一项对11个非线性回归模型的比较研究,突出了自编码器,DBN和SVR,通过SHAP重要性分析增强了大豆分支预测中的重要性
Wei Zhou1, Zhengxiao Yan2, Liting Zhang2
1Florida Agricultural and Mechanical University, Tallahassee, FL, 32307, USA. wei.zhou@famu.edu.
Scientific reports
|March 12, 2024
概括
人工智能准确地预测大豆分枝使用先进的回归模型,如支持向量回归 (SVR). 这种人工智能驱动的方法通过改进表型预测和实现基于数据的作物改进策略来增强数字育种.
科学领域:
- 植物育种和遗传学 植物育种和遗传学
- 计算生物学和生物信息学
- 农业中的人工智能
背景情况:
- 传统的植物育种在效率和数据利用方面面临挑战.
- 数字育种实践需要强大的工具来准确预测表型.
- 人工智能 (AI) 为复杂的生物预测提供了潜在的解决方案.
研究的目的:
- 评估11个非线性回归人工智能模型来预测大豆分支.
- 确定在植物育种中用于表型预测的最有效的AI模型.
- 探索夏普利添加式扩展 (SHAP) 在人工智能驱动的繁殖中对特征选择的实用性.
主要方法:
- 11个非线性回归AI模型的系统比较,包括深度学习和机器学习方法.
- 使用了1918年加入的大豆分支数据 (表型) 和42k个单核酸多态 (SNP) 数据 (基因型).
- 评估模型使用R平方,平均绝对误差,平均平方误差和平均绝对百分比误差指标.
- 使用变量排名,转换,SHAP和关联矩阵算法评估特征重要性.
主要成果:
- 支持向量回归 (SVR),多项式回归,深度信念网络 (DBN) 回归和自编码器回归显示出卓越的预测准确性.
- SHAP值为基因贡献提供了有价值的见解,有助于为繁殖选择特征.
- 在四个测试的算法中,在特征重要性排名中没有发现显著差异,但由于其详细的信息,SHAP被优先考虑.
结论:
- 人工智能,特别是像SVR这样的模型,在植物育种中显著提升了表型预测.
- 开发的AI系统支持基于数据的育种,超越了传统的基于经验的方法.
- 该方法在量化特征位数挖掘和智能育种系统中具有广泛的应用.
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