Related papers: TreeOTU: Operational Taxonomic Unit Classification…

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,…

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…

Taxonomic classification of ecological families, genera, and species underpins biodiversity monitoring and conservation. Existing computer vision methods typically address fine-grained recognition and long-tailed learning in isolation.…

Ontologies such as taxonomies, product catalogs or web directories are heavily used and hence evolve frequently to meet new requirements or to better reflect the current instance data of a domain. To effectively manage the evolution of…

Tree-based methods are powerful nonparametric techniques in statistics and machine learning. However, their effectiveness, particularly in finite-sample settings, is not fully understood. Recent applications have revealed their surprising…

The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

Most decision tree induction algorithms are based on a greedy top-down recursive partitioning strategy for tree growth. In this paper, we propose several methods for induction of decision trees and their ensembles based on evolutionary…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

One approach in phylogenomics to infer the tree of life is based on concatenated multiple sequence alignments from many genes. Unfortunately, the resulting so-called supermatrix is usually sparse, that is, not every gene sequence is…

Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…

A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…

Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…

A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…

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…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

Decision trees and random forest remain highly competitive for classification on medium-sized, standard datasets due to their robustness, minimal preprocessing requirements, and interpretability. However, a single tree suffers from high…

Statistical analysis of multiple sequence alignments of homologous proteins has revealed groups of coevolving amino acids called sectors. These groups of amino-acid sites feature collective correlations in their amino-acid usage, and they…

A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in…

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…