An Efficient Contrastive Unimodal Pretraining Method for EHR Time Series Data
This addresses computational efficiency problems for clinics using EHR data, though it appears incremental as it builds on existing contrastive learning approaches.
The paper tackles the challenge of training deep neural networks on long clinical timeseries data from EHRs by proposing an efficient contrastive pretraining method that reduces computational demands compared to existing SOTA approaches. The method achieves better performance as model and vocabulary sizes scale and demonstrates transferability across clinical datasets (MIMIC-III to eICU).
Machine learning has revolutionized the modeling of clinical timeseries data. Using machine learning, a Deep Neural Network (DNN) can be automatically trained to learn a complex mapping of its input features for a desired task. This is particularly valuable in Electronic Health Record (EHR) databases, where patients often spend extended periods in intensive care units (ICUs). Machine learning serves as an efficient method for extract meaningful information. However, many state-of-the-art (SOTA) methods for training DNNs demand substantial volumes of labeled data, posing significant challenges for clinics in terms of cost and time. Self-supervised learning offers an alternative by allowing practitioners to extract valuable insights from data without the need for costly labels. Yet, current SOTA methods often necessitate large data batches to achieve optimal performance, increasing computational demands. This presents a challenge when working with long clinical timeseries data. To address this, we propose an efficient method of contrastive pretraining tailored for long clinical timeseries data. Our approach utilizes an estimator for negative pair comparison, enabling effective feature extraction. We assess the efficacy of our pretraining using standard self-supervised tasks such as linear evaluation and semi-supervised learning. Additionally, our model demonstrates the ability to impute missing measurements, providing clinicians with deeper insights into patient conditions. We demonstrate that our pretraining is capable of achieving better performance as both the size of the model and the size of the measurement vocabulary scale. Finally, we externally validate our model, trained on the MIMIC-III dataset, using the eICU dataset. We demonstrate that our model is capable of learning robust clinical information that is transferable to other clinics.