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Found 8 papers, 6 papers with code
On the importance of assessing topological convergence in Bayesian phylogenetic inference
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution.
Random-effects substitution models for phylogenetics via scalable gradient approximations
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process.
Scalable Bayesian divergence time estimation with ratio transformations
Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time.
Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis
Even in the presence of non-trivial phylogenetic model constraints, we show that one may analytically address latent factor uncertainty in a way that (a) aids model flexibility, (b) accelerates computation (by as much as 500-fold) and (c) decreases required tuning.
Deep reinforcement learning for large-scale epidemic control
For this reason, we investigate a deep reinforcement learning approach to automatically learn prevention strategies in the context of pandemic influenza.
Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics
To make this tractable, we present a linear-time algorithm for ${\cal O}\hspace{-0. 2em}\left( N \right)$-dimensional gradient evaluation and apply it to general continuous-time Markov processes of sequence substitution on a phylogenetic tree without a need to assume either stationarity or reversibility.
Computation Populations and Evolution Methodology
Bayesian Best-Arm Identification for Selecting Influenza Mitigation Strategies
We evaluate these algorithms in a realistic experimental setting and demonstrate that it is possible to identify the optimal strategy using only a limited number of model evaluations, i. e., 2-to-3 times faster compared to the uniform sampling method, the predominant technique used for epidemiological decision making in the literature.
Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in South America
Although foot-and-mouth disease virus (FMDV) incidence has decreased in South America over the last years, the pathogen still circulates in the region and the risk of re-emergence in previously FMDV-free areas is a veterinary public health concern.
