相关论文: The comparison of tree-sibling time consistent phy…

The group isomorphism problem in computational complexity asks whether two finite groups given by their Cayley tables are isomorphic or not. Although polynomial-time isomorphism tests exist for many specific types of groups, no general…

In this paper, we investigate the problem of generating the spanning trees of a graph $G$ up to the automorphisms or "symmetries" of $G$. After introducing and surveying this problem for general input graphs, we present algorithms that…

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,…

Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…

Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…

We propose a consistent polynomial-time method for the unseeded node matching problem for networks with smooth underlying structures. Despite widely conjectured by the research community that the structured graph matching problem to be…

Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally…

We prove that the combinatorial Weisfeiler-Leman algorithm of dimension $(3k+4)$ is a complete isomorphism test for the class of all graphs of rank width at most $k$. Rank width is a graph invariant that, similarly to tree width, measures…

A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…

We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…

Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…

It is known that a graph isomorphism testing algorithm is polynomially equivalent to a detecting of a graph non-trivial automorphism algorithm. The polynomiality of the latter algorithm, is obtained by consideration of symmetry properties…

The Graph Isomorphism (GI) problem is a theoretically interesting problem because it has not been proven to be in P nor to be NP-complete. Babai made a breakthrough in 2015 when announcing a quasipolynomial time algorithm for GI problem.…

Bayesian network structure learning is the notoriously difficult problem of discovering a Bayesian network that optimally represents a given set of training data. In this paper we study the computational worst-case complexity of exact…

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…

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 binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…

Strong bisimilarity on normed BPA is polynomial-time decidable, while weak bisimilarity on totally normed BPA is NP-hard. It is natural to ask where the computational complexity of branching bisimilarity on totally normed BPA lies. This…

A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…

Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…