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

TL;DR

This study employs machine learning techniques to analyze genomic data of Perccottus glenii, a fish with freeze tolerance, achieving high accuracy in identifying genes linked to this trait and demonstrating the effectiveness of ML over traditional methods.

Contribution

The paper introduces novel gene sequence vectorization methods, compares multiple classification models, and applies interpretability techniques to identify key genetic features for freeze tolerance.

Findings

Random Forest achieved 99.98% accuracy

K-mer encoding was optimal for sequence vectorization

Top features identified by SHAP relate to freeze tolerance

Abstract

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.