BioInnovate AI: A Machine Learning Platform for Rapid PCR Assay Design in Emerging Infectious Disease Diagnostics

Hung-Hsin Lin, Hsing-Yi Chung, Tai-Han Lin, Chih-Kai Chang, Cherng-Lih Perng, Kuo-Sheng Hung, Katsunori Yanagihara, Hung-Sheng Shang, Ming-Jr Jian

Background/Objectives: Emerging infectious diseases pose significant global threats due to their rapid transmission, limited therapeutic options, and profound socioeconomic impact. Conventional diagnostic techniques that rely on sequencing and polymerase chain reactions (PCR) frequently lack the speed necessary to efficiently respond to rapidly evolving pathogens. This study describes the development of BioInnovate AI to overcome these limitations using machine learning to expedite PCR assay development. Methods: The ability of BioInnovate AI to predict optimal PCR reagents across multiple pathogens was assessed. Additionally, random forest classifier, light gradient boosting machine (LGBM), and gradient boosting classifier models were evaluated for their ability to predict effective PCR primer–probe combinations. Performance metrics, including the area under the curve (AUC), sensitivity, specificity, accuracy, and F1 score, were assessed to identify the optimal model for platform integration. Results: All machine learning models performed well, with the LGBM model achieving the highest metrics (AUC: 0.97, sensitivity: 0.93, specificity: 0.91). BioInnovate AI significantly reduced PCR assay development time by approximately 90%, enabling rapid design and reagent optimization for multiple pathogens. Conclusions: BioInnovate AI provides a rapid, accurate, and efficient method for PCR reagent design, significantly enhancing global diagnostic preparedness by optimizing primers and probes for the timely detection of infectious diseases.