Related papers: Relaxed Agreement Forests
The Forest Augmentation Problem (FAP) asks for a minimum set of additional edges (links) that make a given forest 2-edge-connected while spanning all vertices. A key special case is the Path Augmentation Problem (PAP), where the input…
We study the problem of learning tree-structured Markov random fields (MRF) on discrete random variables with common support when the observations are corrupted by a $k$-ary symmetric noise channel with unknown probability of error. For…
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…
Random forests and, more generally, (decision\nobreakdash-)tree ensembles are widely used methods for classification and regression. Recent algorithmic advances allow to compute decision trees that are optimal for various measures such as…
This paper focuses on unsupervised modeling of morphological families, collectively comprising a forest over the language vocabulary. This formulation enables us to capture edgewise properties reflecting single-step morphological…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted binary phylogenetic trees on taxon set X in time (6r)^r.poly(n), where n=|X|. The novelty of this approach is that it avoids the…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
We introduce and study the general problem of finding a most "scale-free-like" spanning tree of a connected graph. It is motivated by a particular problem in epidemiology, and may be useful in studies of various dynamical processes in…
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
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…
Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees.…
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…
Canonical distances such as Euclidean distance often fail to capture the appropriate relationships between items, subsequently leading to subpar inference and prediction. Many algorithms have been proposed for automated learning of suitable…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
Ordered leaf attachment, Phylo2Vec, and HOP are three recently introduced vector representations for rooted phylogenetic trees where the representation is determined by an ordering of the underlying leaf set X. Comparing the vectors of two…
The number of trees T in the random forest (RF) algorithm for supervised learning has to be set by the user. It is controversial whether T should simply be set to the largest computationally manageable value or whether a smaller T may in…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
The marginal maximum a posteriori probability (MAP) estimation problem, which calculates the mode of the marginal posterior distribution of a subset of variables with the remaining variables marginalized, is an important inference problem…