40 citations · 70 across the 24 of their papers we have counts for
31 papers
Non-Linear Drivers of Population Dynamics: a Nonparametric Coalescent Approach
Filippo Monti, Nuno R. Faria, Xiang Ji +3
Effective population size (Ne(t)) is a fundamental parameter in population genetics and phylodynamics that quantifies genetic diversity and reveals demographic history. Coalescent-…
Inhomogeneous continuous-time Markov chains to infer flexible time-varying evolutionary rates
Pratyusa Datta, Philippe Lemey, Marc A. Suchard
Reconstructing evolutionary histories and estimating the rate of evolution from molecular sequence data is of central importance in evolutionary biology and infectious disease rese…
Detecting Evolutionary Change-Points with Branch-Specific Substitution Models and Shrinkage Priors
Xiang Ji, Benjamin Redelings, Shuo Su +6
Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires pri…
On the importance of assessing topological convergence in Bayesian phylogenetic inference
Marius Brusselmans, Luiz Max Carvalho, Samuel L. Hong +7
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distrib…
Quantum Speedups for Multiproposal MCMC
Chin-Yi Lin, Kuo-Chin Chen, Philippe Lemey +3
Multiproposal Markov chain Monte Carlo (MCMC) algorithms choose from multiple proposals to generate their next chain step in order to sample from challenging target distributions m…
Many-core algorithms for high-dimensional gradients on phylogenetic trees
Karthik Gangavarapu, Xiang Ji, Guy Baele +4
The rapid growth in genomic pathogen data spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters o…
Random-effects substitution models for phylogenetics via scalable gradient approximations
Andrew F. Magee, Andrew J. Holbrook, Jonathan E. Pekar +7
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present…
Accelerating Bayesian inference of dependency between complex biological traits
Zhenyu Zhang, Akihiko Nishimura, Nídia S. Trovão +5
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible wh…
Scalable Bayesian divergence time estimation with ratio transformations
Xiang Ji, Alexander A. Fisher, Shuo Su +5
Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time. With t…
Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis
Gabriel W. Hassler, Brigida Gallone, Leandro Aristide +6
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor…
Shrinkage-based random local clocks with scalable inference
Alexander A. Fisher, Xiang Ji, Akihiko Nishimura +2
Local clock models propose that the rate of molecular evolution is constant within phylogenetic sub-trees. Current local clock inference procedures scale poorly to large taxa probl…
Deep reinforcement learning for large-scale epidemic control
Pieter Libin, Arno Moonens, Timothy Verstraeten +4
Epidemics of infectious diseases are an important threat to public health and global economies. Yet, the development of prevention strategies remains a challenging process, as epid…
Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees
Paul Bastide, Lam Si Tung Ho, Guy Baele +2
Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process alon…
Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction
Mandev S. Gill, Philippe Lemey, Marc A. Suchard +2
Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive…
Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
Zhenyu Zhang, Akihiko Nishimura, Paul Bastide +5
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced f…
Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation
Guy Baele, Mandev S. Gill, Philippe Lemey +1
Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution…
Inferring phenotypic trait evolution on large trees with many incomplete measurements
Gabriel Hassler, Max R. Tolkoff, William L. Allen +3
Comparative biologists are often interested in inferring covariation between multiple biological traits sampled across numerous related taxa. To properly study these relationships,…
Relaxed random walks at scale
Alexander A. Fisher, Xiang Ji, Philippe Lemey +1
Relaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny a…
Gradients do grow on trees: a linear-time -dimensional gradient for statistical phylogenetics
Xiang Ji, Zhenyu Zhang, Andrew Holbrook +5
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 r…
Massive parallelization boosts big Bayesian multidimensional scaling
Andrew Holbrook, Philippe Lemey, Guy Baele +4
Big Bayes is the computationally intensive co-application of big data and large, expressive Bayesian models for the analysis of complex phenomena in scientific inference and statis…
Bayesian Best-Arm Identification for Selecting Influenza Mitigation Strategies
Pieter Libin, Timothy Verstraeten, Diederik M. Roijers +4
Pandemic influenza has the epidemic potential to kill millions of people. While various preventive measures exist (i.a., vaccination and school closures), deciding on strategies th…
Phylogenetic Factor Analysis
Max R. Tolkoff, Michael L. Alfaro, Guy Baele +2
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian di…
Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates
Mandev S. Gill, Philippe Lemey, Shannon N. Bennett +2
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics. Kingman's coalescent process enab…
A Relaxed Drift Diffusion Model for Phylogenetic Trait Evolution
Mandev S. Gill, Lam Si Tung Ho, Guy Baele +2
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of…