Yuliang Jiang

Liang He, Peiran Jin, Yaosen Min et al.

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.

Zhuo Xiao, Fugen Zhou, Jingjing Wang et al.

Accurate multi-needle localization in intraoperative CT images is crucial for optimizing seed placement in pelvic seed implant brachytherapy. However, this task is challenging due to poor image contrast and needle adhesion. This paper presents a novel approach that reframes needle localization as a tip-handle detection and matching problem to overcome these difficulties. An anchor-free network, based on HRNet, is proposed to extract multi-scale features and accurately detect needle tips and handles by predicting their centers and orientations using decoupled branches for heatmap regression and polar angle prediction. To associate detected tips and handles into individual needles, a greedy matching and merging (GMM) method designed to solve the unbalanced assignment problem with constraints (UAP-C) is presented. The GMM method iteratively selects the most probable tip-handle pairs and merges them based on a distance metric to reconstruct 3D needle paths. Evaluated on a dataset of 100 patients, the proposed method demonstrates superior performance, achieving higher precision and F1 score compared to a segmentation-based method utilizing the nnUNet model,thereby offering a more robust and accurate solution for needle localization in complex clinical scenarios.

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.