ArticleSystematic biology2021
Relaxed Random Walks at Scale.
Article in Systematic biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology.Current biology : CB · 2026Article
- SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.Bioinformatics (Oxford, England) · 2026Article
- Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology.bioRxiv : the preprint server for biology · 2026Article
- BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference.Nature methods · 2025Article
- Detecting Evolutionary Change-Points with Branch-Specific Substitution Models and Shrinkage Priors.ArXiv · 2025Article
- Detecting Evolutionary Change-Points with Branch-Specific Substitution Models and Shrinkage Priors.Research square · 2025Article
- The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.Cell · 2025Article
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations.Systematic biology · 2024Article
- Many-core algorithms for high-dimensional gradients on phylogenetic trees.Bioinformatics (Oxford, England) · 2024Article
- Scalable Bayesian Divergence Time Estimation With Ratio Transformations.Systematic biology · 2023Article
- Modeling the Evolution of Rates of Continuous Trait Evolution.Systematic biology · 2023Article
- Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation.Genome biology and evolution · 2023Article
- Data integration in Bayesian phylogenetics.Annual review of statistics and its application · 2023Article
- Scalable Bayesian phylogenetics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis.Methods in ecology and evolution · 2022Article
- From viral evolution to spatial contagion: a biologically modulated Hawkes model.Bioinformatics (Oxford, England) · 2022Article
- Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements.Journal of the American Statistical Association · 2022Article
- Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.Nature communications · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Relaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny and more accurately model overdispersed biological data. Increased taxonomic sampling challenges inference under RRWs as the number of unknown parameters grows with the number of taxa. To solve this problem, we present a scalable method to efficiently fit RRWs and infer this branch-specific variation in a Bayesian framework. We develop a Hamiltonian Monte Carlo (HMC) sampler to approximate the high-dimensional, correlated posterior that exploits a closed-form evaluation of the gradient of the trait data log-likelihood with respect to all branch-rate multipliers simultaneously. Our gradient calculation achieves computational complexity that scales only linearly with the number of taxa under study. We compare the efficiency of our HMC sampler to the previously standard univariable Metropolis-Hastings approach while studying the spatial emergence of the West Nile virus in North America in the early 2000s. Our method achieves at least a 6-fold speed increase over the univariable approach. Additionally, we demonstrate the scalability of our method by applying the RRW to study the correlation between five mammalian life history traits in a phylogenetic tree with $3650$ tips.[Bayesian inference; BEAST; Hamiltonian Monte Carlo; life history; phylodynamics, relaxed random walk.].
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.