28 citations · 40 across the 7 of their papers we have counts for
11 papers
Echofilter: A Deep Learning Segmentation Model Improves the Automation, Standardization, and Timeliness for Post-Processing Echosounder Data in Tidal Energy Streams
Scott C. Lowe, Louise P. McGarry, Jessica Douglas +4
Understanding the abundance and distribution of fish in tidal energy streams is important to assess risks presented by introducing tidal energy devices to the habitat. However tida…
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
Mathieu Fourment, Andrew F. Magee, Chris Whidden +3
The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for…
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…
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…
Calculating 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…
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph
Chris Whidden, Frederick A. Matsen
Statistical phylogenetic inference methods use tree rearrangement operations to perform either hill-climbing local search or Markov chain Monte Carlo across tree topologies. The ca…
Quantifying MCMC Exploration of Phylogenetic Tree Space
Christopher Whidden, Frederick A. Matsen
In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the…
Hybridization Number on Three Rooted Binary Trees is EPT
Leo van Iersel, Steven Kelk, Nela Lekić +2
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. T…
Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees
Chris Whidden, Robert G. Beiko, Norbert Zeh
We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the c…
Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests
Chris Whidden, Robert G. Beiko, Norbert Zeh
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for tw…