Wenbin Xing

Mengran Li, Zelin Zang, Wenbin Xing et al.

Understanding how chemical perturbations propagate through biological systems is essential for robust molecular property prediction. While most existing methods focus on chemical structures alone, recent advances highlight the crucial role of cellular responses such as morphology and gene expression in shaping drug effects. However, current cell-aware approaches face two key limitations: (1) modality incompleteness in external biological data, and (2) insufficient modeling of hierarchical dependencies across molecular, cellular, and genomic levels. We propose CHMR (Cell-aware Hierarchical Multi-modal Representations), a robust framework that jointly models local-global dependencies between molecules and cellular responses and captures latent biological hierarchies via a novel tree-structured vector quantization module. Evaluated on nine public benchmarks spanning 728 tasks, CHMR outperforms state-of-the-art baselines, yielding average improvements of 3.6% on classification and 17.2% on regression tasks. These results demonstrate the advantage of hierarchy-aware, multimodal learning for reliable and biologically grounded molecular representations, offering a generalizable framework for integrative biomedical modeling. The code is in https://github.com/limengran98/CHMR.

Mengran Li, Pengyu Zhang, Wenbin Xing et al.

Graphs are a widely used paradigm for representing non-Euclidean data, with applications ranging from social network analysis to biomolecular prediction. While graph learning has achieved remarkable progress, real-world graph data presents a number of challenges that significantly hinder the learning process. In this survey, we focus on four fundamental data-centric challenges: (1) Incompleteness, real-world graphs have missing nodes, edges, or attributes; (2) Imbalance, the distribution of the labels of nodes or edges and their structures for real-world graphs are highly skewed; (3) Cross-domain Heterogeneity, graphs from different domains exhibit incompatible feature spaces or structural patterns; and (4) Dynamic Instability, graphs evolve over time in unpredictable ways. Recently, Large Language Models (LLMs) offer the potential to tackle these challenges by leveraging rich semantic reasoning and external knowledge. This survey focuses on how LLMs can address four fundamental data-centric challenges in graph-structured data, thereby improving the effectiveness of graph learning. For each challenge, we review both traditional solutions and modern LLM-driven approaches, highlighting how LLMs contribute unique advantages. Finally, we discuss open research questions and promising future directions in this emerging interdisciplinary field. To support further exploration, we have curated a repository of recent advances on graph learning challenges: https://github.com/limengran98/Awesome-Literature-Graph-Learning-Challenges.

Mengran Li, Chaojun Ding, Junzhou Chen et al.

Missing attribute issues are prevalent in the graph learning, leading to biased outcomes in Graph Neural Networks (GNNs). Existing methods that rely on feature propagation are prone to cold start problem, particularly when dealing with attribute resetting and low-degree nodes, which hinder effective propagation and convergence. To address these challenges, we propose AttriReBoost (ARB), a novel method that incorporates propagation-based method to mitigate cold start problems in attribute-missing graphs. ARB enhances global feature propagation by redefining initial boundary conditions and strategically integrating virtual edges, thereby improving node connectivity and ensuring more stable and efficient convergence. This method facilitates gradient-free attribute reconstruction with lower computational overhead. The proposed method is theoretically grounded, with its convergence rigorously established. Extensive experiments on several real-world benchmark datasets demonstrate the effectiveness of ARB, achieving an average accuracy improvement of 5.11% over state-of-the-art methods. Additionally, ARB exhibits remarkable computational efficiency, processing a large-scale graph with 2.49 million nodes in just 16 seconds on a single GPU. Our code is available at https://github.com/limengran98/ARB.

Mengran Li, Bo Li, Jiaying Wang et al.

Virtual Cell Modeling (VCM) requires models that not only predict perturbation responses, but also support targeted revision when predictions fail. Current LLM-assisted modeling workflows face a refinement-routing problem: prediction discrepancies are observed through executable implementations, but the relevant revision may involve the modeling assumption, representation design, implementation, or task constraint. Without structured feedback propagation across these levels, iterative refinement may repair code while failing to revise the assumption responsible for the discrepancy. We propose CellScientist, a dual-space hierarchical framework that couples a high-level hypothesis space with a low-level executable implementation space. CellScientist represents modeling decisions as structured states, realizes them as admissible programs under task and interface constraints, and routes execution discrepancies back to targeted hypothesis or implementation updates. This enables a closed Hypothesis -> Implementation -> Hypothesis loop where failures become structured signals for model refinement rather than debugging events. Across morphology and transcriptomic benchmarks, with additional single-cell perturbation evaluations, the final executable models selected by CellScientist improve over reference baselines under fixed split and evaluation protocols, while the workflow produces auditable refinement traces.

Ronghui Zhang, Wenbin Xing, Mengran Li et al.

Accurate and refined passenger flow prediction is essential for optimizing the collaborative management of multiple collection and distribution modes in large-scale transportation hubs. Traditional methods often focus only on the overall passenger volume, neglecting the interdependence between different modes within the hub. To address this limitation, we propose MM-STFlowNet, a comprehensive multi-mode prediction framework grounded in dynamic spatial-temporal graph modeling. Initially, an integrated temporal feature processing strategy is implemented using signal decomposition and convolution techniques to address data spikes and high volatility. Subsequently, we introduce the Spatial-Temporal Dynamic Graph Convolutional Recurrent Network (STDGCRN) to capture detailed spatial-temporal dependencies across multiple traffic modes, enhanced by an adaptive channel attention mechanism. Finally, the self-attention mechanism is applied to incorporate various external factors, further enhancing prediction accuracy. Experiments on a real-world dataset from Guangzhounan Railway Station in China demonstrate that MM-STFlowNet achieves state-of-the-art performance, particularly during peak periods, providing valuable insight for transportation hub management.