用生成数据训练图神经网络,预测肿瘤异质性
Block Graph Neural Networks for tumor heterogeneity prediction
- 基于肿瘤演化模型生成人工数据,构建图结构特征
- 在合成数据上达到89.67%准确率,优于传统方法
- 适合医学图像与单细胞数据融合研究者参考
精准肿瘤分类对治疗选择至关重要,但现有方法存在局限。标准分级依赖细胞分化程度,但部分分化良好的肿瘤仍为恶性。单细胞测序虽能揭示肿瘤异质性,但成本高且需大量人工干预。多数现有统计机器学习方法仍需复杂预处理MRI与病理图像数据。本文基于模拟肿瘤演化的数学模型(Ożański, 2017),生成人工肿瘤数据集,并通过归一化熵评估肿瘤异质性,设定阈值分类为高低异质性。贡献包括:(1) 从人工数据中提取切片并生成图结构的流程;(2) 设计肿瘤特征;(3) 构建基于图神经网络的块图神经网络(BGNN)以预测异质性。实验显示,所提特征与模型组合在人工数据测试集上达89.67%准确率。结果表明,结合增殖标记(如Ki-67)与死亡标记可提升异质性预测能力,有助于增强传统分级体系。
原文摘要 · Abstract (English)
Accurate tumor classification is essential for selecting effective treatments, but current methods have limitations. Standard tumor grading, which categorizes tumors based on cell differentiation, is not recommended as a stand-alone procedure, as some well-differentiated tumors can be malignant. Tumor heterogeneity assessment via single-cell sequencing offers profound insights but can be costly and may still require significant manual intervention. Many existing statistical machine learning methods for tumor data still require complex pre-processing of MRI and histopathological data. In this paper, we propose to build on a mathematical model that simulates tumor evolution (Ożański (2017)) and generate artificial datasets for tumor classification. Tumor heterogeneity is estimated using normalized entropy, with a threshold to classify tumors as having high or low heterogeneity. Our contributions are threefold: (1) the cut and graph generation processes from the artificial data, (2) the design of tumor features, and (3) the construction of Block Graph Neural Networks (BGNN), a Graph Neural Network-based approach to predict tumor heterogeneity. The experimental results reveal that the combination of the proposed features and models yields excellent results on artificially generated data ($89.67\%$ accuracy on the test data). In particular, in alignment with the emerging trends in AI-assisted grading and spatial transcriptomics, our results suggest that enriching traditional grading methods with birth (e.g., Ki-67 proliferation index) and death markers can improve heterogeneity prediction and enhance tumor classification.
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