Single-cell RNA sequencing enables cellular-level gene expression analysis, but high sparsity and noise pose significant challenges for accurate cell-type identification. Here, we propose sxFusion, a structure-aware clustering method that integrates low-rank representation with orthogonal non-negative matrix factorization. sxFusion first integrates graph-based features using a graph convolutional network and nonlinear embeddings from a multilayer perceptron via dimension-wise gating to enhance feature discriminability and mitigating over-smoothing; it then employs a structure-guided low-rank self-expression model co-optimized with orthogonal non-negative matrix factorization, aligning learned representation directly with clustering assignments, and outputs clustering results straightforward. Benchmarked against eleven state-of-the-art methods on eleven single-cell datasets, sxFusion consistently achieved higher accuracy. Ablation and visualization analyses confirmed the advantages of the fusion and co-optimization modules. These results demonstrate that sxFusion effectively identifies biologically meaningful cell populations, providing robust and interpretable clusters.

While 3D facial animation has made impressive progress, challenges still exist in realizing fine-grained stylized 3D facial expression manipulation due to the lack of appropriate datasets. In this paper, we introduce the AUBlendSet, a 3D facial dataset based on AU-Blendshape representation for fine-grained facial expression manipulation across identities. AUBlendSet is a blendshape data collection based on 32 standard facial action units (AUs) across 500 identities, along with an additional set of facial postures annotated with detailed AUs. Based on AUBlendSet, we propose AUBlendNet to learn AU-Blendshape basis vectors for different character styles. AUBlendNet predicts, in parallel, the AU-Blendshape basis vectors of the corresponding style for a given identity mesh, thereby achieving stylized 3D emotional facial manipulation. We comprehensively validate the effectiveness of AUBlendSet and AUBlendNet through tasks such as stylized facial expression manipulation, speech-driven emotional facial animation, and emotion recognition data augmentation. Through a series of qualitative and quantitative experiments, we demonstrate the potential and importance of AUBlendSet and AUBlendNet in 3D facial animation tasks. To the best of our knowledge, AUBlendSet is the first dataset, and AUBlendNet is the first network for continuous 3D facial expression manipulation for any identity through facial AUs. Our source code is available at https://github.com/wslh852/AUBlendNet.git.

Breast cancer subtyping presents a significant clinical and scientific challenge. The prevalent expression-based Prediction Analysis of the Microarray of 50 genes (PAM50) system and its Immunohistochemistry (IHC) surrogate tests showed substantial inconsistencies and did not apply to the rapidly progressing circulating tumor DNA screenings. We developed Unified Genetic and Epigenetic Subtyping (UGES), a new intrinsic subtype classifier, by integrating large-scale DNA-level omics data with a hierarchy learning algorithm. Our benchmarks showed that both multi-step hierarchical learning and using all DNA-level alteration data are crucial, improving the overall AUC score by over 8.3% compared to the one-step multi-classification method. Based on these insights, we developed UGES, a three-step classifier based on 50831 DNA features of 2065 samples, including mutations, copy number aberrations, and methylations. UGES achieved an overall AUC score of 0.963 and greatly improved the clinical stratification of real-world patients, as each subtype strata's survival difference became statistically more significant, P = 9.7e-55 (UGES) vs. 2.2e-47 (PAM50). Finally, UGES identified 52 subtype-specific DNA biomarkers that can be targeted in early screening technology to expand the time window for precision care. The UGES code is freely available at https://github.com/labxscut/UGES.

UNLABELLED: BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant sub-modules of regulatory networks with high confidence are reconstructed by using our extended sub-network mining algorithm of directed graphs. BNArray can handle microarray datasets with missing data. To evaluate the statistical features of generated Bayesian networks, re-sampling procedures are utilized to yield collections of candidate 1st-order network sets for mining dense coherent sub-networks. AVAILABILITY: The R package and the supplementary documentation are available at http://www.cls.zju.edu.cn/binfo/BNArray/.