Phenotype driven data augmentation methods for transcriptomic data

Abstract

The application of machine learning methods to biomedical applications has seen many successes. However, working with transcriptomic data on supervised learning tasks is challenging due to its high dimensionality, low patient numbers, and class imbalances. Machine learning models tend to overfit these data and do not generalize well on out-of-distribution samples. Data augmentation strategies help alleviate this by introducing synthetic data points and acting as regularizers. However, existing approaches are either computationally intensive, require population parametric estimates, or generate insufficiently diverse samples. To address these challenges, we introduce two classes of phenotype-driven data augmentation approaches—signature-dependent and signature-independent. The signature-dependent methods assume the existence of distinct gene signatures describing some phenotype and are simple, non-parametric, and novel data augmentation methods. The signature-independent methods are a modification of the established Gamma-Poisson and Poisson sampling methods for gene expression data. As case studies, we apply our augmentation methods to transcriptomic data of colorectal and breast cancer. Through discriminative and generative experiments with external validation, we show that our methods improve patient stratification by 5−15% over other augmentation methods in their respective cases. The study additionally provides insights into the limited benefits of over-augmenting data.