A New Approach to Large Multiomics Data Integration

Data reduction and data mining are common practices for handling large-scale data from wide-ranging sources, but high-dimensional omics and imaging data sets present difficult challenges for feature extraction and data mining due to the large number of features that cannot be simultaneously examined. The sample numbers and variables in these methods are constantly growing as new technologies are developed, and computational analysis needs to evolve to keep up with growing demand. In recent years, there has been a rapid uptake of nonlinear dimensionality reduction via methods such as t-distributed stochastic neighbor embedding and uniform manifold approximation and projection. These approaches have revolutionized our ability to visualize and interpret high-dimensional data and have rapidly become preferred methods for analysis of data sets containing an extremely high number of variables. Further to this is the emerging interest in combining information from multiple omics sources to gain a more holistic view of systems biology. Current state-of-the-art algorithms can perform data mining, visualization, and classification on routine data sets but struggle when data sets grow above a certain size. We present a new approach to large and multiomic data integration to extract, mine, and integrate large multiomics data sets that were previously considered prohibitively large. Here, we demonstrate the use of deep learning on subsampled nonlinear dimensionality reduction using t-SNE and UMAP to extract features from large complex data sets including mass spectrometry imaging and chromosome conformation capture. We then go on to demonstrate how this method can be used to learn embeddings from the fusion of different omics data, allowing metabolomics data to be projected into a reduced transcriptomics representation.