The process by which sections in a document are demarcated and labeled is known as section identification. Such sections are helpful to the reader when searching for information and contextualizing specific topics. The goal of this work is to segment the sections of clinical medical domain documentation. The primary contribution of this work is MedSecId, a publicly available set of 2,002 fully annotated medical notes from the MIMIC-III. We include several baselines, source code, a pretrained model and analysis of the data showing a relationship between medical concepts across sections using principal component analysis.
This paper reports on the performance of Edin-burgh_UCL_Health's models in the Social Media Mining for Health (SMM4H) 2022 shared tasks. Our team participated in the tasks related to the Identification of Adverse Drug Events (ADEs), the classification of change in medication (change-med) and the classification of selfreport of vaccination (self-vaccine). Our best performing models are based on DeepADEM-iner (with respective F1= 0.64, 0.62 and 0.39 for ADE identification), on a GloVe model trained on Twitter (with F1=0.11 for the changemed) and finally on a stack embedding including a layer of Glove embedding and two layers of Flair embedding (with F1= 0.77 for selfreport).
Difficulties with social aspects of language are among the hallmarks of autism spectrum disorder (ASD). These communication differences are thought to contribute to the challenges that adults with ASD experience when seeking employment, underscoring the need for interventions that focus on improving areas of weakness in pragmatic and social language. In this paper, we describe a transformer-based framework for identifying linguistic features associated with social aspects of communication using a corpus of conversations between adults with and without ASD and neurotypical conversational partners produced while engaging in collaborative tasks. While our framework yields strong accuracy overall, performance is significantly worse for the language of participants with ASD, suggesting that they use a more diverse set of strategies for some social linguistic functions. These results, while showing promise for the development of automated language analysis tools to support targeted language interventions for ASD, also reveal weaknesses in the ability of large contextualized language models to model neuroatypical language.
Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.