BioAutoML: Democratizing Machine Learning in Life Sciences

• Ano de defesa: 2024
• Autor(a) principal: Bonidia, Robson Parmezan
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: Automated feature engineering; BioAutoML; Biological sequences; Descritores matemáticos; Engenharia de características automatizada; Mathematical descriptors; MathFeature; Meta-aprendizado; Metalearning; Sequências biológicas
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/55/55134/tde-01042024-092414/

Recent technological advances allowed an exponential expansion of biological sequence data, and the extraction of meaningful information through Machine Learning (ML) algorithms. This knowledge improved the understanding of the mechanisms related to several fatal diseases, e.g., Cancer and COVID-19, helping to develop innovative solutions, such as CRISPR-based gene editing, coronavirus vaccine, and precision medicine. These advances benefit our society and economy, directly impacting peoples lives in various areas, such as health care, drug discovery, forensic analysis, and food analysis. Nevertheless, ML approaches applied to biological data require representative, quantitative, and informative features. Necessarily, as many ML algorithms can handle only numerical data, sequences need to be translated into a feature vector. This process, known as feature extraction, is a fundamental step for the elaboration of high-quality ML-based models in bioinformatics, by allowing the feature engineering stage, with the design and selection of suitable features. Feature engineering, ML algorithm selection, and hyperparameter tuning are often manual and time-consuming processes, requiring extensive domain knowledge, and performed manually by a human expert. To deal with this problem, we developed a new package, BioAutoML, which automatically runs an end-to-end ML pipeline. BioAutoML extracts numerical and informative features from biological sequence databases, automating feature selection, recommendation of ML algorithm(s), and tuning of hyperparameters, using Automated ML (AutoML). BioAutoML has two components, divided into four modules, (1) automated feature engineering (feature extraction and selection modules) and (2) Metalearning (algorithm recommendation and hyperparameter tuning modules). Our experimental results, assessing the relevance of our proposal, indicate robust results for different problem domains, such as SARS-CoV-2, anticancer peptides, HIV sequences, and non-coding RNAs. According to our systematic review, our proposal is innovative compared to available studies in the literature, being the first study to propose automated feature engineering and metalearning for biological sequences. BioAutoML has a high potential to significantly reduce the expertise required to use ML pipelines, aiding researchers in combating diseases, particularly in low- and middle-income countries. This initiative can provide biologists, physicians, epidemiologists, and other stakeholders with an opportunity for widespread use of these techniques to enhance the health and well-being of their communities.