Semi-supervised information extraction for cancer pathology reports

Pathology reports are a main source of data for cancer surveillance programs. Manual coding of pathology reports is labor-intensive but necessary for obtaining labeled data to train automated information extraction systems. In this study, we investigated semi-supervised deep learning, improving the performance of a multitask information extraction system for automated annotation of pathology reports. We used a set of over 374,000 pathology reports from the Louisiana Tumor Registry and a novel convolutional attention-based auto-encoder. We performed a set of experiments comparing supervised training augmented with unlabeled data at 1%, 5%, 10%, and 50% of the original data size. We also compared the impact of extending text processing to include unlabeled tokens. We find that semi-supervised training consistently improved individual performance with increased micro-Averaged F-scores between 0.012 and 0.064 and increased macro-Averaged F-scores of up to 0.158. This demonstrates that semantic information learned via unsupervised learning can be used to improve supervised clinical task performance.