相关论文: Two metrics for general phylogenetic networks
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
Quantifying the structural and functional differences of temporal networks is a fundamental and challenging problem in the era of big data. This work proposes a temporal dissimilarity measure for temporal network comparison based on the…
We establish maximal trees and graphs for the difference of average distance and proximity proving thus the corresponding conjecture posed in [4]. We also establish maximal trees for the difference of average eccentricity and remoteness and…
A summary is given of the calibration of the Cepheid scale required in the derivation of distances from observations at V and I, as in the HST work on extragalactic Cepheids. There is some evidence that a small metallicity correction may be…
We propose a novel measure of degree heterogeneity, for unweighted and undirected complex networks, which requires only the degree distribution of the network for its computation. We show that the proposed measure can be applied to all…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
Phylogenetic diversity is a popular measure for quantifying the biodiversity of a collection $Y$ of species, while phylogenetic diversity indices provide a way to apportion phylogenetic diversity to individual species. Typically, for some…
In this paper, we present a framework to compare the differences in the occupation probabilities of two random walk processes, which can be generated by modifications of the network or the transition probabilities between the nodes of the…
We investigate a network model based on an infinite regular square lattice embedded in the Euclidean plane where the node connection probability is given by the geometrical distance of nodes. We show that the degree distribution in the…
Identifying and quantifying structural dissimilarities between complex networks is a fundamental and challenging problem in network science. Previous network comparison methods are based on the structural features, such as the length of…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
Despite the growing interest in characterizing the local geometry leading to the global topology of networks, our understanding of the local structure of complex networks, especially real-world networks, is still incomplete. Here, we…
We introduce a new approach to constructing networks with realistic features. Our method, in spite of its conceptual simplicity (it has only two parameters) is capable of generating a wide variety of network types with prescribed…
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…
Based on the glocal HIM metric and its induced graph kernel, we propose a novel solution in differential network analysis that integrates network comparison and classification tasks. The HIM distance is defined as the one-parameter family…
High order networks are weighted hypergraphs col- lecting relationships between elements of tuples, not necessarily pairs. Valid metric distances between high order networks have been defined but they are difficult to compute when the…
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…
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks…