An Iterative LLM Framework for SIBT utilizing RAG-based Adaptive Weight Optimization

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.

SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in protein modeling. While traditional protein foundation models benefit from pre-training on vast unlabeled datasets, they often struggle to capture critical co-evolutionary information, which evolutionary-based methods excel at. In this study, we introduce a novel pre-training strategy for protein foundation models that emphasizes the interactions among amino acid residues to enhance the extraction of both short-range and long-range co-evolutionary features from sequence data. Trained on a large-scale protein sequence dataset, our model demonstrates superior generalization ability, outperforming established baselines of similar size, including the ESM model, across diverse downstream tasks. Experimental results confirm the model's effectiveness in integrating co-evolutionary information, marking a significant step forward in protein sequence-based modeling.