Multi-task learning for single-cell multi-modality biology

Current biotechnologies can simultaneously measure multi-modality high-dimensional information from the same cell and tissue samples. To analyze the multi-modality data, common tasks such as joint data analysis and cross-modal prediction have been developed. However, current analytical methods are generally designed to process multi-modality data for one specific task without considering the underlying connections between tasks. Here, we present UnitedNet, a multi-task deep neural network that integrates the tasks of joint group identification and cross-modal prediction to analyze multi-modality data. We have found that multi-task learning for joint group identification and cross-modal prediction significantly improves the performance of each task. When applied to various single-cell multi-modality datasets, UnitedNet shows superior performance in each task, achieving better unsupervised and supervised joint group identification and cross-modal prediction performances compared with state-of-the-art methods. Furthermore, by considering the spatial information of cells as one modality, UnitedNet substantially improves the accuracy of tissue region identification and enables spatially resolved cross-modal prediction.