Mengran Li

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, 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.

Mengran Li, Junzhou Chen, Chenyun Yu et al.

With the advancement of information technology, the Social Internet of Things (SIoT) has fostered the integration of physical devices and social networks, deepening the study of complex interaction patterns. Text Attribute Graphs (TAGs) capture both topological structures and semantic attributes, enhancing the analysis of complex interactions within the SIoT. However, existing graph learning methods are typically designed for complete attributed graphs, and the common issue of missing attributes in Attribute Missing Graphs (AMGs) increases the difficulty of analysis tasks. To address this, we propose the Topology-Driven Attribute Recovery (TDAR) framework, which leverages topological data for AMG learning. TDAR introduces an improved pre-filling method for initial attribute recovery using native graph topology. Additionally, it dynamically adjusts propagation weights and incorporates homogeneity strategies within the embedding space to suit AMGs' unique topological structures, effectively reducing noise during information propagation. Extensive experiments on public datasets demonstrate that TDAR significantly outperforms state-of-the-art methods in attribute reconstruction and downstream tasks, offering a robust solution to the challenges posed by AMGs. The code is available at https://github.com/limengran98/TDAR.

Chengyang Zhang, Wenchuan Zhang, Bo Li et al.

Recent advances in Multimodal Large Language Models (MLLMs) and agent workflows have shown strong promise for computational pathology, yet reliable patch-level reasoning remains challenging. End-to-end pathology MLLMs often hallucinate morphological features, while recent agentic systems usually merge tool outputs and retrieved knowledge into a shared context, making decisions vulnerable to conflicting evidence and context contamination. We propose PathoSage, a three-stage framework that explicitly separates knowledge retrieval, evidence collection, and evidence adjudication for patch-level pathology multimodal reasoning. Its core component, Structured Evidence Deliberation, independently evaluates heterogeneous evidence from tools, performs conflict analysis, and generates the final judgment in a fresh context to reduce anchoring bias. We further introduce a training-free Beta-Bernoulli experience system with continuous credit assignment to model long-term tool reliability and construct similarity-weighted priors for future tool use. Experiments show that PathoSage effectively mitigates VQA hallucinations and classifier disagreement, outperforming strong pathology MLLM and agentic baselines. Our results highlight explicit evidence adjudication and reliability-aware tool modeling as key ingredients for robust pathology agents.

Chengyang Zhang, Wenchuan Zhang, Bo Li et al.

Pathology vision-language models (VLMs) have recently progressed rapidly and are commonly evaluated by answer accuracy on pathology VQA benchmarks. However, we dig into current evaluations and identify three overlooked issues: 1) Visual evidence is not always necessary. For instance, Gemini-3-Pro achieves 53.5% average accuracy across 5 VQA benchmarks without any visual input. 2) Domain training can improve accuracy without proportional gains in visual binding. Compared with Qwen2.5-VL-7B, Patho-R1-7B exhibits a 5.8-point lower multimodal gain and a 3.7-point lower attention IoU. 3) Entity-level attention is diffuse and weakly query-specific. On PathVG, attention maps remain highly correlated across different entity queries. These issues can lead to substantial misjudgments of pathology VLMs' actual multimodal capabilities. To this end, we present PathBind, a benchmark comprising 2,600 samples: PathBind-VQA with 1,500 questions across six dimensions, PathBind-PTA with 600 questions from a private pathology teaching atlas, and PathBind-Grounding with 500 expert-curated region-level samples. Each component undergoes task-specific automated filtering and expert review to reduce textual shortcuts and improve entity-region correspondence. We evaluate 18 representative VLMs on VQA samples of PathBind and five existing pathology VQA benchmarks, and further evaluate 10 VLMs on PathBind-Grounding and PathVG. Results show that current pathology VLMs still exhibit a substantial gap between answer-side performance and visual-semantic binding.

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.

Mengran Li, Junzhou Chen, Guanying Jiang et al.

Accurately estimating time of arrival (ETA) for trucks is crucial for optimizing transportation efficiency in logistics. GPS trajectory data offers valuable information for ETA, but challenges arise due to temporal sparsity, variable sequence lengths, and the interdependencies among multiple trucks. To address these issues, we propose the Temporal-Attribute-Spatial Tri-space Coordination (TAS-TsC) framework, which leverages three feature spaces-temporal, attribute, and spatial-to enhance ETA. Our framework consists of a Temporal Learning Module (TLM) using state space models to capture temporal dependencies, an Attribute Extraction Module (AEM) that transforms sequential features into structured attribute embeddings, and a Spatial Fusion Module (SFM) that models the interactions among multiple trajectories using graph representation learning.These modules collaboratively learn trajectory embeddings, which are then used by a Downstream Prediction Module (DPM) to estimate arrival times. We validate TAS-TsC on real truck trajectory datasets collected from Shenzhen, China, demonstrating its superior performance compared to existing methods.

Bo Li, Bob Zhang, Chengyang Zhang et al.

In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step procedures, which can introduce inefficiencies, limit generalizability, and increase potential errors. To address these challenges, we present PhenoProfiler, an innovative model designed to efficiently and effectively extract morphological representations, enabling the elucidation of phenotypic changes induced by treatments. PhenoProfiler is designed as an end-to-end tool that processes whole-slide multi-channel images directly into low-dimensional quantitative representations, eliminating the extensive computational steps required by existing methods. It also includes a multi-objective learning module to enhance robustness, accuracy, and generalization in morphological representation learning. PhenoProfiler is rigorously evaluated on large-scale publicly available datasets, including over 230,000 whole-slide multi-channel images in end-to-end scenarios and more than 8.42 million single-cell images in non-end-to-end settings. Across these benchmarks, PhenoProfiler consistently outperforms state-of-the-art methods by up to 20%, demonstrating substantial improvements in both accuracy and robustness. Furthermore, PhenoProfiler uses a tailored phenotype correction strategy to emphasize relative phenotypic changes under treatments, facilitating the detection of biologically meaningful signals. UMAP visualizations of treatment profiles demonstrate PhenoProfiler ability to effectively cluster treatments with similar biological annotations, thereby enhancing interpretability. These findings establish PhenoProfiler as a scalable, generalizable, and robust tool for phenotypic learning.

Xiaochuan Zhang, Mengran Li, Ye Wang et al.

Attribute graphs are ubiquitous in multimedia applications, and graph representation learning (GRL) has been successful in analyzing attribute graph data. However, incomplete graph data and missing node attributes can have a negative impact on media knowledge discovery. Existing methods for handling attribute missing graph have limited assumptions or fail to capture complex attribute-graph dependencies. To address these challenges, we propose Attribute missing Graph Contrastive Learning (AmGCL), a framework for handling missing node attributes in attribute graph data. AmGCL leverages Dirichlet energy minimization-based feature precoding to encode in missing attributes and a self-supervised Graph Augmentation Contrastive Learning Structure (GACLS) to learn latent variables from the encoded-in data. Specifically, AmGCL utilizies feature reconstruction based on structure-attribute energy minimization while maximizes the lower bound of evidence for latent representation mutual information. Our experimental results on multiple real-world datasets demonstrate that AmGCL outperforms state-of-the-art methods in both feature imputation and node classification tasks, indicating the effectiveness of our proposed method in real-world attribute graph analysis tasks.