Machine Learning Performance in a Microbial Molecular Autopsy Context: A Cross-sectional Postmortem Human Population Study

• NCJ Number: 254118
• Journal: PLoS ONE Volume: 14 Issue: 4 Dated: 2019
• Author(s): Yu Zhang; Jennifer L. Pechal; Carl J. Schmidt; Heahter R. Jordan; Wesley W. Wang; M. E. Barlow; Sing-Hoi Sze
• Date Published: 2019
• Length: 10 pages
• Grant Number(s): 2014-DN-BX-K008
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Report (Grant Sponsored); Program/Project Description
• Award: Utilization of microbial structure and function in investigations of criminal justice

Annotation

This project compared three machine learning methods (boosted algorithms, random forests, and neural networks) for their abilities to predict the following aspects of a death investigation: postmortem interval (PMI), location where death occurred, and manner of death.

Abstract

The postmortem microbiome can provide valuable information to a death investigation and to the human health of the once living. Microbiome sequencing produces, in general, large multi-dimensional datasets that can be difficult to analyze and interpret. Machine learning methods can be useful in overcoming this analytical challenge; however, different methods use distinctive strategies to handle complex datasets. It is unclear whether one method is more appropriate than others for modeling postmortem microbiomes and their ability to predict attributes of interest in death investigations, which require understanding of how the microbial communities change after death and may represent those of the once living host. The current study collected postmortem microbiomes by swabbing five anatomical areas during routine death investigation, sequenced and analyzed from 188 death cases. A comparison of the processing of the three machine learning methods found that all algorithms performed well, but with distinct features to their performance. Xgboost often produced the most accurate predictions, but may also be more prone to overfitting. Random forest was the most stable across predictions that included more anatomic areas. Analysis of postmortem microbiota from more than three anatomic areas appears to yield limited returns on accuracy, with the eyes and rectum providing the most useful information correlating with circumstances of death in most cases for this dataset. (publisher abstract modified)