Related papers: Constructing and Employing Tree Alignment Graphs f…
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…
We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In…
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…
Several methods are known for parsing languages generated by Tree Adjoining Grammars (TAGs) in O(n^6) worst case running time. In this paper we investigate which restrictions on TAGs and TAG derivations are needed in order to lower this…
Given a graph, we can form a spanning forest by first sorting the edges in some order, and then only keep edges incident to a vertex which is not incident to any previous edge. The resulting forest is dependent on the ordering of the edges,…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
Long document classification presents challenges in capturing both local and global dependencies due to their extensive content and complex structure. Existing methods often struggle with token limits and fail to adequately model…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy…
Text-Attributed Graphs (TAGs) enhance graph structures with natural language descriptions, enabling detailed representation of data and their relationships across a broad spectrum of real-world scenarios. Despite the potential for deeper…
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…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
This paper presents two new deterministic algorithms for constructing consensus trees. Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus…
Textual Attribute Graphs (TAGs) are critical for modeling complex networks like citation networks, but effective node classification remains challenging due to difficulties in integrating rich semantics from text with structural graph…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…