Qiangqiang Dai

Ru Zhang, Xunkai Li, Yaxin Deng et al.

Recently, data-centric AI methodology has been a dominant paradigm in single-cell transcriptomics analysis, which treats data representation rather than model complexity as the fundamental bottleneck. In the review of current studies, earlier sequence methods treat cells as independent entities and adapt prevalent ML models to analyze their directly inherited sequence data. Despite their simplicity and intuition, these methods overlook the latent intercellular relationships driven by the functional mechanisms of biological systems and the inherent quality issues of the raw sequence data. Therefore, a series of structured methods has emerged. Although they employ various heuristic rules to capture intricate intercellular relationships and enhance the raw sequencing data, these methods often neglect biological prior knowledge. This omission incurs substantial overhead and yields suboptimal graph representations, thereby hindering the utility of ML models. To address them, we propose DOGMA, a holistic data-centric framework designed for the structural reshaping and semantic enhancement of raw data through multi-level biological prior knowledge. Transcending reliance on stochastic heuristics, DOGMA redefines graph construction by integrating Statistical Anchors with Cell Ontology and Phylogenetic Trees to enable deterministic structure discovery and robust cross-species alignment. Furthermore, Gene Ontology is utilized to bridge the feature-level semantic gap by incorporating functional priors. In complex multi-species and multi-organ benchmarks, DOGMA achieves SOTA performance, exhibiting superior zero-shot robustness and sample efficiency while operating with significantly lower computational cost.

Zekai Chen, Kairui Yang, Xunkai Li et al.

Federated graph learning (FGL) enables collaborative training of graph neural networks (GNNs) across decentralized subgraphs without exposing raw data. While existing FGL methods often achieve high overall accuracy, we show that this average performance can conceal severe degradation on disadvantaged node groups. From a fairness perspective, these disparities arise systematically from three coupled sources: label skew toward majority patterns, topology confounding in message propagation, and aggregation dilution of updates from hard clients. To address this, we propose \textbf{BoostFGL}, a boosting-style framework for fairness-aware FGL. BoostFGL introduces three coordinated mechanisms: \ding{182} \emph{Client-side node boosting}, which reshapes local training signals to emphasize systematically under-served nodes; \ding{183} \emph{Client-side topology boosting}, which reallocates propagation emphasis toward reliable yet underused structures and attenuates misleading neighborhoods; and \ding{184} \emph{Server-side model boosting}, which performs difficulty- and reliability-aware aggregation to preserve informative updates from hard clients while stabilizing the global model. Extensive experiments on 9 datasets show that BoostFGL delivers substantial fairness gains, improving Overall-F1 by 8.43\%, while preserving competitive overall performance against strong FGL baselines.

Yilong Zuo, Xunkai Li, Zhihan Zhang et al.

Multimodal Attributed Graphs (MAGs) have been widely adopted for modeling complex systems by integrating multi-modal information, such as text and images, on nodes. However, we identify a discrepancy between the implicit semantic structure induced by different modality embeddings and the explicit graph structure. For instance, neighbors in the explicit graph structure may be close in one modality but distant in another. Since existing methods typically perform message passing over the fixed explicit graph structure, they inadvertently aggregate dissimilar features, introducing modality-specific noise and impeding effective node representation learning. To address this, we propose OptiMAG, an Unbalanced Optimal Transport-based regularization framework. OptiMAG employs the Fused Gromov-Wasserstein distance to explicitly guide cross-modal structural consistency within local neighborhoods, effectively mitigating structural-semantic conflicts. Moreover, a KL divergence penalty enables adaptive handling of cross-modal inconsistencies. This framework can be seamlessly integrated into existing multimodal graph models, acting as an effective drop-in regularizer. Experiments demonstrate that OptiMAG consistently outperforms baselines across multiple tasks, ranging from graph-centric tasks (e.g., node classification, link prediction) to multimodal-centric generation tasks (e.g., graph2text, graph2image). The source code will be available upon acceptance.

Zhiqiu Zou, Ziqi Yin, Rong-Hua Li et al.

Range-filtered approximate nearest neighbor (RFANN) search is a fundamental operation in modern data systems. Given a set of objects, each with a vector and a numerical attribute, an RFANN query retrieves the nearest neighbors to a query vector among those objects whose numerical attributes fall within the range specified by the query. Existing state-of-the-art methods for RFANN search often require constructing multiple range-specific graph indexes to achieve high query performance, which incurs significant indexing overhead. To address this, we first establish a novel graph indexing theory, the range-aware relative neighborhood graph (RRNG), which jointly considers spatial and attribute proximity. We prove that the RRNG satisfies two crucial properties: (1) monotonic search-ability, which ensures correct nearest neighbor retrieval via beam search; and (2) structural heredity, which guarantees that any range-induced subgraph remains a valid RRNG, thus enabling efficient search with a single graph index. Based on this theoretical foundation, we propose a new graph index called RNSG as a practical solution that efficiently approximates RRNG. We develop fast algorithms for both constructing the RNSG index and processing RFANN queries with it. Extensive experiments on five real-world datasets show that RNSG achieves significantly higher query performance with a more compact index and lower construction cost than existing state-of-the-art methods.