Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
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Publication:2233162
DOI10.1214/20-AOAS1394zbMATH Open1475.62273arXiv1912.09185WikidataQ115021793 ScholiaQ115021793MaRDI QIDQ2233162FDOQ2233162
Authors: Akihiko Nishimura, Paul Bastide, Xiang Ji, Rebecca P. Payne, Philip Goulder, Philippe Lemey, Marc A. Suchard, Zhenyu Zhang 
Publication date: 14 October 2021
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient flexibility and computational efficiency to incorporate multiple continuous and discrete traits as data size increases. To accomplish this, we jointly model mixed-type traits by assuming latent parameters for binary outcome dimensions at the tips of an unknown tree informed by molecular sequences. This gives rise to a phylogenetic multivariate probit model. With large sample sizes, posterior computation under this model is problematic, as it requires repeated sampling from a high-dimensional truncated normal distribution. Current best practices employ multiple-try rejection sampling that suffers from slow-mixing and a computational cost that scales quadratically in sample size. We develop a new inference approach that exploits 1) the bouncy particle sampler (BPS) based on piecewise deterministic Markov processes to simultaneously sample all truncated normal dimensions, and 2) novel dynamic programming that reduces the cost of likelihood and gradient evaluations for BPS to linear in sample size. In an application with 535 HIV viruses and 24 traits that necessitates sampling from a 12,840-dimensional truncated normal, our method makes it possible to estimate the across-trait correlation and detect factors that affect the pathogen's capacity to cause disease. This inference framework is also applicable to a broader class of covariance structures beyond comparative biology.
Full work available at URL: https://arxiv.org/abs/1912.09185
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Applications of statistics to biology and medical sciences; meta analysis (62P10) Measures of association (correlation, canonical correlation, etc.) (62H20)
Cites Work
- MCMC using Hamiltonian dynamics
- Bayesian Gaussian Copula Factor Models for Mixed Data
- The no-U-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo
- Inference from iterative simulation using multiple sequences
- Bayesian data analysis.
- A case study competition among methods for analyzing large spatial data
- Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations (with discussion)
- Sparse Bayesian infinite factor models
- The coalescent
- Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
- Analysis of multivariate probit models
- Equation of state calculations by fast computing machines
- Simple marginally noninformative prior distributions for covariance matrices
- The Bouncy Particle Sampler: A Non-Reversible Rejection-Free Markov Chain Monte Carlo Method
- Generating random correlation matrices based on vines and extended onion method
- Bayesian graphical Lasso models and efficient posterior computation
- Title not available (Why is that?)
- Multilevel latent Gaussian process model for mixed discrete and continuous multivariate response data
- Multivariate stochastic process models for correlated responses of mixed type
- Piecewise deterministic Markov processes for scalable Monte Carlo on restricted domains
- Limit theorems for the zig-zag process
- Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
- Extending ordinal regression with a latent zero-augmented beta distribution
Cited In (11)
- Implicit Copula Variational Inference
- Efficient Bayesian inference of general Gaussian models on large phylogenetic trees
- Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference
- Sampling constrained continuous probability distributions: a review
- Statistical challenges in tracking the evolution of SARS-CoV-2
- Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
- Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements
- Posterior computation with the Gibbs zig-zag sampler
- Bayesian Inference on High-Dimensional Multivariate Binary Responses
- Bayesian Conjugacy in Probit, Tobit, Multinomial Probit and Extensions: A Review and New Results
- Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
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