Question: How many reports are in the new dataset?
Evidence: Cancer is one of the leading causes of death in the world, with over 80,000 deaths registered in Canada in 2017 (Canadian Cancer Statistics 2017). A computer-aided system for cancer diagnosis usually involves a pathologist rendering a descriptive report after examining the tissue glass slides obtained from the biopsy of a patient. A pathology report contains specific analysis of cells and tissues, and other histopathological indicators that are crucial for diagnosing malignancies. An average sized laboratory may produces a large quantity of pathology reports annually (e.g., in excess of 50,000), but these reports are written in mostly unstructured text and with no direct link to the tissue sample. Furthermore, the report for each patient is a personalized document and offers very high variability in terminology due to lack of standards and may even include misspellings and missing punctuation, clinical diagnoses interspersed with complex explanations, different terminology to label the same malignancy, and information about multiple carcinoma appearances included in a single report BIBREF0 .
In Canada, each Provincial and Territorial Cancer Registry (PTCR) is responsible for collecting the data about cancer diseases and reporting them to Statistics Canada (StatCan). Every year, Canadian Cancer Registry (CCR) uses the information sources of StatCan to compile an annual report on cancer and tumor diseases. Many countries have their own cancer registry programs. These programs rely on the acquisition of diagnostic, treatment, and outcome information through manual processing and interpretation from various unstructured sources (e.g., pathology reports, autopsy/laboratory reports, medical billing summaries). The manual classification of cancer pathology reports is a challenging, time-consuming task and requires extensive training BIBREF0 .
With the continued growth in the number of cancer patients, and the increase in treatment complexity, cancer registries face a significant challenge in manually reviewing the large quantity of reports BIBREF1 , BIBREF0 . In this situation, Natural Language Processing (NLP) systems can offer a unique opportunity to automatically encode the unstructured reports into structured data. Since, the registries already have access to the large quantity of historically labeled and encoded reports, a supervised machine learning approach of feature extraction and classification is a compelling direction for making their workflow more effective and streamlined. If successful, such a solution would enable processing reports in much lesser time allowing trained personnel to focus on their research and analysis. However, developing an automated solution with high accuracy and consistency across wide variety of reports is a challenging problem.
For cancer registries, an important piece of information in a pathology report is the associated ICD-O code which describes the patient's histological diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology BIBREF2 . Prediction of the primary diagnosis from a pathology report provides a valuable starting point for exploration of machine learning techniques for automated cancer surveillance. A major application for this purpose would be “auto-reporting” based on analysis of whole slide images, the digitization of the biopsy glass slides. Structured, summarized and categorized reports can be associated with the image content when searching in large archives. Such as system would be able to drastically increase the efficiency of diagnostic processes for the majority of cases where in spite of obvious primary diagnosis, still time and effort is required from the pathologists to write a descriptive report.
The primary objective of our study is to analyze the efficacy of existing machine learning approaches for the automated classification of pathology reports into different diagnosis categories. We demonstrate that TF-IDF feature vectors combined with linear SVM or XGBoost classifier can be an effective method for classification of the reports, achieving up to 83% accuracy. We also show that TF-IDF features are capable of identifying important keywords within a pathology report. Furthermore, we have created a new dataset consisting of 1,949 pathology reports across 37 primary diagnoses. Taken together, our exploratory experiments with a newly introduced dataset on pathology reports opens many new opportunities for researchers to develop a scalable and automatic information extraction from unstructured pathology reports.
Furthermore, we have created a new dataset consisting of 1,949 pathology reports across 37 primary diagnoses.
Answer: The new dataset contains 1,949 pathology reports across 37 primary diagnoses.