Z. Wang

Ping Xu, Zaitian Wang, Zhirui Wang et al.

Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain fragmented, often lacking standardized protocols and failing to incorporate recent advances in artificial intelligence. To fill these gaps, we present scCluBench, a comprehensive benchmark of clustering algorithms for scRNA-seq data. First, scCluBench provides 36 scRNA-seq datasets collected from diverse public sources, covering multiple tissues, which are uniformly processed and standardized to ensure consistency for systematic evaluation and downstream analyses. To evaluate performance, we collect and reproduce a range of scRNA-seq clustering methods, including traditional, deep learning-based, graph-based, and biological foundation models. We comprehensively evaluate each method both quantitatively and qualitatively, using core performance metrics as well as visualization analyses. Furthermore, we construct representative downstream biological tasks, such as marker gene identification and cell type annotation, to further assess the practical utility. scCluBench then investigates the performance differences and applicability boundaries of various clustering models across diverse analytical tasks, systematically assessing their robustness and scalability in real-world scenarios. Overall, scCluBench offers a standardized and user-friendly benchmark for scRNA-seq clustering, with curated datasets, unified evaluation protocols, and transparent analyses, facilitating informed method selection and providing valuable insights into model generalizability and application scope.

Zaitian Wang, Pengfei Wang, Kunpeng Liu et al.

Data augmentation is a series of techniques that generate high-quality artificial data by manipulating existing data samples. By leveraging data augmentation techniques, AI models can achieve significantly improved applicability in tasks involving scarce or imbalanced datasets, thereby substantially enhancing AI models' generalization capabilities. Existing literature surveys only focus on a certain type of specific modality data and categorize these methods from modality-specific and operation-centric perspectives, which lacks a consistent summary of data augmentation methods across multiple modalities and limits the comprehension of how existing data samples serve the data augmentation process. To bridge this gap, this survey proposes a more enlightening taxonomy that encompasses data augmentation techniques for different common data modalities by investigating how to take advantage of the intrinsic relationship between and within instances. Additionally, it categorizes data augmentation methods across five data modalities through a unified inductive approach.

Zhiyuan Ning, Zaitian Wang, Ran Zhang et al.

Graph clustering aims to divide the graph into different clusters. The recently emerging deep graph clustering approaches are largely built on graph neural networks (GNN). However, GNN is designed for general graph encoding and there is a common issue of representation collapse in existing GNN-based deep graph clustering algorithms. We attribute two main reasons for such issues: (i) the inductive bias of GNN models: GNNs tend to generate similar representations for proximal nodes. Since graphs often contain a non-negligible amount of inter-cluster links, the bias results in error message passing and leads to biased clustering; (ii) the clustering guided loss function: most traditional approaches strive to make all samples closer to pre-learned cluster centers, which causes a degenerate solution assigning all data points to a single label thus making all samples similar and less discriminative. To address these challenges, we investigate graph clustering from a graph cut perspective and propose an innovative and non-GNN-based Deep Cut-informed Graph embedding and Clustering framework, namely DCGC. This framework includes two modules: (i) cut-informed graph encoding; (ii) self-supervised graph clustering via optimal transport. For the encoding module, we derive a cut-informed graph embedding objective to fuse graph structure and attributes by minimizing their joint normalized cut. For the clustering module, we utilize the optimal transport theory to obtain the clustering assignments, which can balance the guidance of "proximity to the pre-learned cluster center". With the above two tailored designs, DCGC is more suitable for the graph clustering task, which can effectively alleviate the problem of representation collapse and achieve better performance. We conduct extensive experiments to demonstrate that our method is simple but effective compared with benchmarks.

Zaitian Wang, Jinghan Zhang, Xinhao Zhang et al.

Data augmentation is an essential technique in natural language processing (NLP) for enriching training datasets by generating diverse samples. This process is crucial for improving the robustness and generalization capabilities of NLP models. However, a significant challenge remains: \textit{Insufficient Attention to Sample Distribution Diversity}. Most existing methods focus on increasing the sample numbers while neglecting the sample distribution diversity, which can lead to model overfitting. In response, we explore data augmentation's impact on dataset diversity and propose a \textbf{\underline{D}}iversity-\textbf{\underline{o}}riented data \textbf{\underline{Aug}}mentation framework (\textbf{DoAug}). % \(\mathscr{DoAug}\) Specifically, we utilize a diversity-oriented fine-tuning approach to train an LLM as a diverse paraphraser, which is capable of augmenting textual datasets by generating diversified paraphrases. Then, we apply the LLM paraphraser to a selected coreset of highly informative samples and integrate the paraphrases with the original data to create a more diverse augmented dataset. Finally, we conduct extensive experiments on 12 real-world textual datasets. The results show that our fine-tuned LLM augmenter improves diversity while preserving label consistency, thereby enhancing the robustness and performance of downstream tasks. Specifically, it achieves an average performance gain of \(10.52\%\), surpassing the runner-up baseline with more than three percentage points.

Ping Xu, Zaitian Wang, Zhirui Wang et al.

Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have been developed for tasks such as cell clustering, cell type annotation, and marker gene identification. To fully assess and compare these methods, standardized, analysis-ready datasets are essential. However, such datasets remain scarce, and variations in data formats, preprocessing workflows, and annotation strategies hinder reproducibility and complicate systematic evaluation of existing methods. To address these challenges, we present scUnified, an AI-ready standardized resource for single-cell RNA sequencing data that consolidates 13 high-quality datasets spanning two species (human and mouse) and nine tissue types. All datasets undergo standardized quality control and preprocessing and are stored in a uniform format to enable direct application in diverse computational analyses without additional data cleaning. We further demonstrate the utility of scUnified through experimental analyses of representative biological tasks, providing a reproducible foundation for the standardized evaluation of computational methods on a unified dataset.