Using machine learning to parse breast pathology reports.
Extracting information from electronic medical record is a time-consuming and expensive process when done manually. Rule-based and machine learning techniques are two approaches to solving this problem. In this study, we trained a machine learning model on pathology reports to extract pertinent tumor characteristics, which enabled us to create a large database of attribute searchable pathology reports. This database can be used to identify cohorts of patients with characteristics of interest.



We collected a total of 91,505 breast pathology reports from three Partners hospitals: Massachusetts General Hospital, Brigham and Women's Hospital, and Newton-Wellesley Hospital, covering the period from 1978 to 2016. We trained our system with annotations from two datasets, consisting of 6295 and 10,841 manually annotated reports. The system extracts 20 separate categories of information, including atypia types and various tumor characteristics such as receptors. We also report a learning curve analysis to show how much annotation our model needs to perform reasonably.



The model accuracy was tested on 500 reports that did not overlap with the training set. The model achieved accuracy of 90% for correctly parsing all carcinoma and atypia categories for a given patient. The average accuracy for individual categories was 97%. Using this classifier, we created a database of 91,505 parsed pathology reports.



Our learning curve analysis shows that the model can achieve reasonable results even when trained on a few annotations. We developed a user-friendly interface to the database that allows physicians to easily identify patients with target characteristics and export the matching cohort. This model has the potential to reduce the effort required for analyzing large amounts of data from medical records, and to minimize the cost and time required to glean scientific insight from these data.
Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, USA.
Adam
A
Yala
Department of Electrical Engineering and Computer Science, CSAIL, MIT, Cambridge, USA.
Regina
R
Barzilay
Department of Radiation Oncology, MGH, Boston, USA.
Laura
L
Salama
Division of Surgical Oncology, MGH, Boston, USA. megriff@post.harvard.edu.
Molly
0000-0002-1615-2645
M
Griffin
Geisel School of Medicine at Dartmouth, Hanover, USA.
Grace
G
Sollender
Department of Medical Oncology, MGH, Boston, USA.
Aditya
A
Bardia
Department of Radiology, MGH, Boston, USA.
Constance
C
Lehman
Division of Surgical Oncology, MGH, Boston, USA.
Julliette M
JM
Buckley
Division of Surgical Oncology, MGH, Boston, USA.
Suzanne B
SB
Coopey
Department of Biomedical Informatics, Columbia University, New York, USA.
Fernanda
F
Polubriaginof
Department of Medical Oncology, DFCI, Boston, USA.
Judy E
JE
Garber
Division of Surgical Oncology, MGH, Boston, USA.
Barbara L
BL
Smith
Division of Surgical Oncology, MGH, Boston, USA.
Michele A
MA
Gadd
Division of Surgical Oncology, MGH, Boston, USA.
Michelle C
MC
Specht
Department of Pathology, MGH, Boston, USA.
Thomas M
TM
Gudewicz
Department of Pathology, NWH, Newton, USA.
Anthony J
AJ
Guidi
Department of Radiation Oncology, MGH, Boston, USA.
Alphonse
A
Taghian
Division of Surgical Oncology, MGH, Boston, USA.
Kevin S
KS
Hughes
D001943:Breast Neoplasms / Q000453:epidemiology* / Q000473:pathology; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D057286:Electronic Health Records; D005260:Female; D006801:Humans; D000069550:Machine Learning / Q000706:statistics & numerical data; D060787:Neoplasm Grading; D009362:Neoplasm Metastasis; D009367:Neoplasm Staging; D015203:Reproducibility of Results
Atypia; Breast pathology; Carcinoma in situ; Hyperplasia; Machine learning; Natural language processing; Pathology reports