arXiv:2607.22763cs.LGstat.ML2026-07

用深度学习+统计模型分析叶脉图像,挖掘基因与环境的复杂关联。

An Integrated Deep Learning and Statistical Framework for Whole-Network Gene--Environment Association with Leaf Vascular Architecture

论文配图:An Integrated Deep Learning and Statistical Framework for Whole-Network Gene--Environment Association with Leaf Vascular Architecture
图 1 · 摘自论文原文
  • 将叶脉结构整体视为图像表型,用EDTER模型提取完整网络特征。
  • 在真实杨树数据中发现3个显著的基因-地理交互作用。
  • 适合研究复杂图像表型与多因素关联的生物学家和数据科学家。

叶脉具有显著的形态多样性,但现有基因-环境关联研究多依赖少量低维特征,丢失了图像中的大量结构信息。本文提出一种融合深度学习与统计建模的框架,实现四大突破:首先,将叶脉结构整体表示为全网络图像表型;其次,通过联合学习局部与全局上下文特征,微调基于Transformer的边缘检测模型EDTER,从RGB图像中精准提取完整叶脉网络;第三,整合DiffusionEdge生成的边缘图与伯克利分割数据库(BSDS500),构建新的标注叶像数据库;第四,采用半参数稀疏典型相关分析(SSCCA),在重复测量的高维双变量图像响应与高维预测因子间进行变量选择与建模,并通过截断潜变量高斯互信息模型处理稀疏、零膨胀的边缘图数据。两个模拟研究验证了框架在复杂度提升下的性能。应用于真实杨树数据集,识别出三个与叶脉结构显著相关的基因-地理交互作用,揭示新生物学机制,并建立可推广至高维复杂图像表型的分析方法。

原文摘要 · Abstract (English)

Leaf veins exhibit remarkable diversity in architecture and patterning, yet existing gene--environment association studies have primarily quantified leaf venation using a small collection of low-dimensional summary traits, thereby discarding most of the structural information contained in the original images. We propose an integrated deep learning and statistical framework. The proposed framework achieves four methodological advances. First, it represents the complete leaf vascular architecture as a whole-network image phenotype. Second, it fine-tunes the deep learning-based Edge Detection with Transformers (EDTER) model to accurately extract whole-network leaf vascular architecture from RGB images by jointly learning local and global contextual features. Third, it constructs a new annotated leaf image database by integrating edge maps generated by DiffusionEdge with the Berkeley Segmentation Database (BSDS500). Fourth, it applies Semiparametric Sparse Canonical Correlation Analysis (SSCCA) to perform variable selection and model associations between repeatedly measured high-dimensional Bivariate image responses and high-dimensional predictors while simultaneously accommodating sparse, zero-inflated data represented by edge maps through a truncated latent Gaussian copula model. Two simulation studies demonstrate the performance of the proposed framework under increasing levels of complexity. Application to a real \emph{Populus} dataset identifies three significant gene--geography interactions associated with leaf vascular architecture, providing new biological insights and establishing a broadly applicable methodological framework for high-dimensional complex image phenotypes.

图像表型基因-环境深度学习叶脉分析

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