Qiuwen Wu

Qifeng Wu, Zhengzhe Liu, Han Zhu et al.

This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron Microscopy (cryo-EM). Motivated by the recent progress of vision-language models (VLMs), we propose a CLIP-style framework for aligning 3D protein structures with functional annotations using contrastive learning. For model training, we propose a large-scale dataset of approximately 200,000 protein-caption pairs with rich functional descriptors. We evaluate our model in both in-domain and more challenging cross-database retrieval on Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) dataset, respectively. In both cases, our approach demonstrates promising zero-shot retrieval performance, highlighting the potential of multimodal foundation models for structure-function understanding in protein biology.

Dongrong Yang, Xin Wu, Yibo Xie et al.

Radiation therapy treatment planning is an iterative, expertise-dependent process, and the growing burden of cancer cases has made reliance on manual planning increasingly unsustainable, underscoring the need for automation. In this study, we propose a workflow that leverages a large language model (LLM)-based agent to navigate inverse treatment planning for intensity-modulated radiation therapy (IMRT). The LLM agent was implemented to directly interact with a clinical treatment planning system (TPS) to iteratively extract intermediate plan states and propose new constraint values to guide inverse optimization. The agent's decision-making process is informed by current observations and previous optimization attempts and evaluations, allowing for dynamic strategy refinement. The planning process was performed in a zero-shot inference setting, where the LLM operated without prior exposure to manually generated treatment plans and was utilized without any fine-tuning or task-specific training. The LLM-generated plans were evaluated on twenty head-and-neck cancer cases against clinical manual plans, with key dosimetric endpoints analyzed and reported. The LLM-generated plans achieved comparable organ-at-risk (OAR) sparing relative to clinical plans while demonstrating improved hot spot control (Dmax: 106.5% vs. 108.8%) and superior conformity (conformity index: 1.18 vs. 1.39 for boost PTV; 1.82 vs. 1.88 for primary PTV). This study demonstrates the feasibility of a zero-shot, LLM-driven workflow for automated IMRT treatment planning in a commercial TPS. The proposed approach provides a generalizable and clinically applicable solution that could reduce planning variability and support broader adoption of AI-based planning strategies.

Zhuo Xiao, Qinglong Yao, Jingjing Wang et al.

Seed implant brachytherapy (SIBT) is an effective cancer treatment modality; however, clinical planning often relies on manual adjustment of objective function weights, leading to inefficiencies and suboptimal results. This study proposes an adaptive weight optimization framework for SIBT planning, driven by large language models (LLMs). A locally deployed DeepSeek-R1 LLM is integrated with an automatic planning algorithm in an iterative loop. Starting with fixed weights, the LLM evaluates plan quality and recommends new weights in the next iteration. This process continues until convergence criteria are met, after which the LLM conducts a comprehensive evaluation to identify the optimal plan. A clinical knowledge base, constructed and queried via retrieval-augmented generation (RAG), enhances the model's domain-specific reasoning. The proposed method was validated on 23 patient cases, showing that the LLM-assisted approach produces plans that are comparable to or exceeding clinically approved and fixed-weight plans, in terms of dose homogeneity for the clinical target volume (CTV) and sparing of organs at risk (OARs). The study demonstrates the potential use of LLMs in SIBT planning automation.