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Bowei He

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7 papers

2 author rows

AAAI Conference 2026 Conference Paper

S²Drug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening

Bowei He
Bowen Gao
Yankai Chen
Yanyan Lan
Chen Ma
Philip S. Yu
Ya-Qin Zhang
Wei-Ying Ma

Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent contrastive learning approaches, primarily rely on structural data while overlooking protein sequences, which are more accessible and can enhance generalizability. However, directly integrating protein sequences poses challenges due to the redundancy and noise in large-scale protein-ligand datasets. To address these limitations, we propose S²Drug, a two-stage framework that explicitly incorporates protein Sequence information and 3D Structure context in protein-ligand contrastive representation learning. In the first stage, we perform protein sequence pretraining on ChemBL using an ESM2-based backbone, combined with a tailored data sampling strategy to reduce redundancy and noise on both protein and ligand sides. In the second stage, we fine-tune on PDBBind by fusing sequence and structure information through a residue-level gating module, while introducing an auxiliary binding site prediction task. This auxiliary task guides the model to accurately localize binding residues within the protein sequence and capture their 3D spatial arrangement, thereby refining protein-ligand matching. Across multiple benchmarks, S²Drug consistently improves virtual screening performance and achieves strong results on binding site prediction, demonstrating the value of bridging sequence and structure in contrastive learning.

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ICLR Conference 2025 Conference Paper

Certifying Language Model Robustness with Fuzzed Randomized Smoothing: An Efficient Defense Against Backdoor Attacks

Bowei He
Lihao Yin
Hui-Ling Zhen
Jianping Zhang 0002
Lanqing Hong
Mingxuan Yuan
Chen Ma 0001

The widespread deployment of pre-trained language models (PLMs) has exposed them to textual backdoor attacks, particularly those planted during the pre-training stage. These attacks pose significant risks to high-reliability applications, as they can stealthily affect multiple downstream tasks. While certifying robustness against such threats is crucial, existing defenses struggle with the high-dimensional, interdependent nature of textual data and the lack of access to original poisoned pre-training data. To address these challenges, we introduce **F**uzzed **R**andomized **S**moothing (**FRS**), a novel approach for efficiently certifying language model robustness against backdoor attacks. FRS integrates software robustness certification techniques with biphased model parameter smoothing, employing Monte Carlo tree search for proactive fuzzing to identify vulnerable textual segments within the Damerau-Levenshtein space. This allows for targeted and efficient text randomization, while eliminating the need for access to poisoned training data during model smoothing. Our theoretical analysis demonstrates that FRS achieves a broader certified robustness radius compared to existing methods. Extensive experiments across various datasets, model configurations, and attack strategies validate FRS's superiority in terms of defense efficiency, accuracy, and robustness.

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NeurIPS Conference 2025 Conference Paper

CIDD: Collaborative Intelligence for Structure-Based Drug Design Empowered by LLMs

Bowen Gao
Yanwen Huang
Yiqiao Liu
Wenxuan Xie
Bowei He
Haichuan Tan
Wei-Ying Ma
Ya-Qin Zhang

Structure-guided molecular generation is pivotal in early-stage drug discovery, enabling the design of compounds tailored to specific protein targets. However, despite recent advances in 3D generative modeling, particularly in improving docking scores, these methods often produce rare and intrinsically irrational molecular structures that deviate from drug-like chemical space. To quantify this issue, we propose a novel metric, the Molecule Reasonable Ratio (MRR), which measures structural rationality and reveals a critical gap between existing models and real-world approved drugs. To address this, we introduce the Collaborative Intelligence Drug Design (CIDD) framework, the first approach to unify the 3D interaction modeling capabilities of generative models with the general knowledge and reasoning power of large language models (LLMs). By leveraging LLM-based Chain-of-Thought reasoning, CIDD generates molecules that not only bind effectively to protein pockets but also exhibit strong structural drug-likeness, rationality, and synthetic accessibility. On the CrossDocked2020 benchmark, CIDD consistently improves drug-likeness metrics, including QED, SA, and MRR, across different base generative models, while maintaining competitive binding affinity. Notably, it raises the combined success rate (balancing drug-likeness and binding) from 15. 72% to 34. 59%, more than doubling previous results. These findings demonstrate the value of integrating knowledge reasoning with geometric generation to advance AI-driven drug design.

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NeurIPS Conference 2025 Conference Paper

Preserving LLM Capabilities through Calibration Data Curation: From Analysis to Optimization

Bowei He
Lihao Yin
Hui-Ling Zhen
Shuqi LIU
Han Wu
Xiaokun Zhang
Mingxuan Yuan
Chen Ma

Post-training compression has been a widely employed approach to scale down large language model (LLM) and facilitate efficient inference. In various proposed compression methods, including pruning and quantization, calibration data plays a vital role by informing the weight importance and activation dynamic ranges. However, how calibration data impacts the LLM capability after compression is less explored. Few of the existing works, though recognizing the significance of this study, only investigate the language modeling or commonsense reasoning performance degradation from limited angles, like the data sources or sample amounts. More systematic research is still needed to examine the impacts on different LLM capabilities in terms of compositional properties and domain correspondence of calibration data. In this work, we aim at bridging this gap and further analyze underlying influencing mechanisms from the activation pattern perspective. Especially, we explore the calibration data's impacts on high-level complex reasoning capabilities, like math problem solving and code generation. Delving into the underlying mechanism, we find that the representativeness and diversity in activation space more fundamentally determine the quality of calibration data. Finally, we propose a calibration data curation framework based on such observations and analysis, enhancing the performance of existing post-training compression methods on preserving critical LLM capabilities. Our code is provided in Link.

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NeurIPS Conference 2025 Conference Paper

Semantic Retrieval Augmented Contrastive Learning for Sequential Recommendation

Ziqiang Cui
Yunpeng Weng
Xing Tang
Xiaokun Zhang
Shiwei Li
Peiyang Liu
Bowei He
Dugang Liu

Contrastive learning has shown effectiveness in improving sequential recommendation models. However, existing methods still face challenges in generating high-quality contrastive pairs: they either rely on random perturbations that corrupt user preference patterns or depend on sparse collaborative data that generates unreliable contrastive pairs. Furthermore, existing approaches typically require predefined selection rules that impose strong assumptions, limiting the model's ability to autonomously learn optimal contrastive pairs. To address these limitations, we propose a novel approach named Semantic Retrieval Augmented Contrastive Learning (SRA-CL). SRA-CL leverages the semantic understanding and reasoning capabilities of LLMs to generate expressive embeddings that capture both user preferences and item characteristics. These semantic embeddings enable the construction of candidate pools for inter-user and intra-user contrastive learning through semantic-based retrieval. To further enhance the quality of the contrastive samples, we introduce a learnable sample synthesizer that optimizes the contrastive sample generation process during model training. SRA-CL adopts a plug-and-play design, enabling seamless integration with existing sequential recommendation architectures. Extensive experiments on four public datasets demonstrate the effectiveness and model-agnostic nature of our approach. Our code is available at https: //github. com/ziqiangcui/SRA-CL

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UAI Conference 2023 Conference Paper

MMEL: A Joint Learning Framework for Multi-Mention Entity Linking

Chengmei Yang
Bowei He
Yimeng Wu
Chao Xing
Lianghua He
Chen Ma 0001

Entity linking, bridging mentions in the contexts with their corresponding entities in the knowledge bases, has attracted wide attention due to many potential applications. Recently, plenty of multimodal entity linking approaches have been proposed to take full advantage of the visual information rather than solely the textual modality. Although feasible, these methods mainly focus on the single-mention scenarios and neglect the scenarios where multiple mentions exist simultaneously in the same context, which limits the performance. In fact, such multi-mention scenarios are pretty common in public datasets and real-world applications. To solve this challenge, we first propose a joint feature extraction module to learn the representations of context and entity candidates, from both the visual and textual perspectives. Then, we design a pairwise training scheme (for training) and a multi-mention collaborative ranking method (for testing) to model the potential connections between different mentions. We evaluate our method on a public dataset and a self-constructed dataset, NYTimes-MEL, under both text-only and multimodal scenarios. The experimental results demonstrate that our method can largely outperform the state-of-the-art methods, especially in multi-mention scenarios. Our dataset and source code are publicly available at https: //github. com/ycm094/MMEL-main.

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NeurIPS Conference 2023 Conference Paper

Offline Imitation Learning with Variational Counterfactual Reasoning

Zexu Sun
Bowei He
Jinxin Liu
Xu Chen
Chen Ma
Shuai Zhang

In offline imitation learning (IL), an agent aims to learn an optimal expert behavior policy without additional online environment interactions. However, in many real-world scenarios, such as robotics manipulation, the offline dataset is collected from suboptimal behaviors without rewards. Due to the scarce expert data, the agents usually suffer from simply memorizing poor trajectories and are vulnerable to the variations in the environments, lacking the capability of generalizing to new environments. To automatically generate high-quality expert data and improve the generalization ability of the agent, we propose a framework named \underline{O}ffline \underline{I}mitation \underline{L}earning with \underline{C}ounterfactual data \underline{A}ugmentation (OILCA) by doing counterfactual inference. In particular, we leverage identifiable variational autoencoder to generate \textit{counterfactual} samples for expert data augmentation. We theoretically analyze the influence of the generated expert data and the improvement of generalization. Moreover, we conduct extensive experiments to demonstrate that our approach significantly outperforms various baselines on both \textsc{DeepMind Control Suite} benchmark for in-distribution performance and \textsc{CausalWorld} benchmark for out-of-distribution generalization.

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