arXiv:2503.16582cs.LGcs.AI2025-03

用机器学习分析水稻基因序列,预测重金属响应基因。

Machine Learning-Based Genomic Linguistic Analysis (Gene Sequence Feature Learning): A Case Study on Predicting Heavy Metal Response Genes in Rice

  • 融合卷积神经网络与随机森林,从基因序列中提取特征。
  • 模型预测精度达0.89,F1分数为0.82,经实验验证有效。
  • 适合研究作物抗逆机制或基因功能挖掘的科研人员。

本研究探索了基于机器学习的基因语言学在识别水稻(Oryza sativa)重金属响应基因中的应用。通过整合卷积神经网络与随机森林算法,构建了能够从基因序列中提取并学习有意义特征(如k-mer频率和理化性质)的混合模型。该模型在基因数据集上训练并测试,取得高预测性能(精确率:0.89,F1得分:0.82)。对暴露于Hg⁰的水稻叶片进行RNA-seq和qRT-PCR实验,发现与重金属响应相关的基因差异表达,验证了模型预测结果。共表达网络分析识别出103个相关基因,文献回顾表明这些基因极可能参与重金属相关生物过程。通过与差异表达基因(DEGs)分析结果对比,进一步证实了新方法的有效性。研究表明,结合机器学习与基因语言学可高效实现大规模基因预测,为揭示重金属响应的分子机制提供了一种成本低、效率高的方法,具有培育抗逆作物品种的潜在应用价值。

原文摘要 · Abstract (English)

This study explores the application of machine learning-based genetic linguistics for identifying heavy metal response genes in rice (Oryza sativa). By integrating convolutional neural networks and random forest algorithms, we developed a hybrid model capable of extracting and learning meaningful features from gene sequences, such as k-mer frequencies and physicochemical properties. The model was trained and tested on datasets of genes, achieving high predictive performance (precision: 0.89, F1-score: 0.82). RNA-seq and qRT-PCR experiments conducted on rice leaves which exposed to Hg0, revealed differential expression of genes associated with heavy metal responses, which validated the model's predictions. Co-expression network analysis identified 103 related genes, and a literature review indicated that these genes are highly likely to be involved in heavy metal-related biological processes. By integrating and comparing the analysis results with those of differentially expressed genes (DEGs), the validity of the new machine learning method was further demonstrated. This study highlights the efficacy of combining machine learning with genetic linguistics for large-scale gene prediction. It demonstrates a cost-effective and efficient approach for uncovering molecular mechanisms underlying heavy metal responses, with potential applications in developing stress-tolerant crop varieties.

基因预测机器学习水稻重金属

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