AggMapNet: enhanced and explainable low-sample omics deep learning with feature-aggregated multi-channel networks

Omics-based biomedical learning frequently relies on data of high-dimensions (up to thousands) and low-sample sizes (dozens to hundreds), which challenges efficient deep learning (DL) algorithms, particularly for low-sample omics investigations. Here, an unsupervised novel feature aggregation tool AggMap was developed to Aggregate and Map omics features into multi-channel 2D spatial-correlated image-like feature maps (Fmaps) based on their intrinsic correlations. AggMap exhibits strong feature reconstruction capabilities on a randomized benchmark dataset, outperforming existing methods. With AggMap multi-channel Fmaps as inputs, newly-developed multi-channel DL AggMapNet models outperformed the state-of-the-art machine learning models on 18 low-sample omics benchmark tasks. AggMapNet exhibited better robustness in learning noisy data and disease classification. The AggMapNet explainable module Simply-explainer identified key metabolites and proteins for COVID-19 detections and severity predictions. The unsupervised AggMap algorithm of good feature restructuring abilities combined with supervised explainable AggMapNet architecture establish a pipeline for enhanced learning and interpretability of low-sample omics data.

Automated summary

This study developed a feature aggregation tool called AggMap, which can map high-dimensional omics features into 2D spatial-correlated feature maps. The results showed that using AggMap and AggMapNet models can effectively learn low-sample omics data and outperform existing methods. Additionally, the explainable module Simply-explainer of AggMapNet identified key metabolites and proteins for COVID-19 detection and severity prediction.