相关论文: Two metrics for general phylogenetic networks
Graph comparison plays a major role in many network applications. We often need a similarity metric for comparing networks according to their structural properties. Various network features - such as degree distribution and clustering…
The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two…
To improve our understanding of connected systems, different tools derived from statistics, signal processing, information theory and statistical physics have been developed in the last decade. Here, we will focus on the graph comparison…
The widespread relevance of complex networks is a valuable tool in the analysis of a broad range of systems. There is a demand for tools which enable the extraction of meaningful information and allow the comparison between different…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
In recent years, networks with higher-order interactions have emerged as a powerful tool to model complex systems. Comparing these higher-order systems remains however a challenge. Traditional similarity measures designed for pairwise…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
Due to the ever rising importance of the network paradigm across several areas of science, comparing and classifying graphs represent essential steps in the networks analysis of complex systems. Both tasks have been recently tackled via…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
We present the distance matrix evolution for different types of networks: exponential, scale-free and classical random ones. Statistical properties of these matrices are discussed as well as topological features of the networks. Numerical…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
We study the diversity of the features learned by a two-layer neural network trained with the least squares loss. We measure the diversity by the average $L_2$-distance between the hidden-layer features and theoretically investigate how…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
Tree-child networks are an important network class which are used in phylogenetics to model reticulate evolution. In a recent paper, Pons and Batle (2021) conjectured a relation between tree-child networks and certain words. In this short…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…
The dynamic character of most social networks requires to model evolution of networks in order to enable complex analysis of theirs dynamics. The following paper focuses on the definition of differences between network snapshots by means of…
The degree distribution is an important characteristic of complex networks. In many applications, quantification of degree distribution in the form of a fixed-length feature vector is a necessary step. On the other hand, we often need to…