Faculty, Staff and Student Publications
Publication Date
7-14-2022
Journal
BMC Bioinformatics
Abstract
BACKGROUND: Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health's Bridge2AI initiative to address the FAIR challenges with artificial intelligence-based machine learning models for biomedical research. We present our early undertaking in developing an ontology for capturing the conceptual-level information embedded in model card reports.
RESULTS: Sourcing from existing ontologies and developing the core framework, we generated the Model Card Report Ontology. Our development efforts yielded an OWL2-based artifact that represents and formalizes model card report information. The current release of this ontology utilizes standard concepts and properties from OBO Foundry ontologies. Also, the software reasoner indicated no logical inconsistencies with the ontology. With sample model cards of machine learning models for bioinformatics research (HIV social networks and adverse outcome prediction for stent implantation), we showed the coverage and usefulness of our model in transforming static model card reports to a computable format for machine-based processing.
CONCLUSIONS: The benefit of our work is that it utilizes expansive and standard terminologies and scientific rigor promoted by biomedical ontologists, as well as, generating an avenue to make model cards machine-readable using semantic web technology. Our future goal is to assess the veracity of our model and later expand the model to include additional concepts to address terminological gaps. We discuss tools and software that will utilize our ontology for potential application services.
Keywords
Artificial Intelligence, Biological Ontologies, Computational Biology, Machine Learning, Semantics, Software
DOI
10.1186/s12859-022-04797-6
PMID
35836130
PMCID
PMC9284683
PubMedCentral® Posted Date
7-14-2022
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
