Applying methods in natural language processing on electronic health records (EHR) data has attracted rising interests. Existing corpus and annotation focus on modeling textual features and relation prediction. However, there are a paucity of annotated corpus built to model clinical diagnostic thinking, a processing involving text understanding, domain knowledge abstraction and reasoning. In this work, we introduce a hierarchical annotation schema with three stages to address clinical text understanding, clinical reasoning and summarization. We create an annotated corpus based on a large collection of publicly available daily progress notes, a type of EHR that is time-sensitive, problem-oriented, and well-documented by the format of Subjective, Objective, Assessment and Plan (SOAP). We also define a new suite of tasks, Progress Note Understanding, with three tasks utilizing the three annotation stages. This new suite aims at training and evaluating future NLP models for clinical text understanding, clinical knowledge representation, inference and summarization.

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.

Sequence-to-sequence models are appealing because they allow both encoder and decoder to be shared across many tasks by formulating those tasks as text-to-text problems. Despite recently reported successes of such models, we find that engineering input/output representations for such text-to-text models is challenging. On the Clinical TempEval 2016 relation extraction task, the most natural choice of output representations, where relations are spelled out in simple predicate logic statements, did not lead to good performance. We explore a variety of input/output representations, with the most successful prompting one event at a time, and achieving results competitive with standard pairwise temporal relation extraction systems.

Transformer-based neural language models have led to breakthroughs for a variety of natural language processing (NLP) tasks. However, most models are pretrained on general domain data. We propose a methodology to produce a model focused on the clinical domain: continued pretraining of a model with a broad representation of biomedical terminology (PubMedBERT) on a clinical corpus along with a novel entity-centric masking strategy to infuse domain knowledge in the learning process. We show that such a model achieves superior results on clinical extraction tasks by comparing our entity-centric masking strategy with classic random masking on three clinical NLP tasks: cross-domain negation detection, document time relation (DocTimeRel) classification, and temporal relation extraction. We also evaluate our models on the PubMedQA dataset to measure the models’ performance on a non-entity-centric task in the biomedical domain. The language addressed in this work is English.

Recently BERT has achieved a state-of-the-art performance in temporal relation extraction from clinical Electronic Medical Records text. However, the current approach is inefficient as it requires multiple passes through each input sequence. We extend a recently-proposed one-pass model for relation classification to a one-pass model for relation extraction. We augment this framework by introducing global embeddings to help with long-distance relation inference, and by multi-task learning to increase model performance and generalizability. Our proposed model produces results on par with the state-of-the-art in temporal relation extraction on the THYME corpus and is much “greener” in computational cost.

We present refinements over existing temporal relation annotations in the Electronic Medical Record clinical narrative. We refined the THYME corpus annotations to more faithfully represent nuanced temporality and nuanced temporal-coreferential relations. The main contributions are in re-defining CONTAINS and OVERLAP relations into CONTAINS, CONTAINS-SUBEVENT, OVERLAP and NOTED-ON. We demonstrate that these refinements lead to substantial gains in learnability for state-of-the-art transformer models as compared to previously reported results on the original THYME corpus. We thus establish a baseline for the automatic extraction of these refined temporal relations. Although our study is done on clinical narrative, we believe it addresses far-reaching challenges that are corpus- and domain- agnostic.

In this paper we describe an evaluation of the potential of classical information extraction methods to extract drug-related attributes, including adverse drug events, and compare to more recently developed neural methods. We use the 2018 N2C2 shared task data as our gold standard data set for training. We train support vector machine classifiers to detect drug and drug attribute spans, and pair these detected entities as training instances for an SVM relation classifier, with both systems using standard features. We compare to baseline neural methods that use standard contextualized embedding representations for entity and relation extraction. The SVM-based system and a neural system obtain comparable results, with the SVM system doing better on concepts and the neural system performing better on relation extraction tasks. The neural system obtains surprisingly strong results compared to the system based on years of research in developing features for information extraction.

Classic methods for clinical temporal relation extraction focus on relational candidates within a sentence. On the other hand, break-through Bidirectional Encoder Representations from Transformers (BERT) are trained on large quantities of arbitrary spans of contiguous text instead of sentences. In this study, we aim to build a sentence-agnostic framework for the task of CONTAINS temporal relation extraction. We establish a new state-of-the-art result for the task, 0.684F for in-domain (0.055-point improvement) and 0.565F for cross-domain (0.018-point improvement), by fine-tuning BERT and pre-training domain-specific BERT models on sentence-agnostic temporal relation instances with WordPiece-compatible encodings, and augmenting the labeled data with automatically generated “silver” instances.

A large percentage of medical information is in unstructured text format in electronic medical record systems. Manual extraction of information from clinical notes is extremely time consuming. Natural language processing has been widely used in recent years for automatic information extraction from medical texts. However, algorithms trained on data from a single healthcare provider are not generalizable and error-prone due to the heterogeneity and uniqueness of medical documents. We develop a two-stage federated natural language processing method that enables utilization of clinical notes from different hospitals or clinics without moving the data, and demonstrate its performance using obesity and comorbities phenotyping as medical task. This approach not only improves the quality of a specific clinical task but also facilitates knowledge progression in the whole healthcare system, which is an essential part of learning health system. To the best of our knowledge, this is the first application of federated machine learning in clinical NLP.

Mining electronic health records for patients who satisfy a set of predefined criteria is known in medical informatics as phenotyping. Phenotyping has numerous applications such as outcome prediction, clinical trial recruitment, and retrospective studies. Supervised machine learning for phenotyping typically relies on sparse patient representations such as bag-of-words. We consider an alternative that involves learning patient representations. We develop a neural network model for learning patient representations and show that the learned representations are general enough to obtain state-of-the-art performance on a standard comorbidity detection task.

Neural network models are oftentimes restricted by limited labeled instances and resort to advanced architectures and features for cutting edge performance. We propose to build a recurrent neural network with multiple semantically heterogeneous embeddings within a self-training framework. Our framework makes use of labeled, unlabeled, and social media data, operates on basic features, and is scalable and generalizable. With this method, we establish the state-of-the-art result for both in- and cross-domain for a clinical temporal relation extraction task.

Token sequences are often used as the input for Convolutional Neural Networks (CNNs) in natural language processing. However, they might not be an ideal representation for time expressions, which are long, highly varied, and semantically complex. We describe a method for representing time expressions with single pseudo-tokens for CNNs. With this method, we establish a new state-of-the-art result for a clinical temporal relation extraction task.

We experiment with neural architectures for temporal relation extraction and establish a new state-of-the-art for several scenarios. We find that neural models with only tokens as input outperform state-of-the-art hand-engineered feature-based models, that convolutional neural networks outperform LSTM models, and that encoding relation arguments with XML tags outperforms a traditional position-based encoding.