MOTIVATION: Single-cell RNA sequencing (scRNA-seq) enables high-throughput transcriptomic profiling at single-cell resolution. The inherent spatial location is crucial for understanding how single cells orchestrate multicellular functions and drive diseases. However, spatial information is often lost during tissue dissociation. Spatial transcriptomic (ST) technologies can provide precise spatial gene expression atlas, while their practicality is constrained by the number of genes they can assay or the associated costs at a larger scale and the fine-grained cell-type annotation. By transferring knowledge between scRNA-seq and ST data through cell correspondence learning, it is possible to recover the spatial properties inherent in scRNA-seq datasets. RESULTS: In this study, we introduce COME, a COntrastive Mapping lEarning approach that learns mapping between ST and scRNA-seq data to recover the spatial information of scRNA-seq data. Extensive experiments demonstrate that the proposed COME method effectively captures precise cell-spot relationships and outperforms previous methods in recovering spatial location for scRNA-seq data. More importantly, our method is capable of precisely identifying biologically meaningful information within the data, such as the spatial structure of missing genes, spatial hierarchical patterns, and the cell-type compositions for each spot. These results indicate that the proposed COME method can help to understand the heterogeneity and activities among cells within tissue environments. AVAILABILITY AND IMPLEMENTATION: The COME is freely available in GitHub (https://github.com/cindyway/COME).

Single-cell RNA sequencing (scRNA-seq) technology has transformed gene expression studies by enabling analysis at the individual cell level, offering unprecedented insights into cellular heterogeneity. A key challenge in scRNA-seq data analysis is cell type identification, which requires grouping cells with similar gene expression profiles using unsupervised clustering methods. However, the high dimensionality, inherent noise, and significant sparsity of scRNA-seq data present substantial obstacles to accurately determining relationships among cell samples. To address these challenges, we propose a novel deep subspace clustering approach for cell type identification that captures a more reliable subspace structure from scRNA-seq data. Our method leverages a robust self-representation learning framework to effectively characterize and learn the underlying cluster structure. This framework is optimized through an integrated strategy combining a structure-guided approach with an optimal transport algorithm, enhancing the robustness of the subspace clustering process. By mitigating the effects of noise and sparsity in scRNA-seq data, this approach enables more accurate cell clustering. Experimental results on 18 real scRNA-seq datasets demonstrate that our method outperforms several state-of-the-art clustering approaches tailored for scRNA-seq data, excelling in both accuracy and interpretability.

Facial makeup transfer aims to replicate reference makeup on target face, and the existing methods are mainly based on a generic adversarial training process. In this work, we design a Reference-conditional Makeup-aware Discrimination approach (RcMD) to facilitate makeup transfer. Specifically, we perform region-wise semantic feature extraction from a reference makeup image and a source image without makeup. A generator learns to capture and render the reference makeup by modulating the region-wise intermediate features. To ensure precise makeup on target face, we incorporate a reference-conditional discrimination network, which learns to measure the regional makeup consistency between reference and synthesized images. Considering the discrepancy between reference and target faces, an alignment module is trained to fuse the extracted features, conditioned on the reference style. Based on the feature statistics, we perform regional real-synthesized makeup discrimination to ensure precise makeup rendering. Extensive experiments are performed to demonstrate the effectiveness of our designed modules and the superior performance of RcMD in transferring diverse real-world facial makeup.

Partially View-aligned Clustering (PVC) presents a challenge as it requires a comprehensive exploration of complementary and consistent information in the presence of partial alignment of view data. Existing PVC methods typically learn view correspondence based on latent features that are expected to contain common semantic information. However, latent features obtained from heterogeneous spaces, along with the enforcement of alignment into the same feature dimension, can introduce cross-view discrepancies. In particular, partially view-aligned data lacks sufficient shared correspondences for the critical common semantic feature learning, resulting in inaccuracies in establishing meaningful correspondences between latent features across different views. While feature representations may differ across views, instance relationships within each view could potentially encode consistent common semantics across views. Motivated by this, our aim is to learn view correspondence based on graph distribution metrics that capture semantic view-invariant instance relationships. To achieve this, we utilize similarity graphs to depict instance relationships and learn view correspondence by aligning semantic similarity graphs through optimal transport with graph distribution. This facilitates the precise learning of view alignments, even in the presence of heterogeneous view-specific feature distortions. Furthermore, leveraging well-established cross-view correspondence, we introduce a cross-view contrastive learning to learn semantic features by exploiting consistency information. The resulting meaningful semantic features effectively isolate shared latent patterns, avoiding the inclusion of irrelevant private information. We conduct extensive experiments on several real datasets, demonstrating the effectiveness of our proposed method for the PVC task.

The spatial reconstruction of single-cell RNA sequencing (scRNA-seq) data into spatial transcriptomics (ST) is a rapidly evolving field that addresses the significant challenge of aligning gene expression profiles to their spatial origins within tissues. This task is complicated by the inherent batch effects and the need for precise gene expression characterization to accurately reflect spatial information. To address these challenges, we developed SELF-Former, a transformer-based framework that utilizes multi-scale structures to learn gene representations, while designing spatial correlation constraints for the reconstruction of corresponding ST data. SELF-Former excels in recovering the spatial information of ST data and effectively mitigates batch effects between scRNA-seq and ST data. A novel aspect of SELF-Former is the introduction of a gene filtration module, which significantly enhances the spatial reconstruction task by selecting genes that are crucial for accurate spatial positioning and reconstruction. The superior performance and effectiveness of SELF-Former's modules have been validated across four benchmark datasets, establishing it as a robust and effective method for spatial reconstruction tasks. SELF-Former demonstrates its capability to extract meaningful gene expression information from scRNA-seq data and accurately map it to the spatial context of real ST data. Our method represents a significant advancement in the field, offering a reliable approach for spatial reconstruction.