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Wenyu Zhu

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4 papers

2 author rows

AAAI Conference 2026 Conference Paper

Learning Protein–Ligand Binding in Hyperbolic Space

Jianhui Wang
Wenyu Zhu
Bowen Gao
Xin Hong
Ya-Qin Zhang
Wei-Ying Ma
Yanyan Lan

Protein-ligand binding prediction is central to virtual screening and affinity ranking, two fundamental tasks in drug discovery. While recent retrieval-based methods embed ligands and protein pockets into Euclidean space for similarity-based search, the geometry of Euclidean embeddings often fails to capture the hierarchical structure and fine-grained affinity variations intrinsic to molecular interactions. In this work, we propose HypSeek, a hyperbolic representation learning framework that embeds ligands, protein pockets, and sequences into Lorentz-model hyperbolic space. By leveraging the exponential geometry and negative curvature of hyperbolic space, HypSeek enables expressive, affinity-sensitive embeddings that can effectively model both global activity and subtle functional differences–particularly in challenging cases such as activity cliffs, where structurally similar ligands exhibit large affinity gaps. Our model unifies virtual screening and affinity ranking in a single framework, introducing a protein-guided three-tower architecture to enhance representational structure. HypSeek improves early enrichment in virtual screening on DUD-E from 42.63 to 51.44 (+20.7%) and affinity ranking correlation on JACS from 0.5774 to 0.7239 (+25.4%), demonstrating the benefits of hyperbolic geometry across both tasks and highlighting its potential as a powerful inductive bias for protein-ligand modeling.

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ICLR Conference 2025 Conference Paper

A Benchmark for Semantic Sensitive Information in LLMs Outputs

Qingjie Zhang
Han Qiu 0001
Di Wang
Yiming Li 0004
Tianwei Zhang 0004
Wenyu Zhu
Haiqin Weng
Liu Yan

Large language models (LLMs) can output sensitive information, which has emerged as a novel safety concern. Previous works focus on structured sensitive information (e.g. personal identifiable information). However, we notice that sensitive information can also be at semantic level, i.e. semantic sensitive information (SemSI). Particularly, *simple natural questions* can let state-of-the-art (SOTA) LLMs output SemSI. %which is hard to be detected compared with structured ones. Compared to previous work of structured sensitive information in LLM's outputs, SemSI are hard to define and are rarely studied. Therefore, we propose a novel and large-scale investigation on the existence of SemSI in SOTA LLMs induced by simple natural questions. First, we construct a comprehensive and labeled dataset of semantic sensitive information, SemSI-Set, by including three typical categories of SemSI. Then, we propose a large-scale benchmark, SemSI-Bench, to systematically evaluate semantic sensitive information in 25 SOTA LLMs. Our finding reveals that SemSI widely exists in SOTA LLMs' outputs by querying with simple natural questions. We open-source our project at https://semsi-project.github.io/.

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NeurIPS Conference 2025 Conference Paper

AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation

Wenyu Zhu
Jianhui Wang
Bowen Gao
Yinjun Jia
Haichuan Tan
Ya-Qin Zhang
Wei-Ying Ma
Yanyan Lan

Virtual screening (VS) is a critical component of modern drug discovery, yet most existing methods—whether physics-based or deep learning-based—are developed around holo protein structures with known ligand-bound pockets. Consequently, their performance degrades significantly on apo or predicted structures such as those from AlphaFold2, which are more representative of real-world early-stage drug discovery, where pocket information is often missing. In this paper, we introduce an alignment-and-aggregation framework to enable accurate virtual screening under structural uncertainty. Our method comprises two core components: (1) a tri-modal contrastive learning module that aligns representations of the ligand, the holo pocket, and cavities detected from structures, thereby enhancing robustness to pocket localization error; and (2) a cross-attention based adapter for dynamically aggregating candidate binding sites, enabling the model to learn from activity data even without precise pocket annotations. We evaluated our method on a newly curated benchmark of apo structures, where it significantly outperforms state-of-the-art methods in blind apo setting, improving the early enrichment factor (EF1\%) from 11. 75 to 37. 19. Notably, it also maintains strong performance on holo structures. These results demonstrate the promise of our approach in advancing first-in-class drug discovery, particularly in scenarios lacking experimentally resolved protein-ligand complexes. Our implementation is publicly available at https: //github. com/Wiley-Z/AANet.

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NeurIPS Conference 2025 Conference Paper

FIGRDock: Fast Interaction-Guided Regression for Flexible Docking

Shikun Feng
Bicheng Lin
Yuanhuan Mo
Yuyan Ni
Wenyu Zhu
Bowen Gao
Wei-Ying Ma
Haitao Li

Flexible docking, which predicts the binding conformations of both proteins and small molecules by modeling their structural flexibility, plays a vital role in structure-based drug design. Although recent generative approaches, particularly diffusion-based models, have shown promising results, they require iterative sampling to generate candidate structures and depend on separate scoring functions for pose selection. This leads to an inefficient pipeline that is difficult to scale in real-world drug discovery workflows. To overcome these challenges, we introduce FIGRDock, a fast and accurate flexible docking framework that understands complicated interactions between molecules and proteins with a regression-based approach. FIGRDock leverages initial docking poses from conventional tools to distill interaction-aware distance patterns, which serve as explicit structural conditions to directly guide the prediction of the final protein-ligand complex via a regression model. This one-shot inference paradigm enables rapid and precise pose prediction without reliance on multi-step sampling or external scoring stages. Experimental results show that FIGRDock achieves up to 100× faster inference than diffusion-based docking methods, while consistently surpassing them in accuracy across standard benchmarks. These results suggest that FIGRDock has the potential to offer a scalable and efficient solution for flexible docking, advancing the pace of structure-based drug discovery.

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