Related papers: Vector encoding of phylogenetic trees by ordered l…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
A combinatorial Gray code for a set of combinatorial objects is a sequence of all combinatorial objects in the set so that each object is derived from the preceding object by changing a small part. In this paper we design a Gray code for…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
We show that for any two values $\alpha, \beta >0 $ for which $\alpha+\beta>1$ then there is a value $N$ so that for all $n \geq N$ the following holds. For any binary phylogenetic tree $T$ on $n$ leaves there is a set of $\lfloor n^\alpha…
A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
While a considerable amount of semantic parsing approaches have employed RNN architectures for code generation tasks, there have been only few attempts to investigate the applicability of Transformers for this task. Including hierarchical…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method, the data is organized into a binary…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
We study the problem of generating, ranking and unranking of unlabeled ordered trees whose nodes have maximum degree of $\Delta$. This class of trees represents a generalization of chemical trees. A chemical tree is an unlabeled tree in…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
We propose a novel distance to calculate distance between high dimensional vector pairs, utilizing vector quantization generated encodings. Vector quantization based methods are successful in handling large scale high dimensional data.…
We construct bijections giving three "codes" for trees. These codes follow naturally from the Matrix Tree Theorem of Tutte and have many advantages over the one produced by Prufer in 1918. One algorithm gives explicitly a bijection that is…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…