Jinhao Bi

Fukang Ge, Jiarui Zhu, Linjie Zhang et al.

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

Kunyu Zhang, Fukang Ge, Binyang Wang et al.

Unlike nature image classification where groundtruth label is explicit and of no doubt, physicians commonly interpret medical image conditioned on certainty like using phrase "probable" or "likely". Existing medical image datasets either simply overlooked the nuance and polarise into binary label. Here, we propose a novel framework that leverages a Large Language Model (LLM) to directly mine medical reports to utilise the uncertainty relevant expression for supervision signal. At first, we collect uncertainty keywords from medical reports. Then, we use Qwen-3 4B to identify the textual uncertainty and map them into an adaptive Generalized Label Smoothing (GLS) rate. This rate allows our model to treat uncertain labels not as errors, but as informative signals, effectively incorporating expert skepticism into the training process. We establish a new clinical expert uncertainty-aware benchmark to rigorously evaluate this problem. Experiments demonstrate that our approach significantly outperforms state-of-the-art methods in medical disease detection. The curated uncertainty words database, code, and benchmark will be made publicly available upon acceptance.