Related papers: Path lengths in tree-child time consistent hybridi…
In this paper, we are concerned with mean hitting time $\langle\mathcal{H}\rangle$ for random walks on recursive growth tree networks that are built based on an arbitrary tree as the seed via implementing various primitive graphic…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
Transportation and distribution networks are a class of spatial networks that have been of interest in recent years. These networks are often characterized by the presence of complex structures such as central loops paired with peripheral…
Networks having the geometry and the connectivity of trees are considered as the spatial support of spatiotemporal dynamical processes. A tree is characterized by two parameters: its ramification and its depth. The local dynamics at the…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for bicombining tree-child networks in which…
Tree projections provide a unifying framework to deal with most structural decomposition methods of constraint satisfaction problems (CSPs). Within this framework, a CSP instance is decomposed into a number of sub-problems, called views,…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
We develop a framework for applying treewidth-based dynamic programming on graphs with "hybrid structure", i.e., with parts that may not have small treewidth but instead possess other structural properties. Informally, this is achieved by…
Structure and dynamics of complex networks usually deal with degree distributions, clustering, shortest path lengths and other graph properties. Although these concepts have been analysed for graphs on abstract spaces, many networks happen…
We introduce the tree distance, a new distance measure on graphs. The tree distance can be computed in polynomial time with standard methods from convex optimization. It is based on the notion of fractional isomorphism, a characterization…
In many complex networks the vertices are ordered in time, and edges represent causal connections. We propose methods of analysing such directed acyclic graphs taking into account the constraints of causality and highlighting the causal…
In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
We study the problem of inferring network topology from information cascades, in which the amount of time taken for information to diffuse across an edge in the network follows an unknown distribution. Unlike previous studies, which assume…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Information networks are becoming increasingly popular to capture complex relationships across various disciplines, such as social networks, citation networks, and biological networks. The primary challenge in this domain is measuring…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…