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Prime VI

RESOURCE

Publicly Accessible Repository
https://github.com/sandialabs/PRIME-VI
https://doi.org/10.11578/dc.20250905.9

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Abstract

SAND2025-03757O Prime VI is a distribution-of-disease outbreak model calibration code based on variational inference. It accompanies a publication for submission to Statistics in Medicine journal, and the code will be maintained for open-source use on Sandia's GitLab. The software provides methods for calibrating an epidemiological model to measured case-count data for a multitude of correlated spatial regions. The code solves a Bayesian inverse problem for model calibration where the posterior over-model parameters are approximated through a custom implementation of variational inference. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Developers:
Safta, Cosmin [1][2][3] ;  Ray, Jaideep [1][2][3] ;  Bridgman, Wyatt [1][2][3]
  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  2. Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
  3. Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)
Release Date:
2024-08-04
Project Type:
Open Source, Publicly Available Repository
Software Type:
Scientific
Programming Languages:
Python 3.11.5
Version:
0.1
Licenses:
BSD 2-clause "Simplified" License
Sponsoring Org.:
Code ID:
162810
Site Accession Number:
SCR #3072.0
Research Org.:
Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)
Country of Origin:
United States

RESOURCE

Publicly Accessible Repository
https://github.com/sandialabs/PRIME-VI
https://doi.org/10.11578/dc.20250905.9

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Citation Formats

Safta, Cosmin, Ray, Jaideep, and Bridgman, Wyatt. Prime VI. Computer Software. https://github.com/sandialabs/PRIME-VI. USDOE. 04 Aug. 2024. Web. doi:10.11578/dc.20250905.9.
Safta, Cosmin, Ray, Jaideep, & Bridgman, Wyatt. (2024, August 04). Prime VI. [Computer software]. https://github.com/sandialabs/PRIME-VI. https://doi.org/10.11578/dc.20250905.9.
Safta, Cosmin, Ray, Jaideep, and Bridgman, Wyatt. "Prime VI." Computer software. August 04, 2024. https://github.com/sandialabs/PRIME-VI. https://doi.org/10.11578/dc.20250905.9.
@misc{ doecode_162810,
title = {Prime VI},
author = {Safta, Cosmin and Ray, Jaideep and Bridgman, Wyatt},
abstractNote = {SAND2025-03757O Prime VI is a distribution-of-disease outbreak model calibration code based on variational inference. It accompanies a publication for submission to Statistics in Medicine journal, and the code will be maintained for open-source use on Sandia's GitLab. The software provides methods for calibrating an epidemiological model to measured case-count data for a multitude of correlated spatial regions. The code solves a Bayesian inverse problem for model calibration where the posterior over-model parameters are approximated through a custom implementation of variational inference. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.},
doi = {10.11578/dc.20250905.9},
url = {https://doi.org/10.11578/dc.20250905.9},
howpublished = {[Computer Software] \url{https://doi.org/10.11578/dc.20250905.9}},
year = {2024},
month = {aug}
}