Related papers: Graph-based method for constructing consensus tree…
We present a link-by-link rule-based method for constructing all members of the ensemble of spanning trees for any recursively generated, finitely articulated graph, such as the DGM net. The recursions allow for many large-scale properties…
Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…
We consider the tree consensus problem, an important problem in bioinformatics. Given a rooted tree $t$ and another tree $T$, one would like to incorporate compatible information from $T$ to $t$. This problem is a subproblem in the tree…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Provenance is a record that describes how entities, activities, and agents have influenced a piece of data; it is commonly represented as graphs with relevant labels on both their nodes and edges. With the growing adoption of provenance in…
In this work, we propose the novel Prototypical Graph Regression Self-explainable Trees (ProGReST) model, which combines prototype learning, soft decision trees, and Graph Neural Networks. In contrast to other works, our model can be used…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
The goal of branch length estimation in phylogenetic inference is to estimate the divergence time between a set of sequences based on compositional differences between them. A number of software is currently available facilitating branch…
In this article we present a protocol for building dense numeration in network with unknown topology. Additionally to a unique number each node as result of the protocol will get information about a spanning tree. This spanning tree is…
We define the beta diffusion tree, a random tree structure with a set of leaves that defines a collection of overlapping subsets of objects, known as a feature allocation. A generative process for the tree structure is defined in terms of…
A method for creating a forest of model trees to fit samples of a function defined on images is described in several steps: down-sampling the images, determining a tree's hyperplanes, applying convolutions to the hyperplanes to handle small…
Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
Credible intervals and credible sets, such as highest posterior density (HPD) intervals, form an integral statistical tool in Bayesian phylogenetics, both for phylogenetic analyses and for development. Readily available for continuous…
Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
This paper proposes FREEtree, a tree-based method for high dimensional longitudinal data with correlated features. Popular machine learning approaches, like Random Forests, commonly used for variable selection do not perform well when there…
We address unsupervised discontinuous constituency parsing, where we observe a high variance in the performance of the only previous model in the literature. We propose to build an ensemble of different runs of the existing discontinuous…