Related papers: Tropical Data Science

We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

Group-based models appear in algebraic statistics as mathematical models coming from evolutionary biology, respectively the study of mutations of organisms. Both theoretically and in terms of applications, we are interested in determining…

Latent tree analysis seeks to model the correlations among a set of random variables using a tree of latent variables. It was proposed as an improvement to latent class analysis --- a method widely used in social sciences and medicine to…

Probabilistic models over strings have played a key role in developing methods allowing indels to be treated as phylogenetically informative events. There is an extensive literature on using automata and transducers on phylogenies to do…

The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…

Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…

Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…

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…

In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. We show that the most naive approach fails to produce reliable…

Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…

In this working paper, we present a simple theoretical framework based on network theory to study how speciation, the process by which new species appear, shapes spatial patterns of diversity. We show that this framework can be expanded to…

We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…

Deep neural networks show great success when input vectors are in an Euclidean space. However, those classical neural networks show a poor performance when inputs are phylogenetic trees, which can be written as vectors in the tropical…

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…

Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…

To fully exploit the potential of computational phylogenetic methods for cognate data one needs to leverage specific (complex) models an machine learning-based techniques. However, both approaches require datasets that are substantially…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…