RoleMAG: Learning Neighbor Roles in Multimodal Graphs

Multimodal attributed graphs (MAGs) combine multimodal node attributes with structured relations. However, existing methods usually perform shared message passing on a single graph and implicitly assume that the same neighbors are equally useful for all modalities. In practice, neighbors that benefit one modality may interfere with another, blurring modality-specific signals under shared propagation. To address this issue, we propose RoleMAG, a multimodal graph framework that learns how different neighbors should participate in propagation. Concretely, RoleMAG distinguishes whether a neighbor should provide shared, complementary, or heterophilous signals, and routes them through separate propagation channels. This enables cross-modal completion from complementary neighbors while keeping heterophilous ones out of shared smoothing. Extensive experiments on three graph-centric MAG benchmarks show that RoleMAG achieves the best results on RedditS and Bili\_Dance, while remaining competitive on Toys. Ablation, robustness, and efficiency analyses further support the effectiveness of the proposed role-aware propagation design. Our code is available at https://anonymous.4open.science/r/RoleMAG-7EE0/

TMTE: Effective Multimodal Graph Learning with Task-aware Modality and Topology Co-evolution

Multimodal-attributed graphs (MAGs) are a fundamental data structure for multimodal graph learning (MGL), enabling both graph-centric and modality-centric tasks. However, our empirical analysis reveals inherent topology quality limitations in real-world MAGs, including noisy interactions, missing connections, and task-agnostic relational structures. A single graph derived from generic relationships is therefore unlikely to be universally optimal for diverse downstream tasks. To address this challenge, we propose Task-aware Modality and Topology co-Evolution (TMTE), a novel MGL framework that jointly and iteratively optimizes graph topology and multimodal representations toward the target task. TMTE is motivated by the bidirectional coupling between modality and topology: multimodal attributes induce relational structures, while graph topology shapes modality representations. Concretely, TMTE casts topology evolution as multi-perspective metric learning over modality embeddings with an anchor-based approximation, and formulates modality evolution as smoothness-regularized fusion with cross-modal alignment, yielding a closed-loop task-aware co-evolution process. Extensive experiments on 9 MAG datasets and 1 non-graph multimodal dataset across 6 graph-centric and modality-centric tasks show that TMTE consistently achieves state-of-the-art performance. Our code is available at https://anonymous.4open.science/r/TMTE-1873.

TFPS: A Temporal Filtration-enhanced Positive Sample Set Construction Method for Implicit Collaborative Filtering

The negative sampling strategy can effectively train collaborative filtering (CF) recommendation models based on implicit feedback by constructing positive and negative samples. However, existing methods primarily optimize the negative sampling process while neglecting the exploration of positive samples. Some denoising recommendation methods can be applied to denoise positive samples within negative sampling strategies, but they ignore temporal information. Existing work integrates sequential information during model aggregation but neglects time interval information, hindering accurate capture of users' current preferences. To address this problem, from a data perspective, we propose a novel temporal filtration-enhanced approach to construct a high-quality positive sample set. First, we design a time decay model based on interaction time intervals, transforming the original graph into a weighted user-item bipartite graph. Then, based on predefined filtering operations, the weighted user-item bipartite graph is layered. Finally, we design a layer-enhancement strategy to construct a high-quality positive sample set for the layered subgraphs. We provide theoretical insights into why TFPS can improve Recall@k and NDCG@k, and extensive experiments on three real-world datasets demonstrate the effectiveness of the proposed method. Additionally, TFPS can be integrated with various implicit CF recommenders or negative sampling methods to enhance its performance.

OpenMAG: A Comprehensive Benchmark for Multimodal-Attributed Graph

Multimodal-Attributed Graph (MAG) learning has achieved remarkable success in modeling complex real-world systems by integrating graph topology with rich attributes from multiple modalities. With the rapid proliferation of novel MAG models capable of handling intricate cross-modal semantics and structural dependencies, establishing a rigorous and unified evaluation standard has become imperative. Although existing benchmarks have facilitated initial progress, they exhibit critical limitations in domain coverage, encoder flexibility, model diversity, and task scope, presenting significant challenges to fair evaluation. To bridge this gap, we present OpenMAG, a comprehensive benchmark that integrates 19 datasets across 6 domains and incorporates 16 encoders to support both static and trainable feature encoding. OpenMAG further implements a standardized library of 24 state-of-the-art models and supports 8 downstream tasks, enabling fair comparisons within a unified framework. Through systematic assessment of necessity, data quality, effectiveness, robustness, and efficiency, we derive 14 fundamental insights into MAG learning to guide future advancements. Our code is available at https://github.com/YUKI-N810/OpenMAG.

Toward Effective Multimodal Graph Foundation Model: A Divide-and-Conquer Based Approach

Graph Foundation Models (GFMs) have achieved remarkable success in generalizing across diverse domains. However, they mainly focus on Text-Attributed Graphs (TAGs), leaving Multimodal-Attributed Graphs (MAGs) largely untapped. Developing Multimodal Graph Foundation Models (MGFMs) allows for leveraging the rich multimodal information in MAGs, and extends applicability to broader types of downstream tasks. While recent MGFMs integrate diverse modality information, our empirical investigation reveals two fundamental limitations of existing MGFMs: (1)they fail to explicitly model modality interaction, essential for capturing intricate cross-modal semantics beyond simple aggregation, and (2)they exhibit sub-optimal modality alignment, which is critical for bridging the significant semantic disparity between distinct modal spaces. To address these challenges, we propose PLANET (graPh topoLogy-aware modAlity iNteraction and alignmEnT), a novel framework employing a Divide-and-Conquer strategy to decouple modality interaction and alignment across distinct granularities. At the embedding granularity, (1)Embedding-wise Domain Gating (EDG) performs local semantic enrichment by adaptively infusing topology-aware cross-modal context, achieving modality interaction. At the node granularity, (2)Node-wise Discretization Retrieval (NDR) ensures global modality alignment by constructing a Discretized Semantic Representation Space (DSRS) to bridge modality gaps. Extensive experiments demonstrate that PLANET significantly outperforms state-of-the-art baselines across diverse graph-centric and multimodal generative tasks.

DOGMA: Weaving Structural Information into Data-centric Single-cell Transcriptomics Analysis

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.

OpenDDI: A Comprehensive Benchmark for DDI Prediction

Drug-Drug Interactions (DDIs) significantly influence therapeutic efficacy and patient safety. As experimental discovery is resource-intensive and time-consuming, efficient computational methodologies have become essential. The predominant paradigm formulates DDI prediction as a drug graph-based link prediction task. However, further progress is hindered by two fundamental challenges: (1) lack of high-quality data: most studies rely on small-scale DDI datasets and single-modal drug representations; (2) lack of standardized evaluation: inconsistent scenarios, varied metrics, and diverse baselines. To address the above issues, we propose OpenDDI, a comprehensive benchmark for DDI prediction. Specifically, (1) from the data perspective, OpenDDI unifies 6 widely used DDI datasets and 2 existing forms of drug representation, while additionally contributing 3 new large-scale LLM-augmented datasets and a new multimodal drug representation covering 5 modalities. (2) From the evaluation perspective, OpenDDI unifies 20 SOTA model baselines across 3 downstream tasks, with standardized protocols for data quality, effectiveness, generalization, robustness, and efficiency. Based on OpenDDI, we conduct a comprehensive evaluation and derive 10 valuable insights for DDI prediction while exposing current limitations to provide critical guidance for this rapidly evolving field. Our code is available at https://github.com/xiaoriwuguang/OpenDDI

Scalable Topology-Preserving Graph Coarsening with Graph Collapse

Graph coarsening reduces the size of a graph while preserving certain properties. Most existing methods preserve either spectral or spatial characteristics. Recent research has shown that preserving topological features helps maintain the predictive performance of graph neural networks (GNNs) trained on the coarsened graph but suffers from exponential time complexity. To address these problems, we propose Scalable Topology-Preserving Graph Coarsening (STPGC) by introducing the concepts of graph strong collapse and graph edge collapse extended from algebraic topology. STPGC comprises three new algorithms, GStrongCollapse, GEdgeCollapse, and NeighborhoodConing based on these two concepts, which eliminate dominated nodes and edges while rigorously preserving topological features. We further prove that STPGC preserves the GNN receptive field and develop approximate algorithms to accelerate GNN training. Experiments on node classification with GNNs demonstrate the efficiency and effectiveness of STPGC.

OptiMAG: Structure-Semantic Alignment via Unbalanced Optimal Transport

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.

MM-OpenFGL: A Comprehensive Benchmark for Multimodal Federated Graph Learning

Multimodal-attributed graphs (MMAGs) provide a unified framework for modeling complex relational data by integrating heterogeneous modalities with graph structures. While centralized learning has shown promising performance, MMAGs in real-world applications are often distributed across isolated platforms and cannot be shared due to privacy concerns or commercial constraints. Federated graph learning (FGL) offers a natural solution for collaborative training under such settings; however, existing studies largely focus on single-modality graphs and do not adequately address the challenges unique to multimodal federated graph learning (MMFGL). To bridge this gap, we present MM-OpenFGL, the first comprehensive benchmark that systematically formalizes the MMFGL paradigm and enables rigorous evaluation. MM-OpenFGL comprises 19 multimodal datasets spanning 7 application domains, 8 simulation strategies capturing modality and topology variations, 6 downstream tasks, and 57 state-of-the-art methods implemented through a modular API. Extensive experiments investigate MMFGL from the perspectives of necessity, effectiveness, robustness, and efficiency, offering valuable insights for future research on MMFGL.