Related papers: Computing the Distribution of a Tree Metric
The quartet distance is a measure of similarity used to compare two unrooted phylogenetic trees on the same set of $n$ leaves, defined as the number of subsets of four leaves related by a different topology in both trees. After a series of…
We describe the use of an unsupervised Random Forest for similarity learning and improved unsupervised anomaly detection. By training a Random Forest to discriminate between real data and synthetic data sampled from a uniform distribution…
Distributional Random Forest (DRF) is a flexible forest-based method to estimate the full conditional distribution of a multivariate output of interest given input variables. In this article, we introduce a variable importance algorithm for…
This paper proposes a novel method to estimate the rate parameter of the Poisson distribution. The proposed method employs the Cramer-von Mises type optimization which has been commonly used in estimating parameters of continuous…
Random Forests are one of the most popular classifiers in machine learning. The larger they are, the more precise is the outcome of their predictions. However, this comes at a cost: their running time for classification grows linearly with…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
The purpose of this paper is to analyze certain statistics of a recently introduced non-uniform random tree model, biased recursive trees. This model is based on constructing a random tree by establishing a correspondence with non-uniform…
A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree.…
The paper describes an application of the tree classification method Random Forest (RF), as used in the analysis of data from the ground-based gamma telescope MAGIC. In such telescopes, cosmic gamma-rays are observed and have to be…
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…
Rotation distance between trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. In the case of ordered rooted trees, we…
Random forests are considered one of the best out-of-the-box classification and regression algorithms due to their high level of predictive performance with relatively little tuning. Pairwise proximities can be computed from a trained…
We prove a lower bound on the number of spanning two-forests in a graph, in terms of the number of vertices, edges, and spanning trees. This implies an upper bound on the average cut size of a random two-forest. The main tool is an identity…
Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the…
The Random Forest (RF) classifier is often claimed to be relatively well calibrated when compared with other machine learning methods. Moreover, the existing literature suggests that traditional calibration methods, such as isotonic…
SpectralNet is a graph clustering method that uses neural network to find an embedding that separates the data. So far it was only used with $k$-nn graphs, which are usually constructed using a distance metric (e.g., Euclidean distance).…
In [3], algorithms to compute the density of the distance to a random variable uniformly distributed in (a) a ball, (b) a disk, (c) a line segment, or (d) a polygone were introduced. For case (d), the algorithm, based on Green's theorem,…
Random forest (RF) missing data algorithms are an attractive approach for dealing with missing data. They have the desirable properties of being able to handle mixed types of missing data, they are adaptive to interactions and nonlinearity,…
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…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…