Dongfang Xu

Yanjun Gao, Dmitriy Dligach, Timothy Miller et al. · harvard

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.

Dongfang Xu, Shan Chen, Timothy Miller

In this paper, we present our work participating in the BioCreative VII Track 3 - automatic extraction of medication names in tweets, where we implemented a multi-task learning model that is jointly trained on text classification and sequence labelling. Our best system run achieved a strict F1 of 80.4, ranking first and more than 10 points higher than the average score of all participants. Our analyses show that the ensemble technique, multi-task learning, and data augmentation are all beneficial for medication detection in tweets.

Dongfang Xu, Peter Jansen, Jaycie Martin et al.

Prior work has demonstrated that question classification (QC), recognizing the problem domain of a question, can help answer it more accurately. However, developing strong QC algorithms has been hindered by the limited size and complexity of annotated data available. To address this, we present the largest challenge dataset for QC, containing 7,787 science exam questions paired with detailed classification labels from a fine-grained hierarchical taxonomy of 406 problem domains. We then show that a BERT-based model trained on this dataset achieves a large (+0.12 MAP) gain compared with previous methods, while also achieving state-of-the-art performance on benchmark open-domain and biomedical QC datasets. Finally, we show that using this model's predictions of question topic significantly improves the accuracy of a question answering system by +1.7% P@1, with substantial future gains possible as QC performance improves.