arXiv subjects

Andrew J. Holbrook

Publications and source records attributed to Andrew J. Holbrook.

21 records · Page 2Linked to original sources

arXiv2021

Bayesian mitigation of spatial coarsening for a Hawkes model applied to gunfire, wildfire and viral contagion

Self-exciting spatiotemporal Hawkes processes have found increasing use in the study of large-scale public health threats ranging from gun violence and earthquakes to wildfires and viral contagion. Whereas many such applications feature locational uncertainty, i.e., the exact spatial positions of individual events are unknown, most Hawkes model analyses to date have ignored spatial coarsening present in the data. Three particular 21st century public health crises -- urban gun violence, rural wildfires and global viral spread -- present qualitatively and quantitatively varying uncertainty regimes that exhibit (a) different collective magnitudes of spatial coarsening, (b) uniform and mixed magnitude coarsening, (c) differently shaped uncertainty regions and -- less orthodox -- (d) locational data distributed within the `wrong' effective space. We explicitly model such uncertainties in a Bayesian manner and jointly infer unknown locations together with all parameters of a reasonably flexible Hawkes model, obtaining results that are practically and statistically distinct from those obtained while ignoring spatial coarsening. This work also features two different secondary contributions: first, to facilitate Bayesian inference of locations and background rate parameters, we make a subtle yet crucial change to an established kernel-based rate model; and second, to facilitate the same Bayesian inference at scale, we develop a massively parallel implementation of the model's log-likelihood gradient with respect to locations and thus avoid its quadratic computational cost in the context of Hamiltonian Monte Carlo. Our examples involve thousands of observations and allow us to demonstrate practicality at moderate scales.

stat.ME↗

arXiv2021

Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis

Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the evolutionary history of a group of organisms. Scientists seeking to employ this modeling framework confront numerous modeling and implementation decisions, the details of which pose computational and replicability challenges. General and impactful community employment requires a data scientific analysis plan that balances flexibility, speed and ease of use, while minimizing model and algorithm tuning. Even in the presence of non-trivial phylogenetic model constraints, we show that one may analytically address latent factor uncertainty in a way that (a) aids model flexibility, (b) accelerates computation (by as much as 500-fold) and (c) decreases required tuning. We further present practical guidance on inference and modeling decisions as well as diagnosing and solving common problems in these analyses. We codify this analysis plan in an automated pipeline that distills the potentially overwhelming array of modeling decisions into a small handful of (typically binary) choices. We demonstrate the utility of these methods and analysis plan in four real-world problems of varying scales.

q-bio.PE↗

arXiv2020

Scalable Bayesian inference for self-excitatory stochastic processes applied to big American gunfire data

The Hawkes process and its extensions effectively model self-excitatory phenomena including earthquakes, viral pandemics, financial transactions, neural spike trains and the spread of memes through social networks. The usefulness of these stochastic process models within a host of economic sectors and scientific disciplines is undercut by the processes' computational burden: complexity of likelihood evaluations grows quadratically in the number of observations for both the temporal and spatiotemporal Hawkes processes. We show that, with care, one may parallelize these calculations using both central and graphics processing unit implementations to achieve over 100-fold speedups over single-core processing. Using a simple adaptive Metropolis-Hastings scheme, we apply our high-performance computing framework to a Bayesian analysis of big gunshot data generated in Washington D.C. between the years of 2006 and 2019, thereby extending a past analysis of the same data from under 10,000 to over 85,000 observations. To encourage wide-spread use, we provide hpHawkes, an open-source R package, and discuss high-level implementation and program design for leveraging aspects of computational hardware that become necessary in a big data setting.

stat.AP↗