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

TL;DR

This study uses deep learning to improve schizophrenia prediction by identifying and filtering out genetic outliers in case-control datasets.

Contribution

A novel two-stage deep learning approach is introduced to detect and filter outliers in schizophrenia datasets, enhancing model performance.

Findings

Outlying genetic profiles in case-control datasets can hinder classification model performance.

Filtering outliers improves deep learning results and aligns them with heritability estimates for schizophrenia.

The approach enhances understanding of schizophrenia's genetic background and supports precision medicine in mental health.

Abstract

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.

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