Related papers: The comparison of tree-sibling time consistent phy…
Given a network represented by a weighted directed graph G, we consider the problem of finding a bounded cost set of nodes S such that the influence spreading from S in G, within a given time bound, is as large as possible. The dynamic that…
The tree-depth problem can be seen as finding an elimination tree of minimum height for a given input graph $G$. We introduce a bicriteria generalization in which additionally the width of the elimination tree needs to be bounded by some…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
For a given set $\mathcal{L}$ of species and a set $\mathcal{T}$ of triplets on $\mathcal{L}$, one wants to construct a phylogenetic network which is consistent with $\mathcal{T}$, i.e which represents all triplets of $\mathcal{T}$. The…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
The Subgraph Isomorphism problem is of considerable importance in computer science. We examine the problem when the pattern graph H is of bounded treewidth, as occurs in a variety of applications. This problem has a well-known algorithm via…
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 present a complete classification of the deterministic distributed time complexity for a family of graph problems: binary labeling problems in trees. These are locally checkable problems that can be encoded with an alphabet of size two…
We prove that Nakhleh's latest dissimilarity measure for phylogenetic networks is a metric on the classes of tree-child phylogenetic networks, of semi-binary time consistent tree-sibling phylogenetic networks, and of multi-labeled…
In this paper, a new information theoretic framework for graph matching is introduced. Using this framework, the graph isomorphism and seeded graph matching problems are studied. The maximum degree algorithm for graph isomorphism is…
The P versus NP problem asks whether every language verifiable in polynomial time can also be decided in deterministic polynomial time. In this paper, we present a constructive proof that P = NP by introducing a universal, graph-based…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
We continue the study of graph classes in which the treewidth can only be large due to the presence of a large clique, and, more specifically, of graph classes with bounded tree-independence number. In [Dallard, Milani\v{c}, and…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
For graphs $G$ and $H$, a \emph{homomorphism} from $G$ to $H$ is an edge-preserving mapping from the vertex set of $G$ to the vertex set of $H$. For a fixed graph $H$, by \textsc{Hom($H$)} we denote the computational problem which asks…
It is well-known that the graph isomorphism problem can be posed as an equivalent problem of determining whether an auxiliary graph structure contains a clique of specific order. However, the algorithms that have been developed so far for…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
We claimed that there is a polynomial algorithm to test if two graphs are isomorphic. But the algorithm is wrong. It only tests if the adjacency matrices of two graphs have the same eigenvalues. There is a counterexample of two…
In this article, we revisit and expand our prior work on graph similarity. As with our earlier work, we focus on a view of similarity which does not require node correspondence between graphs under comparison. Our work is suited to the…