Ensembling classical machine learning and deep learning approaches for morbidity identification from clinical notes

The past decade has seen an explosion of the amount of digital information generated within the healthcare domain. Digital data exist in the form of images, video, speech, transcripts, electronic health records, clinical records, and free-text. Analysis and interpretation of healthcare data is a daunting task, and it demands a great deal of time, resources, and human effort. In this paper, we focus on the problem of co-morbidity recognition from patient’s clinical records. To this aim, we employ both classical machine learning and deep learning approaches.We use word embeddings and bag-of-words representations, coupled with feature selection techniques. The goal of our work is to develop a classification system to identify whether a certain health condition occurs for a patient by studying his/her past clinical records. In more detail, we have used pre-trained word2vec, domain-trained, GloVe, fastText, and universal sentence encoder embeddings to tackle the classification of sixteen morbidity conditions within clinical records. We have compared the outcomes of classical machine learning and deep learning approaches with the employed feature representation methods and feature selection methods. We present a comprehensive discussion of the performances and behaviour of the employed classical machine learning and deep learning approaches. Finally, we have also used ensemble learning techniques over a large number of combinations of classifiers to improve the single model performance. For our experiments, we used the n2c2 natural language processing research dataset, released by Harvard Medical School. The dataset is in the form of clinical notes that contain patient discharge summaries. Given the unbalancedness of the data and their small size, the experimental results indicate the advantage of the ensemble learning technique with respect to single classifier models. In particular, the ensemble learning technique has slightly improved the performances of single classification models but has greatly reduced the variance of predictions stabilizing the accuracies (i.e., the lower standard deviation in comparison with single classifiers). In real-life scenarios, our work can be employed to identify with high accuracy morbidity conditions of patients by feeding our tool with their current clinical notes. Moreover, other domains where classification is a common problem might benefit from our approach as well.