ArticleMolecular biology and evolution2020
Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Genomic epidemiology of dengue virus serotype 3 lineage 3III_B.3.2 in Brazil: insights into its spread and dengue severity amid co-circulation of multiple dengue serotypes.Lancet regional health. Americas · 2026Article
- Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence.bioRxiv : the preprint server for biology · 2026Article
- Frequent introductions and climate suitability drive increasing dengue risk in Florida.medRxiv : the preprint server for health sciences · 2026Article
- Two Coding-Complete Genomes of Tick-Borne Encephalitis Virus Sequenced fromPathogens (Basel, Switzerland) · 2026Article
- Dispersal, adaptation and persistence of H5N1 in the sub-Antarctic and Antarctica.bioRxiv : the preprint server for biology · 2026Article
- torchtree: Flexible Phylogenetic Model Development and Inference Using PyTorch.Systematic biology · 2026Article
- Phylograd: fast column-specific calculation of substitution model gradients.BMC bioinformatics · 2025Article
- 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
- International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain.Communications medicine · 2025Article
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Dispersal history of SARS-CoV-2 in Galicia, Spain.Journal of medical virology · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.PLoS computational biology · 2024Article
- Dispersal history of SARS-CoV-2 in Galicia, Spain.medRxiv : the preprint server for health sciences · 2024Article
- Many-core algorithms for high-dimensional gradients on phylogenetic trees.Bioinformatics (Oxford, England) · 2024Article
- On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Shrinkage-based Random Local Clocks with Scalable Inference.Molecular biology and evolution · 2023Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.bioRxiv : the preprint server for biology · 2023Article
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8 authors.
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Abstract
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order O(N)-dimensional gradient calculations based on the standard pruning algorithm require O(N2) operations, where N is the number of sampled molecular sequences. With the advent of high-throughput sequencing, recent phylogenetic studies have analyzed hundreds to thousands of sequences, with an apparent trend toward even larger data sets as a result of advancing technology. Such large-scale analyses challenge phylogenetic reconstruction by requiring inference on larger sets of process parameters to model the increasing data heterogeneity. To make these analyses tractable, we present a linear-time algorithm for O(N)-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. We apply this approach to learn the branch-specific evolutionary rates of three pathogenic viruses: West Nile virus, Dengue virus, and Lassa virus. Our proposed algorithm significantly improves inference efficiency with a 126- to 234-fold increase in maximum-likelihood optimization and a 16- to 33-fold computational performance increase in a Bayesian framework.
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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.