Related papers: Graph-based method for constructing consensus tree…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
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…
We establish average consensus on graphs with dynamic topologies prescribed by evolutionary games among strategic agents. Each agent possesses a private reward function and dynamically decides whether to create new links and/or whether to…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
The Composition Vector Tree (CVTree) method, developed under the leadership of Professor Hao Bailin, is an alignment-free algorithm for constructing phylogenetic trees. Although initially designed for studying prokaryotic evolution based on…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
General graphs are difficult for learning due to their irregular structures. Existing works employ message passing along graph edges to extract local patterns using customized graph kernels, but few of them are effective for the integration…
Decision trees are commonly used predictive models due to their flexibility and interpretability. This paper is directed at quantifying the uncertainty of decision tree predictions by employing a Bayesian inference approach. This is…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
Chordal graphs form one of the most studied graph classes. Several graph problems that are NP-hard in general become solvable in polynomial time on chordal graphs, whereas many others remain NP-hard. For a large group of problems among the…
A new synthesis scheme is proposed to effectively generate a random vector with prescribed joint density that induces a (latent) Gaussian tree structure. The quality of synthesis is measured by total variation distance between the…
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…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
Solving fastest distributed consensus averaging problem (i.e., finding weights on the edges to minimize the second-largest eigenvalue modulus of the weight matrix) over networks with different topologies is one of the primary areas of…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
We study the height of a spanning tree $T$ of a graph $G$ obtained by starting with a single vertex of $G$ and repeatedly selecting, uniformly at random, an edge of $G$ with exactly one endpoint in $T$ and adding this edge to $T$.
Mixture model-based frameworks are very popular for statistical inference in clustering. While convenient for producing probabilistic estimates of cluster assignments and uncertainty, they are prone to misspecification, which can lead to…