Chris Whidden
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View article: Modeling dynamics of adult female lice at salmon farming sites in Eastern Canada: a stochastic, state-based approach
Modeling dynamics of adult female lice at salmon farming sites in Eastern Canada: a stochastic, state-based approach Open
Introduction Sea lice are parasitic copepods that harm salmon health, reduce farm productivity, and create ecological and economic challenges for aquaculture. Methods A stochastic, state-based, time-dependent epidemiological model was deve…
View article: Monitoring harmful algae blooms in Darlings Lake, New Brunswick, using K-means clustering of multi-spectral imagery
Monitoring harmful algae blooms in Darlings Lake, New Brunswick, using K-means clustering of multi-spectral imagery Open
Darlings Lake, located in the Saint John River watershed, Canada, experienced lake-wide cyanobacteria blooms in the summers of 2021 and 2022. This study uses high spatial and temporal resolution satellite imagery from Planet Labs (Planet L…
View article: Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon
Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon Open
Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large‐e…
View article: Ranked Subtree Prune and Regraft
Ranked Subtree Prune and Regraft Open
Phylogenetic trees are a mathematical formalisation of evolutionary histories between organisms, species, genes, cancer cells, etc. For many applications, e.g. when analysing virus transmission trees or cancer evolution, (phylogenetic) tim…
View article: Ranked Subtree Prune and Regraft
Ranked Subtree Prune and Regraft Open
Phylogenetic trees are a mathematical formalisation of evolutionary histories between organisms, species, genes, cancer cells, etc. For many applications, e.g. when analysing virus transmission trees or cancer evolution, (phylogenetic) tim…
View article: Toward low-cost automated monitoring of life below water with deep learning
Toward low-cost automated monitoring of life below water with deep learning Open
Oceans will play a crucial role in our efforts to combat the growing climate emergency. Researchers have proposed several strategies to harness greener energy through oceans and use oceans as carbon sinks. However, the risks these strategi…
View article: Parallel genomic basis of age at maturity across spatial scales in Atlantic Salmon
Parallel genomic basis of age at maturity across spatial scales in Atlantic Salmon Open
Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-e…
View article: Echofilter: A Deep Learning Segmention Model Improves the Automation, Standardization, and Timeliness for Post-Processing Echosounder Data in Tidal Energy Streams
Echofilter: A Deep Learning Segmention Model Improves the Automation, Standardization, and Timeliness for Post-Processing Echosounder Data in Tidal Energy Streams Open
Understanding the abundance and distribution of fish in tidal energy streams is important for assessing the risks presented by the introduction of tidal energy devices into the habitat. However, tidal current flows suitable for tidal energ…
View article: Automated Detection, Classification and Counting of Fish in Fish Passages With Deep Learning
Automated Detection, Classification and Counting of Fish in Fish Passages With Deep Learning Open
The Ocean Aware project, led by Innovasea and funded through Canada's Ocean Supercluster, is developing a fish passage observation platform to monitor fish without the use of traditional tags. This will provide an alternative to standard t…
View article: TBRDist: Calculate Rearrangement Distances Between Unrooted Phylogenetic Trees
TBRDist: Calculate Rearrangement Distances Between Unrooted Phylogenetic Trees Open
An R package to calculate exact and approximage TBR, SPR and Replug rearrangement distances between unrooted phylogenetic trees.
View article: 19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology
19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology Open
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 the posterior density, obtained by integrating the product …
View article: Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies Open
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 space systematically, and never return to the same topology. In…
View article: 19 dubious ways to compute the marginal likelihood of a phylogenetic\n tree topology
19 dubious ways to compute the marginal likelihood of a phylogenetic\n tree topology Open
The marginal likelihood of a model is a key quantity for assessing the\nevidence provided by the data in support of a model. The marginal likelihood is\nthe normalizing constant for the posterior density, obtained by integrating the\nprodu…
View article: Systematic Exploration of the High Likelihood Set of Phylogenetic Tree\n Topologies
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree\n Topologies Open
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because\nit frequently returns to the same tree topology. An alternative strategy would\nbe to explore tree space systematically, and never return to the same topology.\…
View article: Calculating the Unrooted Subtree Prune-and-Regraft Distance
Calculating the Unrooted Subtree Prune-and-Regraft Distance Open
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 transfer, viral recombination, and Markov chain Monte Carlo phylog…
View article: Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees Open
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better u…
View article: The combinatorics of discrete time-trees: theory and open problems
The combinatorics of discrete time-trees: theory and open problems Open
A time-tree is a rooted phylogenetic tree such that all internal nodes are equipped with absolute divergence dates and all leaf nodes are equipped with sampling dates. Such time-trees have become a central object of study in phylogenetics …
View article: The shape of subtree prune and regraft tree space: current progress and open problems
The shape of subtree prune and regraft tree space: current progress and open problems Open
View article: Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance
Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance Open
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 transfer, viral recombination, and Markov chain Monte Carlo phylog…
View article: The combinatorics of discrete time-trees: theory and open problems
The combinatorics of discrete time-trees: theory and open problems Open
A time-tree is a rooted phylogenetic tree such that all internal nodes are equipped with absolute divergence dates and all leaf nodes are equipped with sampling dates. Such time-trees have become a central object of study in phylogenetics …
View article: Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies\n between Phylogenetic Trees
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies\n between Phylogenetic Trees Open
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree\nprune-regraft (SPR) graph on a collection of m phylogenetic trees with n\nleaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used\nto bette…
View article: A Resolution of the Static Formulation Question for the Problem of Computing the History Bound
A Resolution of the Static Formulation Question for the Problem of Computing the History Bound Open
Evolutionary data has been traditionally modeled via phylogenetic trees; however, branching alone cannot model conflicting phylogenetic signals, so networks are used instead. Ancestral recombination graphs (ARGs) are used to model the evol…
View article: Hybridization Number on Three Rooted Binary Trees is EPT
Hybridization Number on Three Rooted Binary Trees is EPT Open
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. The hybridization number of a phylogenetic network is the su…
View article: Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph Open
Statistical phylogenetic inference methods use tree rearrangement operations to perform either hill-climbing local search or Markov chain Monte Carlo across tree topologies. The canonical class of such moves are the subtree-prune-regraft (…
View article: Ricci-Ollivier Curvature of the Rooted Phylogenetic\n Subtree-Prune-Regraft Graph
Ricci-Ollivier Curvature of the Rooted Phylogenetic\n Subtree-Prune-Regraft Graph Open
Statistical phylogenetic inference methods use tree rearrangement operations\nto perform either hill-climbing local search or Markov chain Monte Carlo across\ntree topologies. The canonical class of such moves are the\nsubtree-prune-regraf…
View article: spr_neighbors: spr_neighbors v1.0.0
spr_neighbors: spr_neighbors v1.0.0 Open
Software for computing subtree-prune-and-regraft neighbors of phylogenies. Can be used to quickly build rooted subtree prune-and-regraft graphs. Initial version used for the paper: C. Whidden And F. A. Matsen IV. Ricci-Ollivier Curvature o…
View article: random_spr_walk: Random SPR Walk v1.0.0
random_spr_walk: Random SPR Walk v1.0.0 Open
Software for sampling random walks on rooted phylogenies via subtree-prune-and-regraft (SPR) or nearest neighbor interchange (NNI) moves. Initial version used for the paper: C. Whidden And F. A. Matsen IV. Ricci-Ollivier Curvature of the R…
View article: Quantifying MCMC Exploration of Phylogenetic Tree Space
Quantifying MCMC Exploration of Phylogenetic Tree Space Open
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 MCMC converges to the posterior distribution. In this artic…