MOTIVATION: Clinical trials are the essential stage of every drug development program for the treatment to become available to patients. Despite the importance of well-structured clinical trial databases and their tremendous value for drug discovery and development such instances are very rare. Presently large-scale information on clinical trials is stored in clinical trial registers which are relatively structured, but the mappings to external databases of drugs and diseases are increasingly lacking. The precise production of such links would enable us to interrogate richer harmonized datasets for invaluable insights. RESULTS: We present a neural approach for medical concept normalization of diseases and drugs. Our two-stage approach is based on Bidirectional Encoder Representations from Transformers (BERT). In the training stage, we optimize the relative similarity of mentions and concept names from a terminology via triplet loss. In the inference stage, we obtain the closest concept name representation in a common embedding space to a given mention representation. We performed a set of experiments on a dataset of abstracts and a real-world dataset of trial records with interventions and conditions mapped to drug and disease terminologies. The latter includes mentions associated with one or more concepts (in-KB) or zero (out-of-KB, nil prediction). Experiments show that our approach significantly outperforms baseline and state-of-the-art architectures. Moreover, we demonstrate that our approach is effective in knowledge transfer from the scientific literature to clinical trial data. AVAILABILITY: We make code and data freely available at hidden\_during\_review\_process. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Clinical trials are the essential stage of every drug development program for the treatment to become available to patients. Despite the importance of well-structured clinical trial databases and their tremendous value for drug discovery and development such instances are very rare. Presently large-scale information on clinical trials is stored in clinical trial registers which are relatively structured, but the mappings to external databases of drugs and diseases are increasingly lacking. The precise production of such links would enable us to interrogate richer harmonized datasets for invaluable insights. RESULTS: We present a neural approach for medical concept normalization of diseases and drugs. Our two-stage approach is based on Bidirectional Encoder Representations from Transformers (BERT). In the training stage, we optimize the relative similarity of mentions and concept names from a terminology via triplet loss. In the inference stage, we obtain the closest concept name representation in a common embedding space to a given mention representation. We performed a set of experiments on a dataset of abstracts and a real-world dataset of trial records with interventions and conditions mapped to drug and disease terminologies. The latter includes mentions associated with one or more concepts (in-KB) or zero (out-of-KB, nil prediction). Experiments show that our approach significantly outperforms baseline and state-of-the-art architectures. Moreover, we demonstrate that our approach is effective in knowledge transfer from the scientific literature to clinical trial data. AVAILABILITY: We make code and data freely available at hidden\_during\_review\_process. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.