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Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees.…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Multi-task learning is to improve the performance of the model by transferring and exploiting common knowledge among tasks. Existing MTL works mainly focus on the scenario where label sets among multiple tasks (MTs) are usually the same,…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
Effective decision-making and problem-solving in conversational systems require the ability to identify and acquire missing information through targeted questioning. A key challenge lies in efficiently narrowing down a large space of…
Given a connected, undirected graph whose edges are labelled (or coloured), the minimum labelling spanning tree (MLST) problem seeks a spanning tree whose edges have the smallest number of distinct labels (or colours). In recent work, the…
Consider a tree network T, where each edge acts as an independent copy of a given channel M, and information is propagated from the root. For which T and M does the configuration obtained at level n of T typically contain significant…
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 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…
This paper presents privileged multi-label learning (PrML) to explore and exploit the relationship between labels in multi-label learning problems. We suggest that for each individual label, it cannot only be implicitly connected with other…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
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 (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Multiple (simple) context-free tree grammars are investigated, where "simple" means "linear and nondeleting". Every multiple context-free tree grammar that is finitely ambiguous can be lexicalized; i.e., it can be transformed into an…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…