Pre-trained language models (LMs) have been deployed as the state-of-the-art natural language processing (NLP) approaches for multiple clinical applications. Model generalisability is important in clinical domain due to the low available resources. In this study, we evaluated transfer learning techniques for an important clinical application: detecting suicide attempt (SA) and suicide ideation (SI) in electronic health records (EHRs). Using the annotation guideline provided by the authors of ScAN, we annotated two EHR datasets from different hospitals. We then fine-tuned ScANER, a publicly available SA and SI detection model, to evaluate five different parameter efficient transfer learning techniques, such as adapter-based learning and soft-prompt tuning, on the two datasets. Without any fine-tuning, ScANER achieve macro F1-scores of 0.85 and 0.87 for SA and SI evidence detection across the two datasets. We observed that by fine-tuning less than ~2% of ScANER’s parameters, we were able to further improve the macro F1-score for SA-SI evidence detection by 3% and 5% for the two EHR datasets. Our results show that parameter-efficient transfer learning methods can help improve the performance of publicly available clinical models on new hospital datasets with few annotations.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

Suicide is an important public health concern and one of the leading causes of death worldwide. Suicidal behaviors, including suicide attempts (SA) and suicide ideations (SI), are leading risk factors for death by suicide. Information related to patients’ previous and current SA and SI are frequently documented in the electronic health record (EHR) notes. Accurate detection of such documentation may help improve surveillance and predictions of patients’ suicidal behaviors and alert medical professionals for suicide prevention efforts. In this study, we first built Suicide Attempt and Ideation Events (ScAN) dataset, a subset of the publicly available MIMIC III dataset spanning over 12k+ EHR notes with 19k+ annotated SA and SI events information. The annotations also contain attributes such as method of suicide attempt. We also provide a strong baseline model ScANER (Suicide Attempt and Ideation Events Retriever), a multi-task RoBERTa-based model with a retrieval module to extract all the relevant suicidal behavioral evidences from EHR notes of an hospital-stay and, and a prediction module to identify the type of suicidal behavior (SA and SI) concluded during the patient’s stay at the hospital. ScANER achieved a macro-weighted F1-score of 0.83 for identifying suicidal behavioral evidences and a macro F1-score of 0.78 and 0.60 for classification of SA and SI for the patient’s hospital-stay, respectively. ScAN and ScANER are publicly available.

We explore state-of-the-art neural models for question answering on electronic medical records and improve their ability to generalize better on previously unseen (paraphrased) questions at test time. We enable this by learning to predict logical forms as an auxiliary task along with the main task of answer span detection. The predicted logical forms also serve as a rationale for the answer. Further, we also incorporate medical entity information in these models via the ERNIE architecture. We train our models on the large-scale emrQA dataset and observe that our multi-task entity-enriched models generalize to paraphrased questions ~5% better than the baseline BERT model.

Conversational Machine Comprehension (CMC), a research track in conversational AI, expects the machine to understand an open-domain natural language text and thereafter engage in a multi-turn conversation to answer questions related to the text. While most of the research in Machine Reading Comprehension (MRC) revolves around single-turn question answering (QA), multi-turn CMC has recently gained prominence, thanks to the advancement in natural language understanding via neural language models such as BERT and the introduction of large-scale conversational datasets such as CoQA and QuAC. The rise in interest has, however, led to a flurry of concurrent publications, each with a different yet structurally similar modeling approach and an inconsistent view of the surrounding literature. With the volume of model submissions to conversational datasets increasing every year, there exists a need to consolidate the scattered knowledge in this domain to streamline future research. This literature review attempts at providing a holistic overview of CMC with an emphasis on the common trends across recently published models, specifically in their approach to tackling conversational history. The review synthesizes a generic framework for CMC models while highlighting the differences in recent approaches and intends to serve as a compendium of CMC for future researchers.