Mingyang Li

Zhiyuan Chang, Mingyang Li, Xiaojun Jia et al.

Incorporating external knowledge has emerged as a promising way to mitigate outdated knowledge and hallucinations in LLM. However, external knowledge is often imperfect, encompassing substantial extraneous or even inaccurate content, which interferes with the LLM's utilization of useful knowledge in the context. This paper seeks to characterize the features of preferred external knowledge and perform empirical studies in imperfect contexts. Inspired by the chain of evidence (CoE), we characterize that the knowledge preferred by LLMs should maintain both relevance to the question and mutual support among the textual pieces. Accordingly, we propose a CoE discrimination approach and conduct a comparative analysis between CoE and Non-CoE samples across significance, deceptiveness, and robustness, revealing the LLM's preference for external knowledge that aligns with CoE features. Furthermore, we selected three representative tasks (RAG-based multi-hop QA, external knowledge poisoning and poisoning defense), along with corresponding SOTA or prevalent baselines. By integrating CoE features, the variants achieved significant improvements over the original baselines.

Yiheng Zhu, Mingyang Li, Junlong Liu et al.

Structure-based drug discovery (SBDD) is a systematic scientific process that develops new drugs by leveraging the detailed physical structure of the target protein. Recent advancements in pre-trained models for biomolecules have demonstrated remarkable success across various biochemical applications, including drug discovery and protein engineering. However, in most approaches, the pre-trained models primarily focus on the characteristics of either small molecules or proteins, without delving into their binding interactions which are essential cross-domain relationships pivotal to SBDD. To fill this gap, we propose a general-purpose foundation model named BIT (an abbreviation for Biomolecular Interaction Transformer), which is capable of encoding a range of biochemical entities, including small molecules, proteins, and protein-ligand complexes, as well as various data formats, encompassing both 2D and 3D structures. Specifically, we introduce Mixture-of-Domain-Experts (MoDE) to handle the biomolecules from diverse biochemical domains and Mixture-of-Structure-Experts (MoSE) to capture positional dependencies in the molecular structures. The proposed mixture-of-experts approach enables BIT to achieve both deep fusion and domain-specific encoding, effectively capturing fine-grained molecular interactions within protein-ligand complexes. Then, we perform cross-domain pre-training on the shared Transformer backbone via several unified self-supervised denoising tasks. Experimental results on various benchmarks demonstrate that BIT achieves exceptional performance in downstream tasks, including binding affinity prediction, structure-based virtual screening, and molecular property prediction.