title: Automated classification of free-text pathology reports for registration of incident cases of cancer.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Unité d'épidémiologie, biostatistique et registre des cancers de Poitou-Charentes, Faculté de médecine, Centre Hospitalier Universitaire de Poitiers, Université de Poitiers, Poitiers Cedex, France. vianney. jouhet@gmail.com
authors.forename: V
authors.initials: V
authors.lastname: Jouhet
authors.forename: G
authors.initials: G
authors.lastname: Defossez
authors.forename: A
authors.initials: A
authors.lastname: Burgun
authors.forename: P
authors.initials: P
authors.lastname: le Beux
authors.forename: P
authors.initials: P
authors.lastname: Levillain
authors.forename: P
authors.initials: P
authors.lastname: Ingrand
authors.forename: V
authors.initials: V
authors.lastname: Claveau
mesh_terms: D001185:Artificial Intelligence; D005602:France / Q000453:epidemiology; D006801:Humans; D038801:International Classification of Diseases; D008490:Medical Informatics / Q000458:organization & administration*; D009369:Neoplasms / Q000453:epidemiology / Q000473:pathology*; D010336:Pathology / Q000145:classification*; D012042:Registries; D012660:Semantics