Related papers: Vector encoding of phylogenetic trees by ordered l…

We define the beta diffusion tree, a random tree structure with a set of leaves that defines a collection of overlapping subsets of objects, known as a feature allocation. A generative process for the tree structure is defined in terms of…

Routing tables in ad hoc and wireless routing protocols can be represented using rooted trees. The constant need for communication and storage of these trees in routing protocols demands an efficient rooted tree coding algorithm. This…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

A labeled oriented tree is called injective if each generator occurs at most once as an edge label. We show that injective labeled oriented trees are aspherical. The proof relies on a new relative asphericity test based on a lemma of…

The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…

In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…

The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…

Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…

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…

Transformer-based models have demonstrated significant success in various source code representation tasks. Nonetheless, traditional positional embeddings employed by these models inadequately capture the hierarchical structure intrinsic to…

In this paper, we introduce TreeCoders, a novel family of transformer trees. We moved away from traditional linear transformers to complete k-ary trees. Transformer blocks serve as nodes, and generic classifiers learn to select the best…

We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…

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…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…

Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…

Learning vector representations for programs is a critical step in applying deep learning techniques for program understanding tasks. Various neural network models are proposed to learn from tree-structured program representations, e.g.,…

Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary…

We introduce a new variation of Tree Encoding with Nested Intervals, find connections with Materialized Path, and suggest a method for moving parts of the hierarchy.

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…