相关论文: Overlaid species forests

In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…

An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…

The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…

Interactions are ubiquitous across biological systems. These interactions can be abstracted as patterns of connections among distinct units such as genes, proteins, individual organisms, or species which form a hierarchy of biological…

We describe a new instance-based learning algorithm called the Boundary Forest (BF) algorithm, that can be used for supervised and unsupervised learning. The algorithm builds a forest of trees whose nodes store previously seen examples. It…

For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…

Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…

We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can…

Neural network systems describe complex mappings that can be very difficult to understand. In this paper, we study the inverse problem of determining the input images that get mapped to specific neural network classes. Ultimately, we expect…

Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…

The problem of inferring unknown graph edges from numerical data at a graph's nodes appears in many forms across machine learning. We study a version of this problem that arises in the field of \emph{landscape genetics}, where genetic…

Machine Learning has attracted considerable attention throughout the past decade due to its potential to solve far-reaching tasks, such as image classification, object recognition, anomaly detection, and data forecasting. A standard…

The need to explain predictive models is well-established in modern machine learning. However, beyond model interpretability, understanding pre-processing methods is equally essential. Understanding how data modifications impact model…

Random forests is a state-of-the-art supervised machine learning method which behaves well in high-dimensional settings although some limitations may happen when $p$, the number of predictors, is much larger than the number of observations…

This article describes a new system for induction of oblique decision trees. This system, OC1, combines deterministic hill-climbing with two forms of randomization to find a good oblique split (in the form of a hyperplane) at each node of a…

Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

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…

Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the Network Multispecies Coalescent Model, individual gene trees arising from a network can have any topology, but…