Applicability of an Automated Model and Parameter Selection in the Prediction of Screening-Level PTSD in Danish Soldiers Following Deployment: Development Study of Transferable Predictive Models Using Automated Machine Learning

A characteristic cerebellar biosignature for bipolar disorder, identified with fully automatic machine learning

Background

Transcriptomic profile differences between patients with bipolar disorder and healthy controls can be identified using machine learning and can provide information about the potential role of the cerebellum in the pathogenesis of bipolar disorder.With this aim, user-friendly, fully automated machine learning algorithms can achieve extremely high classification scores and disease-related predictive biosignature identification, in short time frames and scaled down to small datasets.

Method

A fully automated machine learning platform, based on the most suitable algorithm selection and relevant set of hyper-parameter values, was applied on a preprocessed transcriptomics dataset, in order to produce a model for biosignature selection and to classify subjects into groups of patients and controls. The parent GEO datasets were originally produced from the cerebellar and parietal lobe tissue of deceased bipolar patients and healthy controls, using Affymetrix Human Gene 1.0 ST Array.

Results

Patients and controls were classified into two separate groups, with no close-to-the-boundary cases, and this classification was based on the cerebellar transcriptomic biosignature of 25 features (genes), with Area Under Curve 0.929 and Average Precision 0.955. The biosignature includes both genes connected before to bipolar disorder, depression, psychosis or epilepsy, as well as genes not linked before with any psychiatric disease. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed participation of 4 identified features in 6 pathways which have also been associated with bipolar disorder.

Conclusion

Automated machine learning (AutoML) managed to identify accurately 25 genes that can jointly - in a multivariate-fashion - separate bipolar patients from healthy controls with high predictive power. The discovered features lead to new biological insights. Machine Learning (ML) analysis considers the features in combination (in contrast to standard differential expression analysis), removing both irrelevant as well as redundant markers, and thus, focusing to biological interpretation.

Early prediction of mental health problems following military deployment: Integrating pre- and post-deployment factors in neural network models

Military personnel deployed to war zones are at increased risk of mental health problems such as posttraumatic stress disorder (PTSD) or depression. Early pre- or post-deployment identification of those at highest risk of such problems is crucial to target intervention to those in need. However, sufficiently accurate models predicting objectively assessed mental health outcomes have not been put forward. In a sample consisting of all Danish military personnel who deployed to war zones for the first (N = 27,594), second (N = 11,083) and third (N = 5,161) time between 1992 and 2013, we apply neural networks to predict psychiatric diagnoses or use of psychotropic medicine in the years following deployment. Models are based on pre-deployment registry data alone or on pre-deployment registry data in combination with post-deployment questionnaire data on deployment experiences or early post-deployment reactions. Further, we identified the most central predictors of importance for the first, second, and third deployment. Models based on pre-deployment registry data alone had lower accuracy (AUCs ranging from 0.61 (third deployment) to 0.67 (first deployment)) than models including pre- and post-deployment data (AUCs ranging from 0.70 (third deployment) to 0.74 (first deployment)). Age at deployment, deployment year and previous physical trauma were important across deployments. Post-deployment predictors varied across deployments but included deployment exposures as well as early post-deployment symptoms. The results suggest that neural network models combining pre- and early post-deployment data can be utilized for screening tools that identify individuals at risk of severe mental health problems in the years following military deployment.

Just Add Data: automated predictive modeling for knowledge discovery and feature selection

Fully automated machine learning (AutoML) for predictive modeling is becoming a reality, giving rise to a whole new field. We present the basic ideas and principles of Just Add Data Bio (JADBio), an AutoML platform applicable to the low-sample, high-dimensional omics data that arise in translational medicine and bioinformatics applications. In addition to predictive and diagnostic models ready for clinical use, JADBio focuses on knowledge discovery by performing feature selection and identifying the corresponding biosignatures, i.e., minimal-size subsets of biomarkers that are jointly predictive of the outcome or phenotype of interest. It also returns a palette of useful information for interpretation, clinical use of the models, and decision making. JADBio is qualitatively and quantitatively compared against Hyper-Parameter Optimization Machine Learning libraries. Results show that in typical omics dataset analysis, JADBio manages to identify signatures comprising of just a handful of features while maintaining competitive predictive performance and accurate out-of-sample performance estimation.

Forecasting military mental health in a complete sample of Danish military personnel deployed between 1992-2013

OBJECTIVE

Mental health problems (MHP) are a relatively common consequence of deployment to war zones. Early identification of those at risk of post-deployment MHP would improve prevention efforts. However, screening instruments based on linear models have not been successful. Machine learning (ML) has shown promise for providing the methodological frame for better prognostic models.

METHODS

The study population was all Danish military personnel deployed for the first time between January 1, 1992 and December 31, 2013. From extensive registry data, 21 pre- or at-deployment predictors comprising early adversity, social, clinical and demographic variables were used to predict psychiatric contacts (psychiatric diagnosis and/or use of psychotropic medicine) occurring within 6.5 years after homecoming. Four supervised ML methods (penalized logistic regression, random forests, support vector machines and gradient boosting machines) were compared in ability to classify those with high risk of post-deployment MHP and those without.

RESULTS

Of 27594 subjects, 2175 (8%) had a psychiatric contact. All four ML methods applied had performances well above chance (Area under the Receiver-operating Curve 0.62-0.68). Positive predictive value for the best model was 0.16. A range of pre-deployment factors were found to be predictive of post-deployment psychiatric contacts.

CONCLUSIONS

ML methods can be useful in early identification of soldiers with high risk of MPH in the years following their first deployment. However, performances were modest and positive predictive values were low, limiting the applicability of the models for pre-deployment screening. Future studies should include neurobiological data and deployment experiences to increase accuracy of the models.