Deep learning on time series laboratory test results from electronic health records for early detection of pancreatic cancer.

Journal Article (Journal Article)

The multi-modal and unstructured nature of observational data in Electronic Health Records (EHR) is currently a significant obstacle for the application of machine learning towards risk stratification. In this study, we develop a deep learning framework for incorporating longitudinal clinical data from EHR to infer risk for pancreatic cancer (PC). This framework includes a novel training protocol, which enforces an emphasis on early detection by applying an independent Poisson-random mask on proximal-time measurements for each variable. Data fusion for irregular multivariate time-series features is enabled by a "grouped" neural network (GrpNN) architecture, which uses representation learning to generate a dimensionally reduced vector for each measurement set before making a final prediction. These models were evaluated using EHR data from Columbia University Irving Medical Center-New York Presbyterian Hospital. Our framework demonstrated better performance on early detection (AUROC 0.671, CI 95% 0.667 - 0.675, p < 0.001) at 12 months prior to diagnosis compared to a logistic regression, xgboost, and a feedforward neural network baseline. We demonstrate that our masking strategy results greater improvements at distal times prior to diagnosis, and that our GrpNN model improves generalizability by reducing overfitting relative to the feedforward baseline. The results were consistent across reported race. Our proposed algorithm is potentially generalizable to other diseases including but not limited to cancer where early detection can improve survival.

Full Text

Duke Authors

Cited Authors

  • Park, J; Artin, MG; Lee, KE; Pumpalova, YS; Ingram, MA; May, BL; Park, M; Hur, C; Tatonetti, NP

Published Date

  • July 2022

Published In

Volume / Issue

  • 131 /

Start / End Page

  • 104095 -

PubMed ID

  • 35598881

Electronic International Standard Serial Number (EISSN)

  • 1532-0480

International Standard Serial Number (ISSN)

  • 1532-0464

Digital Object Identifier (DOI)

  • 10.1016/j.jbi.2022.104095


  • eng