Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
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ABSTRACT:
SUBMITTER: Wirbel J
PROVIDER: S-EPMC8008609 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Theoretically-driven models of suicide have long guided suicidology; however, an approach employing machine learning models has recently emerged in the field. Some have suggested that machine learning models yield improved prediction as compared to theoretical approaches, but to date, this has not been investigated in a systematic manner. The present work directly compares widely researched theories of suicide (i.e., BioSocial, Biological, Ideation-to-Action, and Hopelessness Theories) to machine learning models, comparing the accuracy between the two differing approaches. We conducted literature searches using PubMed, PsycINFO, and Google Scholar, gathering effect sizes from theoretically-relevant constructs and machine learning models. Eligible studies were longitudinal research articles that predicted suicide ideation, attempts, or death published prior to May 1, 2020. 124 studies met inclusion criteria, corresponding to 330 effect sizes. Theoretically-driven models demonstrated suboptimal prediction of ideation (wOR = 2.87; 95% CI, 2.65-3.09; k = 87), attempts (wOR = 1.43; 95% CI, 1.34-1.51; k = 98), and death (wOR = 1.08; 95% CI, 1.01-1.15; k = 78). Generally, Ideation-to-Action (wOR = 2.41, 95% CI = 2.21-2.64, k = 60) outperformed Hopelessness (wOR = 1.83, 95% CI 1.71-1.96, k = 98), Biological (wOR = 1.04; 95% CI .97-1.11, k = 100), and BioSocial (wOR = 1.32, 95% CI 1.11-1.58, k = 6) theories. Machine learning provided superior prediction of ideation (wOR = 13.84; 95% CI, 11.95-16.03; k = 33), attempts (wOR = 99.01; 95% CI, 68.10-142.54; k = 27), and death (wOR = 17.29; 95% CI, 12.85-23.27; k = 7). Findings from our study indicated that across all theoretically-driven models, prediction of suicide-related outcomes was suboptimal. Notably, among theories of suicide, theories within the Ideation-to-Action framework provided the most accurate prediction of suicide-related outcomes. When compared to theoretically-driven models, machine learning models provided superior prediction of suicide ideation, attempts, and death.
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Project description:(1) Background: Constipation is a common condition that affects the health and the quality of life of patients. Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort. Thus, we aimed to construct a classification model based on fecal bacterial and identify the potential gut microbes' biomarkers. (2) Methods: We collected 3056 fecal amplicon sequence data from five research cohorts. The data were subjected to a series of analyses, including alpha- and beta-diversity analyses, phylogenetic profiling analyses, and systematic machine learning to obtain a comprehensive understanding of the association between constipation and the gut microbiome. (3) Results: The alpha diversity of the bacterial community composition was higher in patients with constipation. Beta diversity analysis evidenced significant partitions between the two groups on the base of gut microbiota composition. Further, machine learning based on feature selection was performed to evaluate the utility of the gut microbiome as the potential biomarker for constipation. The Gradient Boosted Regression Trees after chi2 feature selection was the best model, exhibiting a validation performance of 70.7%. (4) Conclusions: We constructed an accurate constipation discriminant model and identified 15 key genera, including Serratia, Dorea, and Aeromonas, as possible biomarkers for constipation.
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