Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data

Single-cell protein abundance is a fundamental type of information to characterize cell states. Due to high cost and technical barriers, however, direct quantification of proteins is difficult. Single-cell RNA sequencing (scRNA-seq) data, serving as a cost-effective substitute of single-cell proteomics, may not accurately reflect protein expression levels due to measurement error, noise, post-transcriptional and translational regulation, etc. The recently emerging single-cell multimodal omics data, e.g. CITE-seq and REAP-seq, can simultaneously profile RNA and protein abundances in single cells, providing labeled data for predictive modeling in a supervised learning framework. Deep neural network-based transfer learning method has been applied to imputation of surface protein abundances from single-cell transcriptomic data. However, it is unclear if the artificial neural network is the best model, and it is desirable to improve the prediction performance (e.g. accuracy, interpretability) of machine learning models. In this paper, we compared several tree-based ensemble learning methods with neural network models, and found that ensemble learning often performed better than neural network, and Random Forest (RF) performed the best overall. Moreover, we used the feature importance scores from RF to interpret biological mechanisms underlying the prediction. Our study demonstrates the effectiveness of ensemble learning for reliable protein abundances prediction using single-cell multimodal omics data, and paves the way for knowledge discovery by mining single-cell multi-omics data in large scale.