Peijin Guo

Lulu Xue, Shengshan Hu, Linqiang Qian et al.

Machine unlearning is a newly popularized technique for removing specific training data from a trained model, enabling it to comply with data deletion requests. While it protects the rights of users requesting unlearning, it also introduces new privacy risks. Prior works have primarily focused on the privacy of data that has been unlearned, while the risks to retained data remain largely unexplored. To address this gap, we focus on the privacy risks of retained data and, for the first time, reveal the vulnerabilities introduced by machine unlearning under the dual-view setting, where an adversary can query both the original and the unlearned models. From an information-theoretic perspective, we introduce the concept of {privacy knowledge gain} and demonstrate that the dual-view setting allows adversaries to obtain more information than querying either model alone, thereby amplifying privacy leakage. To effectively demonstrate this threat, we propose DVIA, a Dual-View Inference Attack, which extracts membership information on retained data using black-box queries to both models. DVIA eliminates the need to train an attack model and employs a lightweight likelihood ratio inference module for efficient inference. Experiments across different datasets and model architectures validate the effectiveness of DVIA and highlight the privacy risks inherent in the dual-view setting.

Minghui Li, Yuanhang Wang, Peijin Guo et al.

Accurate prediction of Drug-Target Affinity (DTA) is crucial for reducing experimental costs and accelerating early screening in computational drug discovery. While sequence-based deep learning methods avoid reliance on costly 3D structures, they still overlook simultaneous modeling of global sequence semantic features and local topological structural features within drugs and proteins, and represent drugs as flat sequences without atomic-level, substructural-level, and molecular-level multi-scale features. We propose HiF-DTA, a hierarchical network that adopts a dual-pathway strategy to extract both global sequence semantic and local topological features from drug and protein sequences, and models drugs multi-scale to learn atomic, substructural, and molecular representations fused via a multi-scale bilinear attention module. Experiments on Davis, KIBA, and Metz datasets show HiF-DTA outperforms state-of-the-art baselines, with ablations confirming the importance of global-local extraction and multi-scale fusion.

Peijin Guo, Minghui Li, Hewen Pan et al.

While deep learning models play a crucial role in predicting antibody-antigen interactions (AAI), the scarcity of publicly available sequence-structure pairings constrains their generalization. Current AAI methods often focus on residue-level static details, overlooking fine-grained structural representations of antibodies and their inter-antibody similarities. To tackle this challenge, we introduce a multi-modality representation approach that integates 3D structural and 1D sequence data to unravel intricate intra-antibody hierarchical relationships. By harnessing these representations, we present MuLAAIP, an AAI prediction framework that utilizes graph attention networks to illuminate graph-level structural features and normalized adaptive graph convolution networks to capture inter-antibody sequence associations. Furthermore, we have curated an AAI benchmark dataset comprising both structural and sequence information along with interaction labels. Through extensive experiments on this benchmark, our results demonstrate that MuLAAIP outperforms current state-of-the-art methods in terms of predictive performance. The implementation code and dataset are publicly available at https://github.com/trashTian/MuLAAIP for reproducibility.

Minghui Li, Zikang Guo, Yang Wu et al.

Drug-target interaction is fundamental in understanding how drugs affect biological systems, and accurately predicting drug-target affinity (DTA) is vital for drug discovery. Recently, deep learning methods have emerged as a significant approach for estimating the binding strength between drugs and target proteins. However, existing methods simply utilize the drug's local information from molecular topology rather than global information. Additionally, the features of drugs and proteins are usually fused with a simple concatenation operation, limiting their effectiveness. To address these challenges, we proposed ViDTA, an enhanced DTA prediction framework. We introduce virtual nodes into the Graph Neural Network (GNN)-based drug feature extraction network, which acts as a global memory to exchange messages more efficiently. By incorporating virtual graph nodes, we seamlessly integrate local and global features of drug molecular structures, expanding the GNN's receptive field. Additionally, we propose an attention-based linear feature fusion network for better capturing the interaction information between drugs and proteins. Experimental results evaluated on various benchmarks including Davis, Metz, and KIBA demonstrate that our proposed ViDTA outperforms the state-of-the-art baselines.

Yichen Wang, Hangtao Zhang, Hewen Pan et al.

Vision-Language Models (VLMs), with their strong reasoning and planning capabilities, are widely used in embodied decision-making (EDM) tasks in embodied agents, such as autonomous driving and robotic manipulation. Recent research has increasingly explored adversarial attacks on VLMs to reveal their vulnerabilities. However, these attacks either rely on overly strong assumptions, requiring full knowledge of the victim VLM, which is impractical for attacking VLM-based agents, or exhibit limited effectiveness. The latter stems from disrupting most semantic information in the image, which leads to a misalignment between the perception and the task context defined by system prompts. This inconsistency interrupts the VLM's reasoning process, resulting in invalid outputs that fail to affect interactions in the physical world. To this end, we propose a fine-grained adversarial attack framework, ADVEDM, which modifies the VLM's perception of only a few key objects while preserving the semantics of the remaining regions. This attack effectively reduces conflicts with the task context, making VLMs output valid but incorrect decisions and affecting the actions of agents, thus posing a more substantial safety threat in the physical world. We design two variants of based on this framework, ADVEDM-R and ADVEDM-A, which respectively remove the semantics of a specific object from the image and add the semantics of a new object into the image. The experimental results in both general scenarios and EDM tasks demonstrate fine-grained control and excellent attack performance.

Peijin Guo, Minghui Li, Hewen Pan et al.

Accurate prediction of molecular metabolic stability (MS) is critical for drug research and development but remains challenging due to the complex interplay of molecular interactions. Despite recent advances in graph neural networks (GNNs) for MS prediction, current approaches face two critical limitations: (1) incomplete molecular modeling due to atom-centric message-passing mechanisms that disregard bond-level topological features, and (2) prediction frameworks that lack reliable uncertainty quantification. To address these challenges, we propose TrustworthyMS, a novel contrastive learning framework designed for uncertainty-aware metabolic stability prediction. First, a molecular graph topology remapping mechanism synchronizes atom-bond interactions through edge-induced feature propagation, capturing both localized electronic effects and global conformational constraints. Second, contrastive topology-bond alignment enforces consistency between molecular topology views and bond patterns via feature alignment, enhancing representation robustness. Third, uncertainty modeling through Beta-Binomial uncertainty quantification enables simultaneous prediction and confidence calibration under epistemic uncertainty. Through extensive experiments, our results demonstrate that TrustworthyMS outperforms current state-of-the-art methods in terms of predictive performance.