Yu Xia

Tianze Zheng, Ailun Wang, Xu Han et al.

A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges. In this study, we address this issue using a modern data-driven approach, developing ByteFF, an Amber-compatible force field for drug-like molecules. To create ByteFF, we generated an expansive and highly diverse molecular dataset at the B3LYP-D3(BJ)/DZVP level of theory. This dataset includes 2.4 million optimized molecular fragment geometries with analytical Hessian matrices, along with 3.2 million torsion profiles. We then trained an edge-augmented, symmetry-preserving molecular graph neural network (GNN) on this dataset, employing a carefully optimized training strategy. Our model predicts all bonded and non-bonded MM force field parameters for drug-like molecules simultaneously across a broad chemical space. ByteFF demonstrates state-of-the-art performance on various benchmark datasets, excelling in predicting relaxed geometries, torsional energy profiles, and conformational energies and forces. Its exceptional accuracy and expansive chemical space coverage make ByteFF a valuable tool for multiple stages of computational drug discovery.

Rui Wang, Junda Wu, Yu Xia et al.

Large Language Models (LLMs) are identified as being susceptible to indirect prompt injection attack, where the model undesirably deviates from user-provided instructions by executing tasks injected in the prompt context. This vulnerability stems from LLMs' inability to distinguish between data and instructions within a prompt. In this paper, we propose CachePrune that defends against this attack by identifying and pruning task-triggering neurons from the KV cache of the input prompt context. By pruning such neurons, we encourage the LLM to treat the text spans of input prompt context as only pure data, instead of any indicator of instruction following. These neurons are identified via feature attribution with a loss function induced from an upperbound of the Direct Preference Optimization (DPO) objective. We show that such a loss function enables effective feature attribution with only a few samples. We further improve on the quality of feature attribution, by exploiting an observed triggering effect in instruction following. Our approach does not impose any formatting on the original prompt or introduce extra test-time LLM calls. Experiments show that CachePrune significantly reduces attack success rates without compromising the response quality. Note: This paper aims to defend against indirect prompt injection attacks, with the goal of developing more secure and robust AI systems.