Related papers: Non-hereditary Minimum Deep Coalescence trees

In this research, we investigate the possibility of applying a search strategy to genetic algorithms to explore the entire genetic tree structure. Several methods aid in performing tree searches; however, simpler algorithms such as…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

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…

In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…

The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…

This paper considers "model diagnosis", which we formulate as a classification problem. Given a pre-trained neural network (NN), the goal is to predict the source of failure from a set of failure modes (such as a wrong hyperparameter,…

Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…

Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…

Itemset mining has been an active area of research due to its successful application in various data mining scenarios including finding association rules. Though most of the past work has been on finding frequent itemsets, infrequent…

An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…

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…

Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…

Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary…

Decision tree learning is increasingly being used for pointwise inference. Important applications include causal heterogenous treatment effects and dynamic policy decisions, as well as conditional quantile regression and design of…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…

The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…

A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…