Related papers: Circular Networks from Distorted Metrics

Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…

Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…

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…

Data-driven analysis of complex networks has been in the focus of research for decades. An important area of research is to study how well real networks can be described with a small selection of metrics, furthermore how well network models…

This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…

Network structures are extremely important to the study of political science. Much of the data in its subfields are naturally represented as networks. This includes trade, diplomatic and conflict relationships. The social structure of…

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…

Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…

Daily internet communication relies heavily on tree-structured graphs, embodied by popular data formats such as XML and JSON. However, many recent generative (probabilistic) models utilize neural networks to learn a probability distribution…

We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…

Directed acyclic graphs are a fundamental class of networks that includes citation networks, food webs, and family trees, among others. Here we define a random graph model for directed acyclic graphs and give solutions for a number of the…

Natural numerical networks are introduced as a new classification algorithm based on the numerical solution of nonlinear partial differential equations of forward-backward diffusion type on complete graphs. The proposed natural numerical…

A complex network is a condensed representation of the relational topological framework of a complex system. A main reason for the existence of such networks is the transmission of items through the entities of these complex systems. Here,…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

In real-world and online social networks, individuals receive and transmit information in real time. Cascading information transmissions (e.g. phone calls, text messages, social media posts) may be understood as a realization of a diffusion…

Consider an information source generating a symbol at the root of a tree network whose links correspond to noisy communication channels, and broadcasting it through the network. We study the problem of reconstructing the transmitted symbol…

Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…