Related papers: Computationally Inferred Genealogical Networks Unc…
Many investigations of scientific collaboration are based on statistical analyses of large networks constructed from bibliographic repositories. These investigations often rely on a wealth of bibliographic data, but very little or no other…
Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
We present a technique for clustering categorical data by generating many dissimilarity matrices and averaging over them. We begin by demonstrating our technique on low dimensional categorical data and comparing it to several other…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life.' In this paper we use an…
A pedigree is a directed graph in which each vertex (except the founder vertices) has two parents. The main result in this paper is a construction of an infinite family of counter examples to a reconstruction problem on pedigrees, thus…
Collaborative filtering or recommender systems use a database about user preferences to predict additional topics or products a new user might like. In this paper we describe several algorithms designed for this task, including techniques…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
Community structure identification has been an important research topic in complex networks and there has been many algorithms proposed so far to detect community structures in complex networks, where most of the algorithms are not suitable…
Graphs are used in many disciplines to model the relationships that exist between objects in a complex discrete system. Researchers may wish to compare a network of interest to a "typical" graph from a family (or ensemble) of graphs which…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Human aging is a process controlled by both genetics and environment. Many studies have been conducted to identify a subset of genes related to aging from the human genome. Biologists implicitly categorize age-related genes into genes that…
User-generated family trees are invaluable for constructing population-scale family networks and studying population dynamics over many generations and far into the past. Family trees contain information on individuals such as birth and…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a…
For families, kinship coefficients are quantifications of the amount of genetic sharing between a pair of individuals. These coefficients are critical for understanding the breeding habits and genetic diversity of diploid populations.…
Net-trees are a general purpose data structure for metric data that have been used to solve a wide range of algorithmic problems. We give a simple randomized algorithm to construct net-trees on doubling metrics using $O(n\log n)$ time in…
Inferring the network topology from the dynamics is a fundamental problem with wide applications in geology, biology and even counter-terrorism. Based on the propagation process, we present a simple method to uncover the network topology.…
Several populational networks present complex topologies when implemented in evolutionary algorithms. A common feature of these topologies is the emergence of a power law. Power law behavior with different scaling factors can also be…