Kehan Wu

Qizhi Pei, Wei Zhang, Jinhua Zhu et al.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose $\mathbf{BioT5}$, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. $\mathbf{BioT5}$ utilizes SELFIES for $100%$ robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, $\mathbf{BioT5}$ distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at $\href{https://github.com/QizhiPei/BioT5}{Github}$.

Meixi Zheng, Kehan Wu, Yanbo Fan et al.

The transfer-based black-box adversarial attack setting poses the challenge of crafting an adversarial example (AE) on known surrogate models that remain effective against unseen target models. Due to the practical importance of this task, numerous methods have been proposed to address this challenge. However, most previous methods are heuristically designed and intuitively justified, lacking a theoretical foundation. To bridge this gap, we derive a novel transferability bound that offers provable guarantees for adversarial transferability. Our theoretical analysis has the advantages of \textit{(i)} deepening our understanding of previous methods by building a general attack framework and \textit{(ii)} providing guidance for designing an effective attack algorithm. Our theoretical results demonstrate that optimizing AEs toward flat minima over the surrogate model set, while controlling the surrogate-target model shift measured by the adversarial model discrepancy, yields a comprehensive guarantee for AE transferability. The results further lead to a general transfer-based attack framework, within which we observe that previous methods consider only partial factors contributing to the transferability. Algorithmically, inspired by our theoretical results, we first elaborately construct the surrogate model set in which models exhibit diverse adversarial vulnerabilities with respect to AEs to narrow an instantiated adversarial model discrepancy. Then, a \textit{model-Diversity-compatible Reverse Adversarial Perturbation} (DRAP) is generated to effectively promote the flatness of AEs over diverse surrogate models to improve transferability. Extensive experiments on NIPS2017 and CIFAR-10 datasets against various target models demonstrate the effectiveness of our proposed attack.