Ruiyi Fang

Shuo Wang, Xiangyu Wang, Quanxin Wang et al.

Current evaluation practices in relational learning rely heavily on flat leaderboards that average performance across heterogeneous datasets, implicitly assuming a uniform underlying structure. We show that this assumption introduces systematic bias: it obscures geometry-dependent performance variations and can lead to misleading conclusions about model generalization. In this work, we identify intrinsic geometry as a key latent factor governing model effectiveness. We demonstrate that conventional aggregated metrics mask critical performance trade-offs that only become visible when datasets are stratified by their geometric properties. To address this issue, we introduce a curvature-stratified evaluation framework that partitions datasets into positive, negative, and near-zero curvature regimes. Our benchmark evaluates 18 representative models including Graph Convolutional Networks (GCNs), Graph Foundation Models (GFMs), and tabular learning methods across 14 datasets. We find that model rankings are highly stable within each curvature regime but shift significantly across regimes, indicating that performance is fundamentally geometry-dependent rather than universally transferable. Notably, we identify regimes where GFMs offer diminishing returns compared to geometry-aligned GNNs. Based on these findings, we propose a geometry-aware evaluation protocol that yields more reliable and interpretable comparisons than standard aggregated benchmarks. We release all code, curvature-stratified dataset splits, and evaluation tools to support reproducible and rigorous assessment of future relational learning methods. Code and datasets are provided in our project homepage: https://sirbabbage.github.io/CurvBench_HOME/.

Xiaodong He, Haolan He, Ruiyi Fang et al.

Graph foundation models (GFMs) seek transferable representations across graph domains but are limited by structural heterogeneity and incompatible node feature spaces. We propose Structure-Centric Graph Foundation Models (SCGFM), which treat graph topology as the primary source of transferable knowledge. Modeling graphs as metric measure spaces, SCGFM introduces learnable geometric bases that define a shared structural coordinate system. Graphs are aligned to these bases via Gromov-Wasserstein distances, yielding structure-aligned latent representations that accommodate heterogeneous graph topologies. To address feature incompatibility, SCGFM employs a structure-aware feature re-encoding mechanism that unifies node representations without assuming a fixed feature dimensionality or requiring dataset-specific preprocessing. Experiments on graph- and node-level tasks demonstrate strong in-domain and cross-domain generalization, outperforming existing GFM approaches.

Zihao Jing, Qiuhao Zeng, Ruiyi Fang et al.

Large language models (LLMs) are enabling reasoning over biomolecular structures, yet existing methods remain modality-specific and typically compress structural inputs through sequence-based tokenization or fixed-length query connectors. Such architectures either omit the geometric groundings requisite for mitigating structural hallucinations or impose inflexible modality fusion bottlenecks that concurrently over-compress and suboptimally allocate structural tokens, thereby impeding the realization of generalized all-atom reasoning. We introduce Cuttlefish, a unified all-atom LLM that grounds language reasoning in geometric cues while scaling modality tokens with structural complexity. First, Scaling-Aware Patching leverages an instruction-conditioned gating mechanism to generate variable-size patches over structural graphs, adaptively scaling the query token budget with structural complexity to mitigate fixed-length connector bottlenecks. Second, Geometry Grounding Adapter refines these adaptive tokens via cross-attention to modality embeddings and injects the resulting modality tokens into the LLM, exposing explicit geometric cues to reduce structural hallucination. Experiments across diverse all-atom benchmarks demonstrate that Cuttlefish achieves superior performance in heterogeneous structure-grounded reasoning. Code is available at the project repository.

Jiale Cai, Gezheng Xu, Zhihao Li et al.

Unlearnable examples (UEs) protect training data by injecting imperceptible perturbations so that models fail to extract exploitable representations. In this paper, we reveal that existing UEs exhibit a critical failure once low-pass filtering is applied, indicating that the effective perturbation signals for unlearnability concentrate predominantly in high frequencies. Hence, we argue that reliable UEs should remain effective across the full spectrum. To this end, we propose Full-spectrum Unlearnable examples via Spectral Equalization (FUSE), which aims to generate spectrum-agnostic perturbations by equalizing the contributions from different bands and enforcing cross-band consistency. Specifically, FUSE adopts a Random Spectral Masking (RSM) strategy during generator training, which randomly removes a contiguous frequency band, forcing the remaining bands to maintain unlearnability. In addition, FUSE further integrates Cross-Band Guidance (CBG), which enforces mutual consistency between high- and low-frequency components, thereby further enhancing low-frequency unlearnability and regulating high-frequency perturbations to preserve the semantic fidelity of images. Extensive experiments across multiple datasets, architectures, and spectral filtering demonstrate the strong protection achieved by FUSE.

Bingheng Li, Xuanting Xie, Haoxiang Lei et al.

Graph Neural Networks (GNNs) have garnered significant attention for their success in learning the representation of homophilic or heterophilic graphs. However, they cannot generalize well to real-world graphs with different levels of homophily. In response, the Possion-Charlier Network (PCNet) \cite{li2024pc}, the previous work, allows graph representation to be learned from heterophily to homophily. Although PCNet alleviates the heterophily issue, there remain some challenges in further improving the efficacy and efficiency. In this paper, we simplify PCNet and enhance its robustness. We first extend the filter order to continuous values and reduce its parameters. Two variants with adaptive neighborhood sizes are implemented. Theoretical analysis shows our model's robustness to graph structure perturbations or adversarial attacks. We validate our approach through semi-supervised learning tasks on various datasets representing both homophilic and heterophilic graphs.

Zhihao Li, Gezheng Xu, Jiale Cai et al.

Unlearnable Examples (UEs) serve as a data protection strategy that generates imperceptible perturbations to mislead models into learning spurious correlations instead of underlying semantics. In this paper, we uncover a fundamental vulnerability of UEs that emerges when learning starts from a pretrained model. Crucially, our empirical analysis shows that even when data are protected by carefully crafted perturbations, pretraining priors still furnish rich semantic representations that allow the model to circumvent the shortcuts introduced by UEs and capture genuine features, thereby nullifying unlearnability. To address this, we propose BAIT (Binding Artificial perturbations to Incorrect Targets), a novel bi-level optimization formulation. Specifically, the inner level aims at associating the perturbed samples with real labels to simulate standard data-label alignment, while the outer level actively disrupts this alignment by enforcing a mislabel-perturbation binding that maps samples to designated incorrect targets. This mechanism effectively overrides the semantic guidance of priors, forcing the model to rely on the injected perturbations and consequently preventing the acquisition of true semantics. Extensive experiments on standard benchmarks and multiple pretrained backbones demonstrate that BAIT effectively mitigates the influence of pretraining priors and maintains data unlearnability.

Zihao Jing, Qiuhao Zeng, Ruiyi Fang et al.

Molecular understanding is central to advancing areas such as scientific discovery, yet Large Language Models (LLMs) struggle to understand molecular graphs effectively. Existing graph-LLM bridges often adapt the Q-Former-style connector with fixed-length static tokens, which is originally designed for vision tasks. These designs overlook stereochemistry and substructural context and typically require costly LLM-backbone fine-tuning, limiting efficiency and generalization. We introduce EDT-Former, an Entropy-guided Dynamic Token Transformer that generates tokens aligned with informative molecular patches, thereby preserving both local and global structural features for molecular graph understanding. Beyond prior approaches, EDT-Former enables alignment between frozen graph encoders and LLMs without tuning the LLM backbone (excluding the embedding layer), resulting in computationally efficient finetuning, and achieves stateof-the-art results on MoleculeQA, Molecule-oriented Mol-Instructions, and property prediction benchmarks (TDC, MoleculeNet), underscoring its effectiveness for scalable and generalizable multimodal molecular understanding