Related papers: kdetrees: Nonparametric Estimation of Phylogenetic…
Accurate identification of synergistic treatment combinations and their underlying biological mechanisms is critical across many disease domains, especially cancer. In translational oncology research, preclinical systems such as…
Most current methods for inferring species-level phylogenies under the coalescent model assume that no gene flow occurs following speciation. While some studies have examined the impact of gene flow on estimation accuracy for certain…
Ensemble methods such as random forests have transformed the landscape of supervised learning, offering highly accurate prediction through the aggregation of multiple weak learners. However, despite their effectiveness, these methods often…
Kernel density estimation (KDE) is a popular statistical technique for estimating the underlying density distribution with minimal assumptions. Although they can be shown to achieve asymptotic estimation optimality for any input…
Decision trees are widely used for non-linear modeling, as they capture interactions between predictors while producing inherently interpretable models. Despite their popularity, performing inference on the non-linear fit remains largely…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…
Advancements in cytometry technologies have led to a remarkable increase in the number of markers that can be analyzed simultaneously, presenting significant challenges in data analysis. Traditional approaches, such as dimensional reduction…
We propose a novel method for automatic program synthesis. P-Tree Programming represents the program search space through a single probabilistic prototype tree. From this prototype tree we form program instances which we evaluate on a given…
Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…
We show that the cophylogenetic distance, k-interval cospeciation, is distinct from other metrics and accounts for global congruence between locally incongruent trees. The growth of the neighborhood of trees which satisfy the largest…
Partitioning trees are efficient data structures for $k$-nearest neighbor search. Machine learning libraries commonly use a special type of partitioning trees called $k$d-trees to perform $k$-nn search. Unfortunately, $k$d-trees can be…
Decision Trees (DTs) are commonly used for many machine learning tasks due to their high degree of interpretability. However, learning a DT from data is a difficult optimization problem, as it is non-convex and non-differentiable.…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
Tree shape statistics are important for investigating evolutionary mechanisms mediating phylogenetic trees. As a step towards bridging shape statistics between rooted and unrooted trees, we present a comparison study on two subtree…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include lineage sorting, horizontal gene transfer, and gene…