Deep learning-based integration of genetics with registry data for stratification of schizophrenia and depression

Detecting outliers in case-control cohorts for improving deep learning networks on Schizophrenia prediction

This study delves into the intricate genetic and clinical aspects of Schizophrenia, a complex mental disorder with uncertain etiology. Deep Learning (DL) holds promise for analyzing large genomic datasets to uncover new risk factors. However, based on reports of non-negligible misdiagnosis rates for SCZ, case-control cohorts may contain outlying genetic profiles, hindering compelling performances of classification models. The research employed a case-control dataset sourced from the Swedish populace. A gene-annotation-based DL architecture was developed and employed in two stages. First, the model was trained on the entire dataset to highlight differences between cases and controls. Then, samples likely to be misclassified were excluded, and the model was retrained on the refined dataset for performance evaluation. The results indicate that SCZ prevalence and misdiagnosis rates can affect case-control cohorts, potentially compromising future studies reliant on such datasets. However, by detecting and filtering outliers, the study demonstrates the feasibility of adapting DL methodologies to large-scale biological problems, producing results more aligned with existing heritability estimates for SCZ. This approach not only advances the comprehension of the genetic background of SCZ but also opens doors for adapting DL techniques in complex research for precision medicine in mental health.

Development and Validation of a Machine Learning-Based Model of Mortality Risk in First-Episode Psychosis

Importance

There is an absence of mortality risk assessment tools in first-episode psychosis (FEP) that could enable personalized interventions.

Objective

To examine the feasibility of machine learning (ML) in discerning mortality risk in FEP and to assess whether such risk predictions can inform pharmacotherapy choices.

Design, Setting, and Participants

In this prognostic study, Swedish nationwide cohort data (from July 1, 2006, to December 31, 2021) were harnessed for model development and validation. Finnish cohort data (from January 1, 1998, to December 31, 2017) were used for external validation. Data analyses were completed between December 2022 and December 2023.

Main Outcomes and Measures

Fifty-one nationwide register variables, encompassing demographics and clinical and work-related histories, were subjected to ML to predict future mortality risk. The ML model's performance was evaluated by calculating the area under the receiver operating characteristic curve (AUROC). The comparative effectiveness of pharmacotherapies in patients was assessed and was stratified by the ML model to those with predicted high mortality risk (vs low risk), using the between-individual hazard ratio (HR). The 5 most important variables were then identified and a model was retrained using these variables in the discovery sample.

Results

This study included 24 052 Swedish participants (20 000 in the discovery sample and 4052 in the validation sample) and 1490 Finnish participants (in the validation sample). Swedish participants had a mean (SD) age of 29.1 (8.1) years, 62.1% were men, and 418 died with 2 years. Finnish participants had a mean (SD) age of 29.7 (8.0) years, 61.7% were men, and 31 died within 2 years. The discovery sample achieved an AUROC of 0.71 (95% CI, 0.68-0.74) for 2-year mortality prediction. Using the 5 most important variables (ie, the top 10% [substance use comorbidities, first hospitalization duration due to FEP, male sex, prior somatic hospitalizations, and age]), the final model resulted in an AUROC of 0.70 (95% CI, 0.63-0.76) in the Swedish sample and 0.67 (95% CI, 0.56-0.78) in the Finnish sample. Individuals with predicted high mortality risk had an elevated 15-year risk in the Swedish sample (HR, 3.77 [95% CI, 2.92-4.88]) and an elevated 20-year risk in the Finnish sample (HR, 3.72 [95% CI, 2.67-5.18]). For those with predicted high mortality risk, long-acting injectable antipsychotics (HR, 0.45 [95% CI, 0.23-0.88]) and mood stabilizers (HR, 0.64 [95% CI, 0.46-0.90]) were associated with decreased mortality risk. Conversely, for those predicted to survive, only oral aripiprazole (HR, 0.38 [95% CI, 0.20-0.69]) and risperidone (HR, 0.38 [95% CI, 0.18-0.82]) were associated with decreased mortality risk.

Conclusions and Relevance

In this prognostic study, an ML-based model was developed and validated to predict mortality risk in FEP. These findings may help to develop personalized interventions to mitigate mortality risk in FEP.

Artificial intelligence in psychiatry research, diagnosis, and therapy

Psychiatric disorders are now responsible for the largest proportion of the global burden of disease, and even more challenges have been seen during the COVID-19 pandemic. Artificial intelligence (AI) is commonly used to facilitate the early detection of disease, understand disease progression, and discover new treatments in the fields of both physical and mental health. The present review provides a broad overview of AI methodology and its applications in data acquisition and processing, feature extraction and characterization, psychiatric disorder classification, potential biomarker detection, real-time monitoring, and interventions in psychiatric disorders. We also comprehensively summarize AI applications with regard to the early warning, diagnosis, prognosis, and treatment of specific psychiatric disorders, including depression, schizophrenia, autism spectrum disorder, attention-deficit/hyperactivity disorder, addiction, sleep disorders, and Alzheimer's disease. The advantages and disadvantages of AI in psychiatry are clarified. We foresee a new wave of research opportunities to facilitate and improve AI technology and its long-term implications in psychiatry during and after the COVID-19 era.

Whole Person Modeling: a transdisciplinary approach to mental health research

The growing global burden of mental illness has prompted calls for innovative research strategies. Theoretical models of mental health include complex contributions of biological, psychosocial, experiential, and other environmental influences. Accordingly, neuropsychiatric research has self-organized into largely isolated disciplines working to decode each individual contribution. However, research directly modeling objective biological measurements in combination with cognitive, psychological, demographic, or other environmental measurements is only now beginning to proliferate. This review aims to (1) to describe the landscape of modern mental health research and current movement towards integrative study, (2) to provide a concrete framework for quantitative integrative research, which we call Whole Person Modeling, (3) to explore existing and emerging techniques and methods used in Whole Person Modeling, and (4) to discuss our observations about the scarcity, potential value, and untested aspects of highly transdisciplinary research in general. Whole Person Modeling studies have the potential to provide a better understanding of multilevel phenomena, deliver more accurate diagnostic and prognostic tests to aid in clinical decision making, and test long standing theoretical models of mental illness. Some current barriers to progress include challenges with interdisciplinary communication and collaboration, systemic cultural barriers to transdisciplinary career paths, technical challenges in model specification, bias, and data harmonization, and gaps in transdisciplinary educational programs. We hope to ease anxiety in the field surrounding the often mysterious and intimidating world of transdisciplinary, data-driven mental health research and provide a useful orientation for students or highly specialized researchers who are new to this area.

Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models

The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug-omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug-drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.

Deep Learning for Cross-Diagnostic Prediction of Mental Disorder Diagnosis and Prognosis Using Danish Nationwide Register and Genetic Data

Importance

Diagnoses and treatment of mental disorders are hampered by the current lack of objective markers needed to provide a more precise diagnosis and treatment strategy.

Objective

To develop deep learning models to predict mental disorder diagnosis and severity spanning multiple diagnoses using nationwide register data, family and patient-specific diagnostic history, birth-related measurement, and genetics.

Design, Setting, and Participants

This study was conducted from May 1, 1981, to December 31, 2016. For the analysis, which used a Danish population-based case-cohort sample of individuals born between 1981 and 2005, genotype data and matched longitudinal health register data were taken from the longitudinal Danish population-based Integrative Psychiatric Research Consortium 2012 case-cohort study. Included were individuals with mental disorders (attention-deficit/hyperactivity disorder [ADHD]), autism spectrum disorder (ASD), major depressive disorder (MDD), bipolar disorder (BD), schizophrenia spectrum disorders (SCZ), and population controls. Data were analyzed from February 1, 2021, to January 24, 2022.

Exposure

At least 1 hospital contact with diagnosis of ADHD, ASD, MDD, BD, or SCZ.

Main Outcomes and Measures

The predictability of (1) mental disorder diagnosis and (2) severity trajectories (measured by future outpatient hospital contacts, admissions, and suicide attempts) were investigated using both a cross-diagnostic and single-disorder setup. Predictive power was measured by AUC, accuracy, and Matthews correlation coefficient (MCC), including an estimate of feature importance.

Results

A total of 63 535 individuals (mean [SD] age, 23 [7] years; 34 944 male [55%]; 28 591 female [45%]) were included in the model. Based on data prior to diagnosis, the specific diagnosis was predicted in a multidiagnostic prediction model including the background population with an overall area under the curve (AUC) of 0.81 and MCC of 0.28, whereas the single-disorder models gave AUCs/MCCs of 0.84/0.54 for SCZ, 0.79/0.41 for BD, 0.77/0.39 for ASD, 0.74/0.38, for ADHD, and 0.74/0.38 for MDD. The most important data sets for multidiagnostic prediction were previous mental disorders and age (11%-23% reduction in prediction accuracy when removed) followed by family diagnoses, birth-related measurements, and genetic data (3%-5% reduction in prediction accuracy when removed). Furthermore, when predicting subsequent disease trajectories of the disorder, the most severe cases were the most easily predictable, with an AUC of 0.72.

Conclusions and Relevance

Results of this diagnostic study suggest the possibility of combining genetics and registry data to predict both mental disorder diagnosis and disorder progression in a clinically relevant, cross-diagnostic setting prior to clinical assessment.