Shang Shang

Can Chen, Karla-Luise Herpoldt, Chenchao Zhao et al.

Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity.This paper explores a sequence-only scenario for affinity maturation, using solely antibody and antigen sequences. Recently AlphaFlow wraps AlphaFold within flow matching to generate diverse protein structures, enabling a sequence-conditioned generative model of structure. Building on this, we propose an alternating optimization framework that (1) fixes the sequence to guide structure generation toward high binding affinity using a structure-based affinity predictor, then (2) applies inverse folding to create sequence mutations, refined by a sequence-based affinity predictor for post selection. A key challenge is the lack of labeled data for training both predictors. To address this, we develop a co-teaching module that incorporates valuable information from noisy biophysical energies into predictor refinement. The sequence-based predictor selects consensus samples to teach the structure-based predictor, and vice versa. Our method, AffinityFlow, achieves state-of-the-art performance in affinity maturation experiments. We plan to open-source our code after acceptance.

Baha Rababah, Shang, Wu et al.

The safety and robustness of large language models (LLMs) based applications remain critical challenges in artificial intelligence. Among the key threats to these applications are prompt hacking attacks, which can significantly undermine the security and reliability of LLM-based systems. In this work, we offer a comprehensive and systematic overview of three distinct types of prompt hacking: jailbreaking, leaking, and injection, addressing the nuances that differentiate them despite their overlapping characteristics. To enhance the evaluation of LLM-based applications, we propose a novel framework that categorizes LLM responses into five distinct classes, moving beyond the traditional binary classification. This approach provides more granular insights into the AI's behavior, improving diagnostic precision and enabling more targeted enhancements to the system's safety and robustness.