A Review of Multi-omics and Machine Learning: Advancements and Applications in Cancer Research

This comprehensive review starts with diving into the progress and real-world applications of combining multi-omics data analysis with machine learning techniques in cancer research. Multi-omics involves examining various biological data types like genomics, transcriptomics, proteomics, and metabolomics together to enhance our understanding of complex biological systems. By merging machine learning with multiomics data, we highlight the advantages for cancer studies, the deeper insights they yield and increased performance and results. Furthermore, we explore existing literature that showcases the integration of multi-omics and machine learning in cancer research. As part of our study, we conduct an experiment utilizing a multiomics dataset to predict the survival of breast cancer patients. We compare three distinct machine learning methods-ensemble, DeepProg, and DCAP-for survival prediction and conclude that despite the ensemble method that increased the prediction results of DeepProg over DCAP in multi-model setting, but the primitive capacity for DCAP is better in single model setting and achieves higher accuracy than DeepProg with noticeable margin 0.628 to 0.57 on C-Index metric, which strongly recommends using Denoising Autoencoder as the base for dimensionality reduction over the vanilla Autoencoder. Another empirical results conclude that using gaussian mixture model with diagonal covariance matrix for Clustering, which is used in DeepProg, might hinder the process for identifying reasonable clusters due to the assumption of no or zero correlation between different features which might not hold true in our problem.