Artificial Neural Network System for Cell Classification using Single Cell RNA Expression

We implemented an automated system for single-cell classification using artificial neural networks (ANN). Our system takes single-cell gene expression sparse matrices and trains ANN to classify cell types and subtypes. The assemblies of ANNs predict cell classes by voting. We tested the system in a case study where we trained ANNs with a dataset containing approximately 120,000 single cells and tested the resulting model using an independent data set of 13,000 single cells. The overall accuracy of the 5-class classification was 95%. We trained and tested a total of 100 ANNs in 10 cycles. The prediction system demonstrated excellent reproducibility. The analysis of misclassifications indicated that 2% were likely classification errors, while the remaining 3% were likely due to mislabeled types and subtypes in the test set.