30 citations · 57 across the 7 of their papers we have counts for
10 papers
A Variational Approach to Bayesian Phylogenetic Inference
Cheng Zhang, Frederick A. Matsen
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long r…
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Chris Whidden, Brian C. Claywell, Thayer Fisher +3
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree spac…
Generalizing Tree Probability Estimation via Bayesian Networks
Cheng Zhang, Frederick A. Matsen
Probability estimation is one of the fundamental tasks in statistics and machine learning. However, standard methods for probability estimation on discrete objects do not handle ob…
Probabilistic Path Hamiltonian Monte Carlo
Vu Dinh, Arman Bilge, Cheng Zhang +1
Hamiltonian Monte Carlo (HMC) is an efficient and effective means of sampling posterior distributions on Euclidean space, which has been extended to manifolds with boundary. Howeve…
Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance
Chris Whidden, Frederick A. Matsen
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfe…
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees
Chris Whidden, Frederick A. Matsen
We develop a time-optimal -time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the pr…