ArticleWellcome open research2020
Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework.
Article in Wellcome open research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- Global transmission pathways and adaptive molecular evolution of avian infectious bronchitis GI-23 (Variant 2).Scientific reports · 2026Article
- Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence.bioRxiv : the preprint server for biology · 2026Article
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- Two Coding-Complete Genomes of Tick-Borne Encephalitis Virus Sequenced fromPathogens (Basel, Switzerland) · 2026Article
- The emergence and molecular evolution of H5N1 influenza viruses in United States dairy cattle.bioRxiv : the preprint server for biology · 2026Article
- Dispersal, adaptation and persistence of H5N1 in the sub-Antarctic and Antarctica.bioRxiv : the preprint server for biology · 2026Article
- BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference.Nature methods · 2025Article
- Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature.BMC infectious diseases · 2024Article
- Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean.Nature communications · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.PLoS computational biology · 2024Article
- Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean.Nature communications · 2024Article
- Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean.medRxiv : the preprint server for health sciences · 2023Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.bioRxiv : the preprint server for biology · 2023Article
- Scalable Bayesian Divergence Time Estimation With Ratio Transformations.Systematic biology · 2023Article
- Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.Science (New York, N.Y.) · 2023Article
- Dynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States.Current biology : CB · 2023Article
- Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States.medRxiv : the preprint server for health sciences · 2023Article
- Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status.Virus evolution · 2022Article
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4 authors.
Funding
Abstract
Nonparametric coalescent-based models are often employed to infer past population dynamics over time. Several of these models, such as the skyride and skygrid models, are equipped with a block-updating Markov chain Monte Carlo sampling scheme to efficiently estimate model parameters. The advent of powerful computational hardware along with the use of high-performance libraries for statistical phylogenetics has, however, made the development of alternative estimation methods feasible. We here present the implementation and performance assessment of a Hamiltonian Monte Carlo gradient-based sampler to infer the parameters of the skygrid model. The skygrid is a popular and flexible coalescent-based model for estimating population dynamics over time and is available in BEAST 1.10.5, a widely-used software package for Bayesian pylogenetic and phylodynamic analysis. Taking into account the increased computational cost of gradient evaluation, we report substantial increases in effective sample size per time unit compared to the established block-updating sampler. We expect gradient-based samplers to assume an increasingly important role for different classes of parameters typically estimated in Bayesian phylogenetic and phylodynamic analyses.
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