title: Automated training for algorithms that learn from genomic data.
abstract: Supervised machine learning algorithms are used by life scientists for a variety of objectives. Expert-curated public gene and protein databases are major resources for gathering data to train these algorithms. While these data resources are continuously updated, generally, these updates are not incorporated into published machine learning algorithms which thereby can become outdated soon after their introduction. In this paper, we propose a new model of operation for supervised machine learning algorithms that learn from genomic data. By defining these algorithms in a pipeline in which the training data gathering procedure and the learning process are automated, one can create a system that generates a classifier or predictor using information available from public resources. The proposed model is explained using three case studies on SignalP, MemLoci, and ApicoAP in which existing machine learning models are utilized in pipelines. Given that the vast majority of the procedures described for gathering training data can easily be automated, it is possible to transform valuable machine learning algorithms into self-evolving learners that benefit from the ever-changing data available for gene products and to develop new machine learning algorithms that are similarly capable.
authors.affiliation: School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA.
authors.forename: Gokcen
authors.identifier: 0000-0001-5769-5489
authors.initials: G
authors.lastname: Cilingir
authors.affiliation: School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA ; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA ; Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA.
authors.forename: Shira L
authors.initials: SL
authors.lastname: Broschat
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D008962:Models, Theoretical; D010363:Pattern Recognition, Automated / Q000379:methods*; D012984:Software