Related papers: Fixed-Parameter and Approximation Algorithms for M…
In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…
Given a set of leaf-labeled trees with identical leaf sets, the well-known "Maximum Agreement SubTree" problem (MAST) consists of finding a subtree homeomorphically included in all input trees and with the largest number of leaves. Its…
An algorithm is proposed for constructing directed spanning forests of the minimum weight, in which the maximum possible degree of affinity between the minimum forests is preserved when the number of trees changes. The correctness of the…
In this paper, we propose a new random forest algorithm that constructs the trees using a novel adaptive split-balancing method. Rather than relying on the widely-used random feature selection, we propose a permutation-based balanced…
Recursive partitioning is the core of several statistical methods including CART, random forest, and boosted trees. Despite the popularity of tree based methods, to date, there did not exist methods for combining multiple trees into a…
We demonstrate that adaptively controlling the size of individual regression trees in a random forest can improve predictive performance, contrary to the conventional wisdom that trees should be fully grown. A fast pruning algorithm,…
We give a counterexample to the conjecture of Martin and Thatte that two balanced rooted binary leaf-labelled trees on $n$ leaves have a maximum agreement subtree (MAST) of size at least $n^{\frac{1}{2}}$. In particular, we show that for…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
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…
Wood increment is critical information in forestry management. Previous studies used mathematics models to describe complex growing pattern of forest stand, in order to determine the dynamic status of growing forest stand in multiple…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
The Aho, Hopcroft and Ullman (AHU) algorithm has been the state of the art since the 1970s for determining in linear time whether two unordered rooted trees are isomorphic or not. However, it has been criticized (by Campbell and Radford)…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Max-affine regression refers to a model where the unknown regression function is modeled as a maximum of $k$ unknown affine functions for a fixed $k \geq 1$. This generalizes linear regression and (real) phase retrieval, and is closely…
We present a bounded-error quantum algorithm for evaluating Min-Max trees. For a tree of size N our algorithm makes N^{1/2+o(1)} comparison queries, which is close to the optimal complexity for this problem.
In the $L_0$ Fitting Tree Metrics problem, we are given all pairwise distances among the elements of a set $V$ and our output is a tree metric on $V$. The goal is to minimize the number of pairwise distance disagreements between the input…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
As a flexible nonparametric learning tool, the random forests algorithm has been widely applied to various real applications with appealing empirical performance, even in the presence of high-dimensional feature space. Unveiling the…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We…