arXiv:2410.08867cs.LG2024-10被引 2

用机器学习分析鱼类冻融基因,准确率达99.98%。

Prediction by Machine Learning Analysis of Genomic Data Phenotypic Frost Tolerance in Perccottus glenii

  • 用K-mer编码处理长基因序列,筛选出最优特征表示方法。
  • 随机森林模型准确率达99.98%,显著优于其他模型。
  • 通过SHAP值识别出10个关键基因特征,提升结果可解释性。

对具有耐冻特性的唯一鱼类——日本拟鲤(Perccottus glenii)的基因组序列进行分析,有助于理解生物适应极端环境的机制。传统生物学分析耗时且精度有限,为此我们采用机器学习方法,以海南新鳅(Neodontobutis hainanensis)为对照组,提出五种基因序列向量化方法,并针对序列表示方法展开比较研究,包括序数编码、独热编码和K-mer编码,最终确定最优编码方式。基于从国家生物技术信息中心获取的数据集,使用最优编码方式对序列矩阵进行向量化,构建了随机森林、LightGBM、XGBoost和决策树四类分类模型。其中,随机森林模型表现最佳,分类准确率达到99.98%。通过十折交叉验证与AUC指标评估,并利用SHAP值对最优模型进行可解释性分析,识别出贡献度最高的前10个特征。结果表明,机器学习方法能高效替代传统人工分析,精准识别与冻融耐受表型相关的基因。

原文摘要 · Abstract (English)

Analysis of the genome sequence of Perccottus glenii, the only fish known to possess freeze tolerance, holds significant importance for understanding how organisms adapt to extreme environments, Traditional biological analysis methods are time-consuming and have limited accuracy, To address these issues, we will employ machine learning techniques to analyze the gene sequences of Perccottus glenii, with Neodontobutis hainanens as a comparative group, Firstly, we have proposed five gene sequence vectorization methods and a method for handling ultra-long gene sequences, We conducted a comparative study on the three vectorization methods: ordinal encoding, One-Hot encoding, and K-mer encoding, to identify the optimal encoding method, Secondly, we constructed four classification models: Random Forest, LightGBM, XGBoost, and Decision Tree, The dataset used by these classification models was extracted from the National Center for Biotechnology Information database, and we vectorized the sequence matrices using the optimal encoding method, K-mer, The Random Forest model, which is the optimal model, achieved a classification accuracy of up to 99, 98 , Lastly, we utilized SHAP values to conduct an interpretable analysis of the optimal classification model, Through ten-fold cross-validation and the AUC metric, we identified the top 10 features that contribute the most to the model's classification accuracy, This demonstrates that machine learning methods can effectively replace traditional manual analysis in identifying genes associated with the freeze tolerance phenotype in Perccottus glenii.

基因预测机器学习冻融耐受可解释性

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