AI- and HPC-enabled Lead Generation for SARS-CoV-2: Models and Processes to Extract Druglike Molecules Contained in Natural Language Text

Abstract: Researchers worldwide are seeking to repurpose existing drugs or discover new drugs to counter the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising source of candidates for such studies is molecules that have been reported in the scientific literature to be drug-like in the context of coronavirus research. We report here on a project that leverages both human and artificial intelligence to detect references to drug-like molecules in free text. We engage non-expert humans to create a corpus of labeled text, use this labeled corpus to train a named entity recognition model, and employ the trained model to extract 10912 drug-like molecules from the COVID-19 Open Research Dataset Challenge (CORD-19) corpus of 198875 papers. Performance analyses show that our automated extraction model can achieve performance on par with that of non-expert humans.