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Ensemble machine learning prediction of posttraumatic stress disorder screening status after emergency room hospitalization.

ABSTRACT: Posttraumatic stress disorder (PTSD) develops in a substantial minority of emergency room admits. Inexpensive and accurate person-level assessment of PTSD risk after trauma exposure is a critical precursor to large-scale deployment of early interventions that may reduce individual suffering and societal costs. Toward this aim, we applied ensemble machine learning to predict PTSD screening status three months after severe injury using cost-effective and minimally invasive data. Participants (N = 271) were recruited at a Level 1 Trauma Center where they provided variables routinely collected at the hospital, including pulse, injury severity, and demographics, as well as psychological variables, including self-reported current depression, psychiatric history, and social support. Participant zip codes were used to extract contextual variables including population total and density, average annual income, and health insurance coverage rates from publicly available U.S. Census data. Machine learning yielded good prediction of PTSD screening status 3 months post-hospitalization, AUC?=?0.85 95% CI [0.83, 0.86], and significantly outperformed all benchmark comparison models in a cross-validation procedure designed to yield an unbiased estimate of performance. These results demonstrate that good prediction can be attained from variables that individually have relatively weak predictive value, pointing to the promise of ensemble machine learning approaches that do not rely on strong isolated risk factors.

SUBMITTER: Papini S

PROVIDER: S-EPMC6777842 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Ensemble machine learning prediction of posttraumatic stress disorder screening status after emergency room hospitalization.

Papini Santiago S Pisner Derek D Shumake Jason J Powers Mark B MB Beevers Christopher G CG Rainey Evan E EE Smits Jasper A J JAJ Warren Ann Marie AM

Journal of anxiety disorders 20181030

Posttraumatic stress disorder (PTSD) develops in a substantial minority of emergency room admits. Inexpensive and accurate person-level assessment of PTSD risk after trauma exposure is a critical precursor to large-scale deployment of early interventions that may reduce individual suffering and societal costs. Toward this aim, we applied ensemble machine learning to predict PTSD screening status three months after severe injury using cost-effective and minimally invasive data. Participants (N = ...[more]

PMID: 30419537

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Project description:ImportanceMilitary deployment involves significant risk for life-threatening experiences that can lead to posttraumatic stress disorder (PTSD). Accurate predeployment prediction of PTSD risk may facilitate the development of targeted intervention strategies to enhance resilience.ObjectiveTo develop and validate a machine learning (ML) model to predict postdeployment PTSD.Design, setting, and participantsThis diagnostic/prognostic study included 4771 soldiers from 3 US Army brigade combat teams who completed assessments between January 9, 2012, and May 1, 2014. Predeployment assessments occurred 1 to 2 months before deployment to Afghanistan, and follow-up assessments occurred approximately 3 and 9 months post deployment. Machine learning models to predict postdeployment PTSD were developed in the first 2 recruited cohorts using as many as 801 predeployment predictors from comprehensive self-report assessments. In the development phase, cross-validated performance metrics and predictor parsimony were considered to select an optimal model. Next, the selected model's performance was evaluated with area under the receiver operating characteristics curve and expected calibration error in a temporally and geographically distinct cohort. Data analyses were performed from August 1 to November 30, 2022.Main outcomes and measuresPosttraumatic stress disorder diagnosis was assessed by clinically calibrated self-report measures. Participants were weighted in all analyses to address potential biases related to cohort selection and follow-up nonresponse.ResultsThis study included 4771 participants (mean [SD] age, 26.9 [6.2] years), 4440 (94.7%) of whom were men. In terms of race and ethnicity, 144 participants (2.8%) identified as American Indian or Alaska Native, 242 (4.8%) as Asian, 556 (13.3%) as Black or African American, 885 (18.3%) as Hispanic, 106 (2.1%) as Native Hawaiian or other Pacific Islander, 3474 (72.2%) as White, and 430 (8.9%) as other or unknown race or ethnicity; participants could identify as of more than 1 race or ethnicity. A total of 746 participants (15.4%) met PTSD criteria post deployment. In the development phase, models had comparable performance (log loss range, 0.372-0.375; area under the curve range, 0.75-0.76). A gradient-boosting machine with 58 core predictors was selected over an elastic net with 196 predictors and a stacked ensemble of ML models with 801 predictors. In the independent test cohort, the gradient-boosting machine had an area under the curve of 0.74 (95% CI, 0.71-0.77) and low expected calibration error of 0.032 (95% CI, 0.020-0.046). Approximately one-third of participants with the highest risk accounted for 62.4% (95% CI, 56.5%-67.9%) of the PTSD cases. Core predictors cut across 17 distinct domains: stressful experiences, social network, substance use, childhood or adolescence, unit experiences, health, injuries, irritability or anger, personality, emotional problems, resilience, treatment, anxiety, attention or concentration, family history, mood, and religion.Conclusions and relevanceIn this diagnostic/prognostic study of US Army soldiers, an ML model was developed to predict postdeployment PTSD risk with self-reported information collected before deployment. The optimal model showed good performance in a temporally and geographically distinct validation sample. These results indicate that predeployment stratification of PTSD risk is feasible and may facilitate the development of targeted prevention and early intervention strategies.

Project description:BACKGROUND:In plants, long non-protein coding RNAs are believed to have essential roles in development and stress responses. However, relative to advances on discerning biological roles for long non-protein coding RNAs in animal systems, this RNA class in plants is largely understudied. With comparatively few validated plant long non-coding RNAs, research on this potentially critical class of RNA is hindered by a lack of appropriate prediction tools and databases. Supervised learning models trained on data sets of mostly non-validated, non-coding transcripts have been previously used to identify this enigmatic RNA class with applications largely focused on animal systems. Our approach uses a training set comprised only of empirically validated long non-protein coding RNAs from plant, animal, and viral sources to predict and rank candidate long non-protein coding gene products for future functional validation. RESULTS:Individual stochastic gradient boosting and random forest classifiers trained on only empirically validated long non-protein coding RNAs were constructed. In order to use the strengths of multiple classifiers, we combined multiple models into a single stacking meta-learner. This ensemble approach benefits from the diversity of several learners to effectively identify putative plant long non-coding RNAs from transcript sequence features. When the predicted genes identified by the ensemble classifier were compared to those listed in GreeNC, an established plant long non-coding RNA database, overlap for predicted genes from Arabidopsis thaliana, Oryza sativa and Eutrema salsugineum ranged from 51 to 83% with the highest agreement in Eutrema salsugineum. Most of the highest ranking predictions from Arabidopsis thaliana were annotated as potential natural antisense genes, pseudogenes, transposable elements, or simply computationally predicted hypothetical protein. Due to the nature of this tool, the model can be updated as new long non-protein coding transcripts are identified and functionally verified. CONCLUSIONS:This ensemble classifier is an accurate tool that can be used to rank long non-protein coding RNA predictions for use in conjunction with gene expression studies. Selection of plant transcripts with a high potential for regulatory roles as long non-protein coding RNAs will advance research in the elucidation of long non-protein coding RNA function.

Project description:The necessary requirement of a traumatic event preceding the development of Posttraumatic Stress Disorder, theoretically allows for administering preventive and early interventions in the early aftermath of such events. Machine learning models including biomedical data to forecast PTSD outcome after trauma are highly promising for detection of individuals most in need of such interventions. In the current study, machine learning was applied on biomedical data collected within 48 h post-trauma to forecast individual risk for long-term PTSD, using a multinominal approach including the full spectrum of common PTSD symptom courses within one prognostic model for the first time. N = 417 patients (37.2% females; mean age 46.09 ± 15.88) admitted with (suspected) serious injury to two urban Academic Level-1 Trauma Centers were included. Routinely collected biomedical information (endocrine measures, vital signs, pharmacotherapy, demographics, injury and trauma characteristics) upon ED admission and subsequent 48 h was used. Cross-validated multi-nominal classification of longitudinal self-reported symptom severity (IES-R) over 12 months and bimodal classification of clinician-rated PTSD diagnosis (CAPS-IV) at 12 months post-trauma was performed using extreme Gradient Boosting and evaluated on hold-out sets. SHapley Additive exPlanations (SHAP) values were used to explain the derived models in human-interpretable form. Good prediction of longitudinal PTSD symptom trajectories (multiclass AUC = 0.89) and clinician-rated PTSD at 12 months (AUC = 0.89) was achieved. Most relevant prognostic variables to forecast both multinominal and dichotomous PTSD outcomes included acute endocrine and psychophysiological measures and hospital-prescribed pharmacotherapy. Thus, individual risk for long-term PTSD was accurately forecasted from biomedical information routinely collected within 48 h post-trauma. These results facilitate future targeted preventive interventions by enabling future early risk detection and provide further insights into the complex etiology of PTSD.

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Ensemble machine learning prediction of posttraumatic stress disorder screening status after emergency room hospitalization.

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Ensemble machine learning prediction of posttraumatic stress disorder screening status after emergency room hospitalization.

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