Semi-supervised single-cell cross-modality translation using Polarbear

Abstract The emergence of single-cell co-assays enables us to learn to translate between single-cell modalities, potentially offering valuable insights from datasets where only one modality is available. However, the sparsity of single-cell measurements and the limited number of cells measured in typical co-assay datasets impedes the power of cross-modality translation. Here, we propose Polarbear, a semi-supervised translation framework to predict cross-modality profiles that is trained using a combination of co-assay data and traditional “single-assay” data. Polarbear uses single-assay and co-assay data to train an autoencoder for each modality and then uses just the co-assay data to train a translator between the embedded representations learned by the autoencoders. With this approach, Polarbear is able to translate between modalities with improved accuracy relative to state-of-the-art translation techniques. As an added benefit of the training procedure, we show that Polarbear also produces a matching of cells across modalities.