Related papers: A polynomial time algorithm for calculating the pr…
Given a gene-tree labeled topology $G$ and a species tree $S$, the "ancestral configurations" at an internal node $k$ of $S$ represent the combinatorially different sets of gene lineages that can be present at $k$ when all possible…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
In this paper a general class of tree algorithms is analyzed. It is shown that, by using an appropriate probabilistic representation of the quantities of interest, the asymptotic behavior of these algorithms can be obtained quite easily…
We present a genetic algorithm which is distributed in two novel ways: along genotype and temporal axes. Our algorithm first distributes, for every member of the population, a subset of the genotype to each network node, rather than a…
Analysis of probability distributions conditional on species trees has demonstrated the existence of anomalous ranked gene trees (ARGTs), ranked gene trees that are more probable than the ranked gene tree that accords with the ranked…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…
Control and characterization of networks is a paramount step for the development of many quantum technologies. Even for moderate-sized networks, this amounts to explore an extremely vast parameters space in search for the couplings defining…
We present a deterministic algorithm that given a tree T with n vertices, a starting vertex v and a slackness parameter epsilon > 0, estimates within an additive error of epsilon the cover and return time, namely, the expected time it takes…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
In this research, we investigate the possibility of applying a search strategy to genetic algorithms to explore the entire genetic tree structure. Several methods aid in performing tree searches; however, simpler algorithms such as…
In this paper, we provide algorithms to rank, unrank, and randomly generate certain degree-restricted classes of Cayley trees. Specifically, we consider classes of trees that have a given degree sequence or a given multiset of degrees. If…
We study the growth of a time-ordered rooted tree by probabilistic attachment of new vertices to leaves. We construct a likelihood function of the leaves based on the connectivity of the tree. We take such connectivity to be induced by the…
We consider the problem of estimating the conditional probability of a label in time $O(\log n)$, where $n$ is the number of possible labels. We analyze a natural reduction of this problem to a set of binary regression problems organized in…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
Decision trees and decision rule systems play important roles as classifiers, knowledge representation tools, and algorithms. They are easily interpretable models for data analysis, making them widely used and studied in computer science.…
In this paper we propose a family of algorithms combining tree-clustering with conditioning that trade space for time. Such algorithms are useful for reasoning in probabilistic and deterministic networks as well as for accomplishing…