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Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning

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Research in Computational Molecular Biology (RECOMB 2019)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11467))

Abstract

Objective: Automatic recognition of medical concepts in unstructured text is an important component of many clinical and research applications and its accuracy has a large impact on electronic health record analysis. The mining of such terms is complicated by the broad use of synonyms and non-standard terms in medical documents. Here we presented a machine learning model for concept recognition in large unstructured text which optimizes the use of ontological structures and can identify previously unobserved synonyms for concepts in the ontology.

Materials and Methods: We present a neural dictionary model which can be used to predict if a phrase is synonymous to a concept in a reference ontology. Our model, called Neural Concept Recognizer (NCR), uses a convolutional neural network and utilizes the taxonomy structure to encode input phrases, then rank medical concepts based on the similarity in that space. It also utilizes the biomedical ontology structure to optimize the embedding of various terms and has fewer training constraints than previous methods. We train our model on two biomedical ontologies, the Human Phenotype Ontology (HPO) and SNOMED-CT.

Results: We tested our model trained on HPO on two different data sets: 288 annotated PubMed abstracts and 39 clinical reports. We also tested our model trained on the SNOMED-CT on 2000 MIMIC-III ICU discharge summaries. The results of our experiments show the high accuracy of our model, as well as the value of utilizing the taxonomy structure of the ontology in concept recognition.

Conclusion: Most popular medical concept recognizers rely on rule-based models, which cannot generalize well to unseen synonyms. Also, most machine learning methods typically require large corpora of annotated text that cover all classes of concepts, which can be extremely difficult to get for biomedical ontologies. Without relying on a large-scale labeled training data or requiring any custom training, our model can efficiently generalize to new synonyms and performs as well or better than state-of-the-art methods custom built for specific ontologies.

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Acknowledgements

We thank Michael Glueck for his valuable comments and discussions. We also thank Tudor Groza for his helpful comments and for providing us the BioLarK API used for the experiments.

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Authors and Affiliations

  1. Department of Computer Science, University of Toronto, Toronto, ON, Canada

    Aryan Arbabi, Sanja Fidler & Michael Brudno

  2. Center for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada

    Aryan Arbabi & Michael Brudno

  3. Vector Institute, Toronto, ON, Canada

    Aryan Arbabi, Sanja Fidler & Michael Brudno

  4. Section on Human Biochemical Genetics, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

    David R. Adams

Authors
  1. Aryan Arbabi
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  2. David R. Adams
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  3. Sanja Fidler
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  4. Michael Brudno
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Corresponding author

Correspondence to Michael Brudno .

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Editors and Affiliations

  1. Tufts University, Cambridge, MA, USA

    Lenore J. Cowen

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Arbabi, A., Adams, D.R., Fidler, S., Brudno, M. (2019). Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. In: Cowen, L. (eds) Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science(), vol 11467. Springer, Cham. https://doi.org/10.1007/978-3-030-17083-7_2

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  • DOI: https://doi.org/10.1007/978-3-030-17083-7_2

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  • Online ISBN: 978-3-030-17083-7

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