Universal domain adaptation (UniDA) transfers knowledge from a labelled source domain to an unlabelled target domain under domain-shift and category-shift for annotation. In reality, due to privacy protection or other limits, not only source data but also pre-trained models on it may be unavailable when training on target data. In this paper, we go a step further to explore the black-box universal domain adaptation (B^2-UniDA) problem. It requires tackling the labelling task under shifts by only accessing the interface of pre-trained source models. To this end, we introduce GSS which proposes a novel sample selection criterion based on gradient descent and Bayes' Theorem to identify samples of potential unknown classes. This criterion doesn't require manually-set thresholds depending on data used and is suitable for various datasets. GSS builds an open-set classifier and enables it to estimate probabilities of belonging to each class including the unknown category and adjust estimates adaptively. To overcome class-imbalance, especially imbalance between the unknown and known classes, we propose a balancing mechanism by measuring training status and estimating DA type. In addition to distilling knowledge from source model outputs, we focus on mining the categorical structure of target domain by self-training. Experiments on benchmarks show the state-of-the-art performance of GSS compared to typical methods, including source models or source data dependent methods.

MOTIVATION: The rapid development of single-cell RNA sequencing (scRNA-seq) technologies allows us to explore tissue heterogeneity at the cellular level. The identification of cell types plays an essential role in the analysis of scRNA-seq data, which, in turn, influences the discovery of regulatory genes that induce heterogeneity. As the scale of sequencing data increases, the classical method of combining clustering and differential expression analysis to annotate cells becomes more costly in terms of both labor and resources. Existing scRNA-seq supervised classification method can alleviate this issue through learning a classifier trained on the labeled reference data and then making a prediction based on the unlabeled target data. However, such label transference strategy carries with risks, such as susceptibility to batch effect and further compromise of inherent discrimination of target data. RESULTS: In this article, inspired by unsupervised domain adaptation, we propose a flexible single cell semi-supervised clustering and annotation framework, scSemiCluster, which integrates the reference data and target data for training. We utilize structure similarity regularization on the reference domain to restrict the clustering solutions of the target domain. We also incorporates pairwise constraints in the feature learning process such that cells belonging to the same cluster are close to each other, and cells belonging to different clusters are far from each other in the latent space. Notably, without explicit domain alignment and batch effect correction, scSemiCluster outperforms other state-of-the-art, single-cell supervised classification and semi-supervised clustering annotation algorithms in both simulation and real data. To the best of our knowledge, we are the first to use both deep discriminative clustering and deep generative clustering techniques in the single-cell field. AVAILABILITYAND IMPLEMENTATION: An implementation of scSemiCluster is available from https://github.com/xuebaliang/scSemiCluster. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.