Related papers: Constructing and Employing Tree Alignment Graphs f…
We introduce a comprehensive data structure, tangle structure trees, which simultaneously displays all the $\mathcal{F}$-tangles of an abstract separation system for very general obstruction sets $\mathcal{F}$. It simultaneously also…
In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian methods…
Several real problems ranging from text classification to computational biology are characterized by hierarchical multi-label classification tasks. Most of the methods presented in literature focused on tree-structured taxonomies, but only…
Inferring predictive maps between multiple input and multiple output variables or tasks has innumerable applications in data science. Multi-task learning attempts to learn the maps to several output tasks simultaneously with information…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
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…
Recent years have seen a surge in research on deep interpretable neural networks with decision trees as one of the most commonly incorporated tools. There are at least three advantages of using decision trees over logistic regression…
We present the results of an investigation into how the set of elementary trees of a Lexicalized Tree Adjoining Grammar can be represented in the lexical knowledge representation language DATR (Evans & Gazdar 1989a,b). The LTAG under…
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…
Graph-based semantic representations are valuable in natural language processing, where it is often simple and effective to represent linguistic concepts as nodes, and relations as edges between them. Several attempts has been made to find…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
The inducibility of a graph represents its maximum density as an induced subgraph over all possible sequences of graphs of size growing to infinity. This invariant of graphs has been extensively studied since its introduction in $1975$ by…
We provide a logarithmic upper bound for the disentangling number on unordered lists of leaf labeled trees. This results is useful for analyzing phylogenetic mixture models. The proof depends on interpreting multisets of trees as high…
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…
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Tanglegrams are special graphs that consist of a pair of rooted binary trees with the same number of leaves, and a perfect matching between the two leaf-sets. These objects are of use in phylogenetics and are represented with straightline…
Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic…