Automated Classification of Free-text Pathology Reports for Registration of Incident Cases of Cancer

V. Jouhet; G. Defossez; A. Burgun; P. le Beux; P. Levillain; P. Ingrand; V. Claveau

doi:10.3414/ME11-01-0005

Methods of Information in Medicine, Table of Contents

Methods Inf Med 2012; 51(03): 242-251
DOI: 10.3414/ME11-01-0005

Original Articles

Schattauer GmbH

Automated Classification of Free-text Pathology Reports for Registration of Incident Cases of Cancer

V. Jouhet

¹Unité d’épidémiologie, biostatistique et registre des cancers de Poitou-Charentes, Faculté de médecine, Centre Hospitalier Universitaire de Poitiers, Université de Poitiers, Poitiers, France

,

G. Defossez

¹Unité d’épidémiologie, biostatistique et registre des cancers de Poitou-Charentes, Faculté de médecine, Centre Hospitalier Universitaire de Poitiers, Université de Poitiers, Poitiers, France

,

A. Burgun

²INSERM U936, Faculté de médecine, Université de Rennes 1, Rennes, France

,

P. le Beux

²INSERM U936, Faculté de médecine, Université de Rennes 1, Rennes, France

,

P. Levillain

³Anatomie et cytologie pathologiques, Centre Hospitalier Universitaire de Poitiers, Poitiers, France

⁴Centre de Regroupement Informatique et Statistique en Anatomo-Pathologie de Poitou-Charentes, Faculté de médecine, Université de Poitiers, Poitiers, France

,

P. Ingrand

¹Unité d’épidémiologie, biostatistique et registre des cancers de Poitou-Charentes, Faculté de médecine, Centre Hospitalier Universitaire de Poitiers, Université de Poitiers, Poitiers, France

⁵INSERM, CIC 802, Poitiers, France

,

V. Claveau

⁶IRISA – CNRS UMR 6074, Rennes, France

› Author Affiliations

Abstract

Summary

Objective: Our study aimed to construct and evaluate functions called “classifiers”, produced by supervised machine learning techniques, in order to categorize automatically pathology reports using solely their content.

Methods: Patients from the Poitou-Charentes Cancer Registry having at least one pathology report and a single non-metastatic invasive neoplasm were included. A descriptor weighting function accounting for the distribution of terms among targeted classes was developed and compared to classic methods based on inverse document frequencies. The classification was performed with support vector machine (SVM) and Naive Bayes classifiers. Two levels of granularity were tested for both the topographical and the morphological axes of the ICD-O3 code. The ability to correctly attribute a precise ICD-O3 code and the ability to attribute the broad category defined by the International Agency for Research on Cancer (IARC) for the multiple primary cancer registration rules were evaluated using F1-measures.

Results: 5121 pathology reports produced by 35 pathologists were selected. The best performance was achieved by our class-weighted descriptor, associated with a SVM classifier. Using this method, the pathology reports were properly classified in the IARC categories with F1-measures of 0.967 for both topography and morphology. The ICD-O3 code attribution had lower performance with a 0.715 F1-measure for topography and 0.854 for morphology.

Conclusion: These results suggest that free-text pathology reports could be useful as a data source for automated systems in order to identify and notify new cases of cancer. Future work is needed to evaluate the improvement in performance obtained from the use of natural language processing, including the case of multiple tumor description and possible incorporation of other medical documents such as surgical reports.

Keywords

Medical Informatics - neoplasm - pathology - free text - automated classification

Full Text

References

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