Related papers: A synopsis of comparative metrics for classificati…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Homophily is a graph property describing the tendency of edges to connect similar nodes; the opposite is called heterophily. It is often believed that heterophilous graphs are challenging for standard message-passing graph neural networks…
Graphs are structured data that models complex relations between real-world entities. Heterophilic graphs, where linked nodes are prone to be with different labels or dissimilar features, have recently attracted significant attention and…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Nonlinear metrics, such as the F1-score, Matthews correlation coefficient, and Fowlkes-Mallows index, are often used to evaluate the performance of machine learning models, in particular, when facing imbalanced datasets that contain more…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of…
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First,…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity with a main objective: disentangling the processes that drive species distributions from local to broad…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Assume we are given a set of items from a general metric space, but we neither have access to the representation of the data nor to the distances between data points. Instead, suppose that we can actively choose a triplet of items (A,B,C)…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…