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Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…

We present a detailed analysis of the class of regression decision tree algorithms which employ a regulized piecewise-linear node-splitting criterion and have regularized linear models at the leaves. From a theoretic standpoint, based on…

Clustering under pairwise constraints is an important knowledge discovery tool that enables the learning of appropriate kernels or distance metrics to improve clustering performance. These pairwise constraints, which come in the form of…

Regression forests have long delivered state-of-the-art accuracy, often outperforming regression trees and even neural networks, but they suffer from limited interpretability as ensemble methods. In this work, we revisit forest pruning, an…

The rise of machine learning methods on heavily resource constrained devices requires not only the choice of a suitable model architecture for the target platform, but also the optimization of the chosen model with regard to execution time…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…

CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…

We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…

We present a tree structure algorithm for optimal control problems with state constraints. We prove a convergence result for a discrete time approximation of the value function based on a novel formulation of the constrained problem. Then…

Despite the latest prevailing success of deep neural networks (DNNs), several concerns have been raised against their usage, including the lack of intepretability the gap between DNNs and other well-established machine learning models, and…

Model trees provide an appealing way to perform interpretable machine learning for both classification and regression problems. In contrast to ``classic'' decision trees with constant values in their leaves, model trees can use linear…

Identifying a subset of taxa that maximizes Phylogenetic Diversity (PD) is a cornerstone of quantitative conservation planning. Traditionally, PD is defined over a phylogenetic tree in which leaves resemble present-day taxa and the branch…

Kernels ensuing from tree ensembles such as random forest (RF) or gradient boosted trees (GBT), when used for kernel learning, have been shown to be competitive to their respective tree ensembles (particularly in higher dimensional…

We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…

An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…

In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…

Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…

Tanglegrams are drawings of two rooted binary phylogenetic trees and a matching between their leaf sets. The trees are drawn crossing-free on opposite sides with their leaf sets facing each other on two vertical lines. Instead of minimizing…

In this report we present two new ways of enforcing monotone constraints in regression and classification trees. One yields better results than the current LightGBM, and has a similar computation time. The other one yields even better…