Towards automated patient data cleaning using deep learning: A feasibility study on the standardization of organ labeling

Abstract: Data cleaning consumes about 80% of the time spent on data analysis for clinical research projects. This is a much bigger problem in the era of big data and machine learning in the field of medicine where large volumes of data are being generated. We report an initial effort towards automated patient data cleaning using deep learning: the standardization of organ labeling in radiation therapy. Organs are often labeled inconsistently at different institutions (sometimes even within the same institution) and at different time periods, which poses a problem for clinical research, especially for multi-institutional collaborative clinical research where the acquired patient data is not being used effectively. We developed a convolutional neural network (CNN) to automatically identify each organ in the CT image and then label it with the standardized nomenclature presented at AAPM Task Group 263. We tested this model on the CT images of 54 patients with prostate and 100 patients with head and neck cancer who previously received radiation therapy. The model achieved 100% accuracy in detecting organs and assigning standardized labels for the patients tested. This work shows the feasibility of using deep learning in patient data cleaning that enables standardized datasets to be generated for effective intra- and interinstitutional collaborative clinical research.