existed that would solve the problems in the NP class in…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We find an orientation of a tree with 20 vertices such that the corresponding fixed-template constraint satisfaction problem (CSP) is NP-complete, and prove that for every orientation of a tree with fewer vertices the corresponding CSP can…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…
We study techniques for deciding the computational complexity of infinite-domain constraint satisfaction problems. For certain fundamental algebraic structures Delta, we prove definability dichotomy theorems of the following form: for every…
We perform a refined complexity-theoretic analysis of three classical problems in the context of Hierarchical Task Network Planning: the verification of a provided plan, whether an executable plan exists, and whether a given state can be…
We produce a class of $\omega$-categorical structures with finite signature by applying a model-theoretic construction -- a refinement of the Hrushosvki-encoding -- to $\omega$-categorical structures in a possibly infinite signature. We…
We completely classify the computational complexity of the list H-colouring problem for graphs (with possible loops) in combinatorial and algebraic terms: for every graph H the problem is either NP-complete, NL-complete, L-complete or is…
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…
Symmetries occur naturally in CSP or SAT problems and are not very difficult to discover, but using them to prune the search space tends to be very challenging. Indeed, this usually requires finding specific elements in a group of…
Valued constraint satisfaction problems (VCSPs) constitute a large class of computational optimization problems. It was shown recently that, over finite domains, every VCSP is in P or NP-complete, depending on the admitted cost functions.…
We study the complexity of the valued constraint satisfaction problem (VCSP) for every valued structure with the domain ${\mathbb Q}$ that is preserved by all order-preserving bijections. Such VCSPs will be called temporal, in analogy to…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
We show that under mild assumptions for a problem whose solutions admit a dynamic programming-like recurrence relation, we can still find a solution under additional packing constraints, which need to be satisfied approximately. The number…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
For a first-order theory $T$, the Constraint Satisfaction Problem of $T$ is the computational problem of deciding whether a given conjunction of atomic formulas is satisfiable in some model of $T$. In this article we develop sufficient…