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06/28/2023
On the surprising effectiveness of a simple matrix exponential derivative approximation, with application to global SARS-CoV-2
The continuous-time Markov chain (CTMC) is the mathematical workhorse of...
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05/24/2023
Quantitative bias analysis for outcome phenotype error correction in comparative effect estimation: an empirical and synthetic evaluation
Outcome phenotype measurement error is rarely corrected in comparative e...
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05/19/2023
Bayesian Safety Surveillance with Adaptive Bias Correction
Post-market safety surveillance is an integral part of mass vaccination ...
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03/23/2023
Random-effects substitution models for phylogenetics via scalable gradient approximations
Phylogenetic and discrete-trait evolutionary inference depend heavily on...
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03/08/2023
Many-core algorithms for high-dimensional gradients on phylogenetic trees
The rapid growth in genomic pathogen data spurs the need for efficient i...
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11/09/2022
TreeFlow: probabilistic programming and automatic differentiation for phylogenetics
Probabilistic programming frameworks are powerful tools for statistical ...
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09/23/2022
hdtg: An R package for high-dimensional truncated normal simulation
Simulating from the multivariate truncated normal distribution (MTN) is ...
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07/06/2022
Adjusting for both sequential testing and systematic error in safety surveillance using observational data: Empirical calibration and MaxSPRT
Post-approval safety surveillance of medical products using observationa...
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06/24/2022
Sparse precision matrix estimation in phenotypic trait evolution models
Phylogenetic trait evolution models allow for the estimation of evolutio...
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04/18/2022
Massive Parallelization of Massive Sample-size Survival Analysis
Large-scale observational health databases are increasingly popular for ...
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01/18/2022
Hamiltonian zigzag accelerates large-scale inference for conditional dependencies between complex biological traits
Inferring dependencies between complex biological traits while accountin...
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10/25/2021
Scalable Bayesian divergence time estimation with ratio transformations
Divergence time estimation is crucial to provide temporal signals for da...
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07/02/2021
Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis
Biological phenotypes are products of complex evolutionary processes in ...
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05/15/2021
Shrinkage-based random local clocks with scalable inference
Local clock models propose that the rate of molecular evolution is const...
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04/15/2021
Hamiltonian zigzag sampler got more momentum than its Markovian counterpart: Equivalence of two zigzags under a momentum refreshment limit
Zigzag and other piecewise deterministic Markov process samplers have at...
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03/03/2021
From viral evolution to spatial contagion: a biologically modulated Hawkes model
Mutations sometimes increase contagiousness for evolving pathogens. Duri...
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01/05/2021
Combining Cox Regressions Across a Heterogeneous Distributed Research Network Facing Small and Zero Counts
Studies of the effects of medical interventions increasingly take place ...
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10/06/2020
Bayesian mitigation of spatial coarsening for a fairly flexible spatiotemporal Hawkes model
Self-exciting spatiotemporal Hawkes processes have found increasing use ...
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05/13/2020
Scalable Bayesian inference for self-excitatory stochastic processes applied to big American gunfire data
The Hawkes process and its extensions effectively model self-excitatory ...
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03/23/2020
Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees
Phylogenetic comparative methods correct for shared evolutionary history...
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02/01/2020
Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction
Reconstructing pathogen dynamics from genetic data as they become availa...
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12/19/2019
Large-scale inference of correlation among mixed-type biological traits with Phylogenetic multivariate probit models
Inferring concerted changes among biological traits along an evolutionar...
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11/07/2019
Scalable Algorithms for Large Competing Risks Data
This paper develops two orthogonal contributions to scalable sparse regr...
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11/06/2019
Regularization of Bayesian shrinkage priors and inference via geometrically / uniformly ergodic Gibbs sampler
Use of continuous shrinkage priors — with a "spike" near zero and heavy-...
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06/12/2019
Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation
Markov models of character substitution on phylogenies form the foundati...
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06/11/2019
Relaxed random walks at scale
Relaxed random walk (RRW) models of trait evolution introduce branch-spe...
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06/07/2019
Inferring phenotypic trait evolution on large trees with many incomplete measurements
Comparative biologists are often interested in inferring covariation bet...
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05/29/2019
Gradients do grow on trees: a linear-time O( N )-dimensional gradient for statistical phylogenetics
Calculation of the log-likelihood stands as the computational bottleneck...
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05/17/2019
A Fast and Scalable Implementation Method for Competing Risks Data with the R Package fastcmprsk
Advancements in medical informatics tools and high-throughput biological...
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03/28/2019
Estimating effective population size changes from preferentially sampled genetic sequences
Coalescent theory combined with statistical modeling allows us to estima...
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03/10/2019
On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
Maximum likelihood estimators are used extensively to estimate unknown p...
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10/29/2018
Prior-preconditioned conjugate gradient method for accelerated Gibbs sampling in "large n & large p" sparse Bayesian regression
In a modern observational study based on healthcare databases, the numbe...
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10/29/2018
Prior-preconditioned conjugate gradient for accelerated Gibbs sampling in "large n & large p" sparse Bayesian logistic regression models
In a modern observational study based on healthcare databases, the numbe...
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03/28/2018
A systematic approach to improving the reliability and scale of evidence from health care data
Concerns over reproducibility in science extend to research using existi...
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12/02/2017