Automatic information extraction from childhood cancer pathology reports

Hong Jun Yoon, Alina Peluso, Eric B. Durbin, Xiao Cheng Wu, Antoinette Stroup, Jennifer Doherty, Stephen Schwartz, Charles Wiggins, Linda Coyle, Lynne Penberthy

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Objectives: The International Classification of Childhood Cancer (ICCC) facilitates the effective classification of a heterogeneous group of cancers in the important pediatric population. However, there has been no development of machine learning models for the ICCC classification. We developed deep learning-based information extraction models from cancer pathology reports based on the ICD-O-3 coding standard. In this article, we describe extending the models to perform ICCC classification. Materials and Methods: We developed 2 models, ICD-O-3 classification and ICCC recoding (Model 1) and direct ICCC classification (Model 2), and 4 scenarios subject to the training sample size. We evaluated these models with a corpus consisting of 29 206 reports with age at diagnosis between 0 and 19 from 6 state cancer registries. Results: Our findings suggest that the direct ICCC classification (Model 2) is substantially better than reusing the ICD-O-3 classification model (Model 1). Applying the uncertainty quantification mechanism to assess the confidence of the algorithm in assigning a code demonstrated that the model achieved a micro-F1 score of 0.987 while abstaining (not sufficiently confident to assign a code) on only 14.8% of ambiguous pathology reports. Conclusions: Our experimental results suggest that the machine learning-based automatic information extraction from childhood cancer pathology reports in the ICCC is a reliable means of supplementing human annotators at state cancer registries by reading and abstracting the majority of the childhood cancer pathology reports accurately and reliably.

Original languageEnglish
Article numberooac049
JournalJAMIA Open
Issue number2
StatePublished - Jul 1 2022

Bibliographical note

Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press on behalf of the American Medical Informatics Association.


  • cancer pathology reports
  • information extraction
  • machine learning
  • pediatric cancer

ASJC Scopus subject areas

  • Health Informatics


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