Identifying key soil characteristics for Francisella tularensis classification with optimized Machine learning models

• Published in: Scientific reports Vol. 14; no. 1; pp. 1743 - 18
• Main Authors: Ahmad, Fareed, Javed, Kashif, Tahir, Ahsen, Khan, Muhammad Usman Ghani, Abbas, Mateen, Rabbani, Masood, Shabbir, Muhammad Zubair
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19.01.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/114/1305; 631/326/2521; 631/326/41/1470; 692/700/139; 692/700/459; Bayesian analysis; Classification; Economic impact; Environmental factors; Epidemic models; Epidemiology; Francisella tularensis; Human populations; Humanities and Social Sciences; Learning algorithms; Machine learning; Mathematical models; multidisciplinary; Neural networks; Optimization; Organic matter; Pathogens; Risk reduction; Science; Science (multidisciplinary); Soil characteristics; Soils; Statistical analysis; Statistical methods; Support vector machines
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-51502-z

Francisella tularensis (Ft) poses a significant threat to both animal and human populations, given its potential as a bioweapon. Current research on the classification of this pathogen and its relationship with soil physical–chemical characteristics often relies on traditional statistical methods. In this study, we leverage advanced machine learning models to enhance the prediction of epidemiological models for soil-based microbes. Our model employs a two-stage feature ranking process to identify crucial soil attributes and hyperparameter optimization for accurate pathogen classification using a unique soil attribute dataset. Optimization involves various classification algorithms, including Support Vector Machines (SVM), Ensemble Models (EM), and Neural Networks (NN), utilizing Bayesian and Random search techniques. Results indicate the significance of soil features such as clay, nitrogen, soluble salts, silt, organic matter, and zinc , while identifying the least significant ones as potassium, calcium, copper, sodium, iron, and phosphorus. Bayesian optimization yields the best results, achieving an accuracy of 86.5% for SVM, 81.8% for EM, and 83.8% for NN. Notably, SVM emerges as the top-performing classifier, with an accuracy of 86.5% for both Bayesian and Random Search optimizations. The insights gained from employing machine learning techniques enhance our understanding of the environmental factors influencing Ft’s persistence in soil. This, in turn, reduces the risk of false classifications, contributing to better pandemic control and mitigating socio-economic impacts on communities.