Literature DB >> 34354329

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

Andrew J Holbrook1, Charles E Loeffler2, Seth R Flaxman3, Marc A Suchard1,4,5.   

Abstract

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 widespread 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.

Entities:  

Keywords:  GPU; Massive parallelization; SIMD; Spatiotemporal Hawkes process

Year:  2021        PMID: 34354329      PMCID: PMC8330599          DOI: 10.1007/s11222-020-09980-4

Source DB:  PubMed          Journal:  Stat Comput        ISSN: 0960-3174            Impact factor:   2.559


  10 in total

1.  Open science is a research accelerator.

Authors:  Michael Woelfle; Piero Olliaro; Matthew H Todd
Journal:  Nat Chem       Date:  2011-09-23       Impact factor: 24.427

2.  Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures.

Authors:  Marc A Suchard; Quanli Wang; Cliburn Chan; Jacob Frelinger; Andrew Cron; Mike West
Journal:  J Comput Graph Stat       Date:  2010-06-01       Impact factor: 2.302

3.  Many-core algorithms for statistical phylogenetics.

Authors:  Marc A Suchard; Andrew Rambaut
Journal:  Bioinformatics       Date:  2009-04-15       Impact factor: 6.937

4.  Firearms research: The gun fighter.

Authors:  Meredith Wadman
Journal:  Nature       Date:  2013-04-25       Impact factor: 49.962

5.  Tale of 2 Agencies: CDC Avoids Gun Violence Research But NIH Funds It.

Authors:  Rita Rubin
Journal:  JAMA       Date:  2016-04-26       Impact factor: 56.272

Review 6.  From point process observations to collective neural dynamics: Nonlinear Hawkes process GLMs, low-dimensional dynamics and coarse graining.

Authors:  Wilson Truccolo
Journal:  J Physiol Paris       Date:  2017-05-25

7.  Graphics Processing Units and High-Dimensional Optimization.

Authors:  Hua Zhou; Kenneth Lange; Marc A Suchard
Journal:  Stat Sci       Date:  2010-08-01       Impact factor: 2.901

8.  On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods.

Authors:  Anthony Lee; Christopher Yau; Michael B Giles; Arnaud Doucet; Christopher C Holmes
Journal:  J Comput Graph Stat       Date:  2010-12-01       Impact factor: 2.302

9.  Real-time predictions of the 2018-2019 Ebola virus disease outbreak in the Democratic Republic of the Congo using Hawkes point process models.

Authors:  J Daniel Kelly; Junhyung Park; Ryan J Harrigan; Nicole A Hoff; Sarita D Lee; Rae Wannier; Bernice Selo; Mathias Mossoko; Bathe Njoloko; Emile Okitolonda-Wemakoy; Placide Mbala-Kingebeni; George W Rutherford; Thomas B Smith; Steve Ahuka-Mundeke; Jean Jacques Muyembe-Tamfum; Anne W Rimoin; Frederic Paik Schoenberg
Journal:  Epidemics       Date:  2019-07-23       Impact factor: 4.396

10.  Massive parallelization boosts big Bayesian multidimensional scaling.

Authors:  Andrew J Holbrook; Philippe Lemey; Guy Baele; Simon Dellicour; Dirk Brockmann; Andrew Rambaut; Marc A Suchard
Journal:  J Comput Graph Stat       Date:  2020-06-08       Impact factor: 2.302

  10 in total
  2 in total

1.  BAYESIAN MITIGATION OF SPATIAL COARSENING FOR A HAWKES MODEL APPLIED TO GUNFIRE, WILDFIRE AND VIRAL CONTAGION.

Authors:  Andrew J Holbrook; Xiang Ji; Marc A Suchard
Journal:  Ann Appl Stat       Date:  2022-03-28       Impact factor: 1.959

2.  From viral evolution to spatial contagion: a biologically modulated Hawkes model.

Authors:  Andrew J Holbrook; Xiang Ji; Marc A Suchard
Journal:  Bioinformatics       Date:  2022-01-18       Impact factor: 6.937

  2 in total

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