Automatic structuring of electronic medical records is of high demand for clinical workflow solutions to facilitate extraction, storage, and querying of patient care information. However, developing a scalable solution is extremely challenging, specifically for radiology reports, as most healthcare institutes use either no template or department/institute specific templates. Moreover, radiologists’ reporting style varies from one to another as sentences are written in a telegraphic format and do not follow general English grammar rules. In this work, we present an ensemble method that consolidates the predictions of three models, capturing various attributes of textual information for automatic labeling of sentences with section labels. These three models are: 1) Focus Sentence model, capturing context of the target sentence; 2) Surrounding Context model, capturing the neighboring context of the target sentence; and finally, 3) Formatting/Layout model, aimed at learning report formatting cues. We utilize Bi-directional LSTMs, followed by sentence encoders, to acquire the context. Furthermore, we define several features that incorporate the structure of reports. We compare our proposed approach against multiple baselines and state-of-the-art approaches on a proprietary dataset as well as 100 manually annotated radiology notes from the MIMIC-III dataset, which we are making publicly available. Our proposed approach significantly outperforms other approaches by achieving 97.1% accuracy.
Since the introduction of context-aware token representation techniques such as Embeddings from Language Models (ELMo) and Bidirectional Encoder Representations from Transformers (BERT), there has been numerous reports on improved performance on a variety of natural language tasks. Nevertheless, the degree to which the resulting context-aware representations encode information about morpho-syntactic properties of the word/token in a sentence remains unclear. In this paper, we investigate the application and impact of state-of-the-art neural token representations for automatic cue-conditional speculation and negation scope detection coupled with the independently computed morpho-syntactic information. Through this work, We establish a new state-of-the-art for the BioScope and NegPar corpus. More importantly, we provide a thorough analysis of neural representations and additional features interactions, cue-representation for conditioning, discuss model behavior on different datasets and address the annotation-induced biases in the learned representations.