Prompting Whole Slide Image Based Genetic Biomarker Prediction
<|reference_start|>Prompting Whole Slide Image Based Genetic Biomarker Prediction: Prediction of genetic biomarkers, e.g., microsatellite instability and BRAF in colorectal cancer is crucial for clinical decision making. In this paper, we propose a whole slide image (WSI) based genetic biomarker prediction method via prompting techniques. Our work aims at addressing the following challenges: (1) extracting foreground instances related to genetic biomarkers from gigapixel WSIs, and (2) the interaction among the fine-grained pathological components in WSIs.Specifically, we leverage large language models to generate medical prompts that serve as prior knowledge in extracting instances associated with genetic biomarkers. We adopt a coarse-to-fine approach to mine biomarker information within the tumor microenvironment. This involves extracting instances related to genetic biomarkers using coarse medical prior knowledge, grouping pathology instances into fine-grained pathological components and mining their interactions. Experimental results on two colorectal cancer datasets show the superiority of our method, achieving 91.49% in AUC for MSI classification. The analysis further shows the clinical interpretability of our method. Code is publicly available at https://github.com/DeepMed-Lab-ECNU/PromptBio.<|reference_end|>
@article{zhang2024prompting,
    title={Prompting Whole Slide Image Based Genetic Biomarker Prediction},
    author={Ling Zhang, Boxiang Yun, Xingran Xie, Qingli Li, Xinxing Li, Yan Wang},
    journal={arXiv preprint arXiv:2407.09540},
    year={2024},
    archivePrefix={arXiv},
    eprint={2407.09540},
    primaryClass={eess.IV cs.CE cs.CV cs.LG q-bio.TO}
}