OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks

Abstract The OmicsFootPrint framework addresses the need for advanced multi-omics data analysis methodologies by transforming data into intuitive two-dimensional circular images and facilitating the interpretation of complex diseases. Utilizing Deep Neural Networks and incorporating the SHapley Additive exPlanations (SHAP) algorithm, the framework enhances model interpretability. Tested with The Cancer Genome Atlas (TCGA) data, OmicsFootPrint effectively classified lung and breast cancer subtypes, achieving high Area Under Curve (AUC) scores— 0.98±0.02 for lung cancer subtype differentiation, 0.83±0.07 for breast cancer PAM50 subtypes, and successfully distinguished between invasive lobular and ductal carcinomas in breast cancer, showcasing its robustness. It also demonstrated notable performance in predicting drug responses in cancer cell lines, with a median AUC of 0.74, surpassing nine existing methods. Furthermore, its effectiveness persists even with reduced training sample sizes. OmicsFootPrint marks an enhancement in multi-omics research, offering a novel, efficient, and interpretable approach that contributes to a deeper understanding of disease mechanisms. Competing Interest Statement The authors have declared no competing interest. Footnotes 1. Update of figure 6 (color arrangement and higher resolution) as well as corresponding text and figure legend. 2. Now Methods section comes before the Results section. Change in Supplementary Table. 3. Captions added for Figures.