Related papers: Fast Compatibility Testing for Phylogenies with Ne…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
We propose techniques to incorporate coarse taxonomic labels to train image classifiers in fine-grained domains. Such labels can often be obtained with a smaller effort for fine-grained domains such as the natural world where categories are…
We present a method for constructing taxonomic trees (e.g., WordNet) using pretrained language models. Our approach is composed of two modules, one that predicts parenthood relations and another that reconciles those predictions into trees.…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view…
The data made available for analysis are becoming more and more complex along several directions: high dimensionality, number of examples and the amount of labels per example. This poses a variety of challenges for the existing machine…
Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes is one of the crucial steps in the process and can be accomplished…
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
Classification predicts classes of objects using the knowledge learned during the training phase. This process requires learning from labeled samples. However, the labeled samples usually limited. Annotation process is annoying, tedious,…
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…
An {\em ancestry labeling scheme} labels the nodes of any tree in such a way that ancestry queries between any two nodes in a tree can be answered just by looking at their corresponding labels. The common measure to evaluate the quality of…
The question whether a partition $\mathcal{P}$ and a hierarchy $\mathcal{H}$ or a tree-like split system $\mathfrak{S}$ are compatible naturally arises in a wide range of classification problems. In the setting of phylogenetic trees, one…
Graph isomorphism, subgraph isomorphism, and maximum common subgraphs are classical well-investigated objects. Their (parameterized) complexity and efficiently tractable cases have been studied. In the present paper, for a given set of…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
We consider the problem of clustering partially labeled data from a minimal number of randomly chosen pairwise comparisons between the items. We introduce an efficient local algorithm based on a power iteration of the non-backtracking…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…