arXiv subjects

Yuan Fang

Publications and source records attributed to Yuan Fang.

2 recordsLinked to original sources

arXiv2026

HeTGB: A Comprehensive Benchmark for Heterophilic Text-Attributed Graphs

Graph neural networks (GNNs) have demonstrated success in modeling relational data primarily under the assumption of homophily. However, many real-world graphs exhibit heterophily, where linked nodes belong to different categories or possess diverse attributes, such as webpages, Wikipedia articles, social networks, and e-commerce platforms. Additionally, nodes in many domains are associated with textual descriptions, forming heterophilic text-attributed graphs (TAGs). Despite their significance, heterophilic TAGs remain underexplored due to the lack of dedicated benchmarks that jointly capture heterophilic structures and rich textual attributes. To address this gap, we introduce the \textbf{He}terophilic \textbf{T}ext-attributed \textbf{G}raph \textbf{B}enchmark (HeTGB), a novel benchmark comprising five real-world heterophilic graph datasets from diverse domains, with nodes enriched by extensive textual descriptions. HeTGB enables systematic evaluation of GNNs, pre-trained language models (PLMs) and co-training methods on the node classification task. Through extensive benchmarking experiments, we showcase the utility of text attributes in heterophilic graphs, analyze the challenges posed by heterophilic TAGs and the limitations of existing models, and provide insights into the interplay between graph structures and textual attributes.

cs.CL↗

arXiv2026

MolGA: Molecular Graph Adaptation with Pre-trained 2D Graph Encoder

Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated strong performance, they overlook the rich molecular domain knowledge associated with submolecular instances (atoms and bonds). While molecular pre-training approaches incorporate such knowledge into their pre-training objectives, they typically employ designs tailored to a specific type of knowledge, lacking the flexibility to integrate diverse knowledge present in molecules. Hence, reusing widely available and well-validated pre-trained 2D encoders, while incorporating molecular domain knowledge during downstream adaptation, offers a more practical alternative. In this work, we propose MolGA, which adapts pre-trained 2D graph encoders to downstream molecular applications by flexibly incorporating diverse molecular domain knowledge. First, we propose a molecular alignment strategy that bridge the gap between pre-trained topological representations with domain-knowledge representations. Second, we introduce a conditional adaptation mechanism that generates instance-specific tokens to enable fine-grained integration of molecular domain knowledge for downstream tasks. Finally, we conduct extensive experiments on eleven public datasets, demonstrating the effectiveness of MolGA.

cs.LG↗