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Published on: June 25, 2020
A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal
Camilo Patarroyo1,2, Stéphane Dupas2, Silvia Restrepo3
1Department of Biological Sciences Universidad de los Andes Bogotá Colombia.
Applications in Plant Sciences
|October 3, 2024
Summary
A new machine learning tool, AdaBag, now automates the classification of Phytophthora infestans genotypes into clonal lineages. This aids in managing potato late blight by enabling prompt identification of pathogen spread.
Area of Science:
- Plant Pathology
- Computational Biology
- Machine Learning
Background:
- Accurate classification of Phytophthora infestans isolates into clonal lineages is crucial for managing potato late blight.
- Current methods rely on manual microsatellite genotype comparison, which is time-consuming.
- An automated classification tool is needed to improve efficiency and accuracy.
Purpose of the Study:
- To develop a flexible, machine learning-based classifier for Phytophthora infestans genotypes.
- To automate the process of categorizing pathogen isolates into described clonal lineages.
Main Methods:
- Evaluated the performance of various machine learning algorithms for classifying P. infestans genotypes.
- Compared algorithm performance using decreasing amounts of training data and a complete dataset.
- Implemented the best-performing algorithm in a freely available web application.
Main Results:
- Four algorithms (mlpML, cforest, nnet, AdaBag) achieved near 100% accuracy in preliminary tests.
- AdaBag demonstrated significantly superior performance on the complete dataset (Tukey HSD P < 0.001).
- A web application utilizing AdaBag for automated genotype classification was developed and made publicly available.
Conclusions:
- A gradient boosting-based tool (AdaBag) was successfully developed for automated P. infestans genotype classification.
- This tool provides a valuable resource for rapid identification of spreading clonal lineages.
- Automated classification enhances pathogen management strategies for potato late blight.
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