Search for: All records

Inferring dependencies between mixed-type biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The state-of-the-art approach uses a phylogenetic multivariate probit model to accommodate binary and continuous traits via a latent variable framework, and utilizes an efficient bouncy particle sampler (BPS) to tackle the computational bottleneck—integrating many latent variables from a high-dimensional truncated normal distribution. This approach breaks down as the number of specimens grows and fails to reliably characterize conditional dependencies between traits. Here, we propose an inference pipeline for phylogenetic probit models that greatly outperforms BPS. The novelty lies in 1) a combination of the recent Zigzag Hamiltonian Monte Carlo (Zigzag-HMC) with linear-time gradient evaluations and 2) a joint sampling scheme for highly correlated latent variables and correlation matrix elements. In an application exploring HIV-1 evolution from 535 viruses, the inference requires joint sampling from an 11,235-dimensional truncated normal and a 24-dimensional covariance matrix. Our method yields a 5-fold speedup compared to BPS and makes it possible to learn partial correlations between candidate viral mutations and virulence. Computational speedup now enables us to tackle even larger problems: we study the evolution of influenza H1N1 glycosylations on around 900 viruses. For broader applicability, we extend the phylogenetic probit model to incorporate categorical traits, and demonstrate its use to studyAquilegiaflower and pollinator co-evolution.

Prior information often takes the form of parameter constraints. Bayesian methods include such information through prior distributions having constrained support. By using posterior sampling algorithms, one can quantify uncertainty without relying on asymptotic approximations. However, sharply constrained priors are not necessary in some settings and tend to limit modelling scope to a narrow set of distributions that are tractable computationally. We propose to replace the sharp indicator function of the constraint with an exponential kernel, thereby creating a close-to-constrained neighbourhood within the Euclidean space in which the constrained subspace is embedded. This kernel decays with distance from the constrained space at a rate depending on a relaxation hyperparameter. By avoiding the sharp constraint, we enable use of off-the-shelf posterior sampling algorithms, such as Hamiltonian Monte Carlo, facilitating automatic computation in a broad range of models. We study the constrained and relaxed distributions under multiple settings and theoretically quantify their differences. Application of the method is illustrated through several novel modelling examples.