19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
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 …
the data in support of a model. The marginal likelihood is the normalizing constant for the …
Fidelity of hyperbolic space for Bayesian phylogenetic inference
Bayesian inference for phylogenetics is a gold standard for computing distributions of
phylogenies. However, Bayesian phylogenetics faces the challenging computational …
phylogenies. However, Bayesian phylogenetics faces the challenging computational …
[PDF][PDF] A variational approach to Bayesian phylogenetic inference
C Zhang, FA Matsen IV - 2022 - jmlr.org
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC)
with simple proposal mechanisms. This hinders exploration efficiency and often requires …
with simple proposal mechanisms. This hinders exploration efficiency and often requires …
Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference
Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference Page 1 The
Annals of Applied Statistics 2023, Vol. 17, No. 2, 1419–1443 https://doi.org/10.1214/22-AOAS1676 …
Annals of Applied Statistics 2023, Vol. 17, No. 2, 1419–1443 https://doi.org/10.1214/22-AOAS1676 …
[HTML][HTML] How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
Bayesian inference is a popular and widely-used approach to infer phylogenies
(evolutionary trees). However, despite decades of widespread application, it remains difficult …
(evolutionary trees). However, despite decades of widespread application, it remains difficult …
Differentiable Phylogenetics via Hyperbolic Embeddings with Dodonaphy
M Macaulay, M Fourment - Bioinformatics Advances, 2024 - academic.oup.com
Motivation Navigating the high dimensional space of discrete trees for phylogenetics
presents a challenging problem for tree optimisation. To address this, hyperbolic …
presents a challenging problem for tree optimisation. To address this, hyperbolic …
Testing phylogenetic stability with variable taxon sampling
CLE Powell, FU Battistuzzi - Environmental Microbial Evolution: Methods …, 2022 - Springer
Over the past three decades, computational capabilities have grown at such a rapid rate that
they have given rise to many computationally heavy science fields such as phylogenomics …
they have given rise to many computationally heavy science fields such as phylogenomics …
Assessment of Taxon Sampling on Phylogenetic Reconstructions and Timetrees: A New Methodology and Application
CLE Powell - 2023 - search.proquest.com
Over the past three decades, computational capabilities have grown at such a rapid rate that
they have given rise to many computationally heavy science fields such as phylogenomics …
they have given rise to many computationally heavy science fields such as phylogenomics …
[图书][B] Reliable and interpretable inference of evolutionary history using Bayesian phylogenetic approaches
AF Magee - 2021 - search.proquest.com
Phylogenetic trees are key objects for understanding evolutionary history, first used to
describe relationships between groups of species. Phylogenies help us to fill out the tree of …
describe relationships between groups of species. Phylogenies help us to fill out the tree of …