Related papers: Reconstructing a phylogenetic level-1 network from…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
The vast majority of network datasets contains errors and omissions, although this is rarely incorporated in traditional network analysis. Recently, an increasing effort has been made to fill this methodological gap by developing network…
Many dynamical processes of complex systems can be understood as the dynamics of a group of nodes interacting on a given network structure. However, finding such interaction structure and node dynamics from time series of node behaviours is…
We consider the problem of constructing distributed overlay networks, where nodes in a reconfigurable system can create or sever connections with nodes whose identifiers they know. Initially, each node knows only its own and its neighbors'…
Phylogenetic networks provide a general framework for modeling reticulate evolutionary processes such as hybridization, recombination, and horizontal gene transfer. In this paper, we study the asymptotic counting of binary phylogenetic…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
If the phase retrieval problem can be solved by a method similar to that of solving a system of linear equations under the context of FFT, the time complexity of computer based phase retrieval algorithm would be reduced. Here I present such…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Multiple methods of finding the vertices belonging to a planted dense subgraph in a random dense $G(n, p)$ graph have been proposed, with an emphasis on planted cliques. Such methods can identify the planted subgraph in polynomial time, but…
Discovering the latent structure from many observed variables is an important yet challenging learning task. Existing approaches for discovering latent structures often require the unknown number of hidden states as an input. In this paper,…
While gradient descent has proven highly successful in learning connection weights for neural networks, the actual structure of these networks is usually determined by hand, or by other optimization algorithms. Here we describe a simple…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…