Pathology reports represent a primary source of information for cancer registries. Hospitals routinely process high volumes of free-text reports, a valuable source of information regarding cancer diagnosis for improving clinical care and supporting research. Information extraction and coding of textual unstructured data is typically a manual, labour-intensive process. There is a need to develop automated approaches to extract meaningful information from such texts in a reliable and accurate way. In this scenario, Natural Language Processing (NLP) algorithms offer a unique opportunity to automatically encode the unstructured reports into structured data, thus representing a potential powerful alternative to expensive manual processing. However, notwithstanding the increasing interest in this area, there is still limited availability of NLP approaches for pathology reports in languages other than English, including Italian, to date. The aim of our work was to develop an automated algorithm based on NLP techniques, able to identify and classify the morphological content of pathology reports in the Italian language with micro-averaged performance scores higher than 95%. Specifically, a novel, domain-specific classifier that uses linguistic rules was developed and tested on 27,239 pathology reports from a single Italian oncological centre, following the International Classification of Diseases for Oncology morphology classification standard (ICD-O-M). The proposed classification algorithm achieved successful results with a micro-F1 score of 98.14% on 9594 pathology reports in the test dataset. This algorithm relies on rules defined on data from a single hospital that is specifically dedicated to cancer, but it is based on general processing steps which can be applied to different datasets. Further research will be important to demonstrate the generalizability of the proposed approach on a larger corpus from different hospitals.

Automated classification of cancer morphology from Italian pathology reports using Natural Language Processing techniques: A rule-based approach

Hammami L.;Paglialonga A.;Caiani E. G.;
2021

Abstract

Pathology reports represent a primary source of information for cancer registries. Hospitals routinely process high volumes of free-text reports, a valuable source of information regarding cancer diagnosis for improving clinical care and supporting research. Information extraction and coding of textual unstructured data is typically a manual, labour-intensive process. There is a need to develop automated approaches to extract meaningful information from such texts in a reliable and accurate way. In this scenario, Natural Language Processing (NLP) algorithms offer a unique opportunity to automatically encode the unstructured reports into structured data, thus representing a potential powerful alternative to expensive manual processing. However, notwithstanding the increasing interest in this area, there is still limited availability of NLP approaches for pathology reports in languages other than English, including Italian, to date. The aim of our work was to develop an automated algorithm based on NLP techniques, able to identify and classify the morphological content of pathology reports in the Italian language with micro-averaged performance scores higher than 95%. Specifically, a novel, domain-specific classifier that uses linguistic rules was developed and tested on 27,239 pathology reports from a single Italian oncological centre, following the International Classification of Diseases for Oncology morphology classification standard (ICD-O-M). The proposed classification algorithm achieved successful results with a micro-F1 score of 98.14% on 9594 pathology reports in the test dataset. This algorithm relies on rules defined on data from a single hospital that is specifically dedicated to cancer, but it is based on general processing steps which can be applied to different datasets. Further research will be important to demonstrate the generalizability of the proposed approach on a larger corpus from different hospitals.
Cancer morphology
Italian language
Natural Language Processing
Pathology Reports
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11311/1213397
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