Related papers: An algorithm to represent inbreeding trees
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Binary trait data record the presence or absence of distinguishing traits in individuals. We treat the problem of estimating ancestral trees with time depth from binary trait data. Simple analysis of such data is problematic. Each homology…
This paper describes experiments, on two domains, to investigate the effect of averaging over predictions of multiple decision trees, instead of using a single tree. Other authors have pointed out theoretical and commonsense reasons for…
We introduce a novel interpretable tree based algorithm for prediction in a regression setting. Our motivation is to estimate the unknown regression function from a functional decomposition perspective in which the functional components…
Convolution trees, loopy belief propagation, and fast numerical p-convolution are combined for the first time to efficiently solve networks with several additive constraints between random variables. An implementation of this "convolution…
We model a social-encounter network where linked nodes match for reproduction in a manner depending probabilistically on each node`s attractiveness. The developed model reveals that increasing either the network`s mean degree or the…
The spanning tree heuristic is a commonly adopted procedure in network inference and estimation. It allows one to generalize an inference method developed for trees, which is usually based on a statistically rigorous approach, to a…
We consider the probability that a spanning tree chosen uniformly at random from a graph can be partitioned into a fixed number $k$ of trees of equal size by removing $k-1$ edges. In that case, the spanning tree is called {\em splittable}.…
This paper studies a Markov chain for phylogenetic reconstruction which uses a popular transition between tree topologies known as subtree pruning-and-regrafting (SPR). We analyze the Markov chain in the simpler setting that the generating…
Bayesian Decision Trees are known for their probabilistic interpretability. However, their construction can sometimes be costly. In this article we present a general Bayesian Decision Tree algorithm applicable to both regression and…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
In the design and analysis of political redistricting maps, it is often useful to be able to sample from the space of all partitions of the graph of census blocks into connected subgraphs of equal population. There are influential Markov…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
Highly dynamic networks are characterized by frequent changes in the availability of communication links. These networks are often partitioned into several components, which split and merge unpredictably. We present a distributed algorithm…
Polyploidy is an important speciation mechanism, particularly in land plants. Allopolyploid species are formed after hybridization between otherwise intersterile parental species. Recent theoretical progress has led to successful…