Physiological sensor data cleaning with autoencoders

Objective. Physiological sensor data (e.g. photoplethysmograph) is important for remotely monitoring patients' vital signals, but is often affected by measurement noise. Existing feature-based models for signal cleaning can be limited as they might not capture the full signal characteristics. Approach. In this work we present a deep learning framework for sensor signal cleaning based on dilated convolutions which capture the coarse- and fine-grained structure in order to classify whether a signal is noisy or clean. However, since obtaining annotated physiological data is costly and time-consuming we propose an autoencoder-based semi-supervised model which is able to learn a representation of the sensor signal characteristics, also adding an element of interpretability. Main results. Our proposed models are over 8% more accurate than existing feature-based approaches with half the false positive/negative rates. Finally, we show that with careful tuning (that can be improved further), the semi-supervised model outperforms supervised approaches suggesting that incorporating the large amounts of available unlabeled data can be advantageous for achieving high accuracy (over 90%) and minimizing the false positive/negative rates. Significance. Our approach enables us to reliably separate clean from noisy physiological sensor signal that can pave the development of reliable features and eventually support decisions regarding drug efficacy in clinical trials.