The Revival of the Notes Field: Leveraging the Unstructured Content in Electronic Health Records

Problem: Clinical practice requires the production of a time- and resource-consuming great amount of notes. They contain relevant information, but their secondary use is almost impossible, due to their unstructured nature. Researchers are trying to address this problems, with traditional and promising novel techniques. Application in real hospital settings seems not to be possible yet, though, both because of relatively small and dirty dataset, and for the lack of language-specific pre-trained models.Aim: Our aim is to demonstrate the potential of the above techniques, but also raise awareness of the still open challenges that the scientific communities of IT and medical practitioners must jointly address to realize the full potential of unstructured content that is daily produced and digitized in hospital settings, both to improve its data quality and leverage the insights from data-driven predictive models.Methods: To this extent, we present a narrative literature review of the most recent and relevant contributions to leverage the application of Natural Language Processing techniques to the free-text content electronic patient records. In particular, we focused on four selected application domains, namely: data quality, information extraction, sentiment analysis and predictive models, and automated patient cohort selection. Then, we will present a few empirical studies that we undertook at a major teaching hospital specializing in musculoskeletal diseases.Results: We provide the reader with some simple and affordable pipelines, which demonstrate the feasibility of reaching literature performance levels with a single institution non-English dataset. In such a way, we bridged literature and real world needs, performing a step further toward the revival of notes fields

On the effects of low-quality training data on information extraction from clinical reports

In the last five years there has been a flurry of work on information extraction from clinical documents, that is, on algorithms capable of extracting, from the informal and unstructured texts that are generated during everyday clinical practice, mentions of concepts relevant to such practice. Many of these research works are about methods based on supervised learning, that is, methods for training an information extraction system from manually annotated examples. While a lot of work has been devoted to devising learning methods that generate more and more accurate information extractors, nowork has been devoted to investigating the effect of the quality of training data on the learning process for the clinical domain. Low quality in training data often derives from the fact that the person who has annotated the data is different from the one against whose judgment the automatically annotated data must be evaluated. In this article, we test the impact of such data quality issues on the accuracy of information extraction systems as applied to the clinical domain. We do this by comparing the accuracy deriving from training data annotated by the authoritative coder (i.e., the one who has also annotated the test data and by whose judgment we must abide) with the accuracy deriving from training data annotated by a different coder, equally expert in the subject matter. The results indicate that, although the disagreement between the two coders (as measured on the training set) is substantial, the difference is (surprisingly enough) not always statistically significant. While the dataset used in the present work originated in a clinical context, the issues we study in this work are of more general interest