Yangzhe Peng

Yangzhe Peng, Haiquan Qiu, Quanming Yao et al.

LLMs have recently shown strong potential in enhancing node-level tasks on text-attributed graphs (TAGs) by providing explanation features. However, their practical use is severely limited by the high computational and monetary cost of repeated LLM queries. To illustrate, naively generating explanations for all nodes on a medium-sized benchmark like Photo (48k nodes) using a representative method (e.g., TAPE) would consume days of processing time. In this paper, we propose Bilevel-Optimized Sparse Querying (BOSQ), a general framework that selectively leverages LLM-derived explanation features to enhance performance on node-level tasks on TAGs. We design an adaptive sparse querying strategy that selectively decides when to invoke LLMs, avoiding redundant or low-gain queries and significantly reducing computation overhead. Extensive experiments on six real-world TAG datasets involving two types of node-level tasks demonstrate that BOSQ achieves orders of magnitude speedups over existing GraphLLM methods while consistently delivering on-par or superior performance.

Yangzhe Peng, Kaiyuan Gao, Liang He et al.

Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due to their strong, enduring binding nature. However, most existing docking methods and deep learning approaches hardly account for the formation of covalent bonds and the associated structural changes. To address this gap, we introduce a comprehensive benchmark for covalent docking, CovDocker, which is designed to better capture the complexities of covalent binding. We decompose the covalent docking process into three main tasks: reactive location prediction, covalent reaction prediction, and covalent docking. By adapting state-of-the-art models, such as Uni-Mol and Chemformer, we establish baseline performances and demonstrate the effectiveness of the benchmark in accurately predicting interaction sites and modeling the molecular transformations involved in covalent binding. These results confirm the role of the benchmark as a rigorous framework for advancing research in covalent drug design. It underscores the potential of data-driven approaches to accelerate the discovery of selective covalent inhibitors and addresses critical challenges in therapeutic development.