Hierarchy-aware Adverse Reaction Embeddings for Signal Detection.

Post-market drug surveillance monitors new and evolving treatments for their effectiveness and safety in real-world conditions. A large amount of drug safety surveillance data is captured by spontaneous reporting systems such as the FAERS. Developing automated methods to identify actionable safety signals from these databases is an active area of research. In this paper, we propose two novel network representation learning methods (HARE and T-HARE) for signal detection that jointly utilize association information between drugs and medical outcomes from the FAERS and ancestral information in medical ontologies. We evaluate these methods using two publicly available reference datasets, EU-ADR and OMOP corpus. Experimental results showed that the proposed methods significantly outper-formed standard methodologies based on disproportionality metrics and the existing state-of-the-art aer2vec method with statistically significant improvements on both EU-ADR and OMOP datasets. Through quantitative and qualitative analysis, we demonstrate the potential of the proposed methods for effective signal detection.

AI-assisted tracking of worldwide non-pharmaceutical interventions for COVID-19.

The Coronavirus disease 2019 (COVID-19) global pandemic has transformed almost every facet of human society throughout the world. Against an emerging, highly transmissible disease, governments worldwide have implemented non-pharmaceutical interventions (NPIs) to slow the spread of the virus. Examples of such interventions include community actions, such as school closures or restrictions on mass gatherings, individual actions including mask wearing and self-quarantine, and environmental actions such as cleaning public facilities. We present the Worldwide Non-pharmaceutical Interventions Tracker for COVID-19 (WNTRAC), a comprehensive dataset consisting of over 6,000 NPIs implemented worldwide since the start of the pandemic. WNTRAC covers NPIs implemented across 261 countries and territories, and classifies NPIs into a taxonomy of 16 NPI types. NPIs are automatically extracted daily from Wikipedia articles using natural language processing techniques and then manually validated to ensure accuracy and veracity. We hope that the dataset will prove valuable for policymakers, public health leaders, and researchers in modeling and analysis efforts to control the spread of COVID-19.

Reducing Physicians' Cognitive Load During Chart Review: A Problem-Oriented Summary of the Patient Electronic Record.

Overabundance of information within electronic health records (EHRs) has resulted in a need for automated systems to mitigate the cognitive burden on physicians utilizing today's EHR systems. We present ProSPER, a Problem-oriented Summary of the Patient Electronic Record that displays a patient summary centered around an auto-generated problem list and disease-specific views for chronic conditions. ProSPER was developed using 1,500 longitudinal patient records from two large multi-specialty medical groups in the United States, and leverages multiple natural language processing (NLP) components targeting various fundamental (e.g. syntactic analysis), clinical (e.g. adverse drug event extraction) and summarizing (e.g. problem list generation) tasks. We report evaluation results for each component and discuss how specific components address existing physician challenges in reviewing EHR data. This work demonstrates the need to leverage holistic information in EHRs to build a comprehensive summarization application, and the potential for NLP-based applications to support physicians and improve clinical care.

Extraction of Information Related to Drug Safety Surveillance From Electronic Health Record Notes: Joint Modeling of Entities and Relations Using Knowledge-Aware Neural Attentive Models.

BACKGROUND: An adverse drug event (ADE) is commonly defined as "an injury resulting from medical intervention related to a drug." Providing information related to ADEs and alerting caregivers at the point of care can reduce the risk of prescription and diagnostic errors and improve health outcomes. ADEs captured in structured data in electronic health records (EHRs) as either coded problems or allergies are often incomplete, leading to underreporting. Therefore, it is important to develop capabilities to process unstructured EHR data in the form of clinical notes, which contain a richer documentation of a patient's ADE. Several natural language processing (NLP) systems have been proposed to automatically extract information related to ADEs. However, the results from these systems showed that significant improvement is still required for the automatic extraction of ADEs from clinical notes. OBJECTIVE: This study aims to improve the automatic extraction of ADEs and related information such as drugs, their attributes, and reason for administration from the clinical notes of patients. METHODS: This research was conducted using discharge summaries from the Medical Information Mart for Intensive Care III (MIMIC-III) database obtained through the 2018 National NLP Clinical Challenges (n2c2) annotated with drugs, drug attributes (ie, strength, form, frequency, route, dosage, duration), ADEs, reasons, and relations between drugs and other entities. We developed a deep learning-based system for extracting these drug-centric concepts and relations simultaneously using a joint method enhanced with contextualized embeddings, a position-attention mechanism, and knowledge representations. The joint method generated different sentence representations for each drug, which were then used to extract related concepts and relations simultaneously. Contextualized representations trained on the MIMIC-III database were used to capture context-sensitive meanings of words. The position-attention mechanism amplified the benefits of the joint method by generating sentence representations that capture long-distance relations. Knowledge representations were obtained from graph embeddings created using the US Food and Drug Administration Adverse Event Reporting System database to improve relation extraction, especially when contextual clues were insufficient. RESULTS: Our system achieved new state-of-the-art results on the n2c2 data set, with significant improvements in recognizing crucial drug-reason (F1=0.650 versus F1=0.579) and drug-ADE (F1=0.490 versus F1=0.476) relations. CONCLUSIONS: This study presents a system for extracting drug-centric concepts and relations that outperformed current state-of-the-art results and shows that contextualized embeddings, position-attention mechanisms, and knowledge graph embeddings effectively improve deep learning-based concepts and relation extraction. This study demonstrates the potential for deep learning-based methods to help extract real-world evidence from unstructured patient data for drug safety surveillance.

Adverse Drug Events Detection in Clinical Notes by Jointly Modeling Entities and Relations Using Neural Networks.

BACKGROUND AND SIGNIFICANCE: Adverse drug events (ADEs) occur in approximately 2-5% of hospitalized patients, often resulting in poor outcomes or even death. Extraction of ADEs from clinical narratives can accelerate and automate pharmacovigilance. Using state-of-the-art deep-learning neural networks to jointly model concept and relation extraction, we achieved the highest integrated task score in the 2018 Medication and Adverse Drug Event (MADE) 1.0 challenge. METHODS: We used a combined bidirectional long short-term memory (BiLSTM) and conditional random fields (CRF) neural network to detect medical entities relevant to ADEs and a combined BiLSTM and attention network to determine relations, including the adverse drug reaction relation between medication and sign or symptom entities. Using these models, we conducted three experiments: (1) separate and sequential modeling of entities and relations; (2) joint modeling where relations between medications and sign or symptoms determined ADE and indication entities; (3) use of information from external resources such as the US FDA's adverse event database as additional input to the second method. RESULTS: Joint modeling improved the overall task accuracy from 0.62 to 0.65 F measure, and the additional use of external resources improved the accuracy to 0.66 F measure. Given the gold-standard medical entity labels, the joint model plus external resources method achieved F measures of 0.83 for ADE-relevant medical entity detection and 0.87 for relation detection. CONCLUSION: It is important to use joint modeling techniques and external resources for effectively detecting ADEs from clinical narratives in electronic health record (EHR) systems. While the extraction of entities and relations individually achieved high accuracy, the integrated task still has room for further improvement.

A convolutional route to abbreviation disambiguation in clinical text.

OBJECTIVE: Abbreviations sense disambiguation is a special case of word sense disambiguation. Machine learning methods based on neural networks showed promising results for word sense disambiguation (Festag and Spreckelsen, 2017) [1] and, here we assess their effectiveness for abbreviation sense disambiguation. METHODS: Convolutional Neural Network (CNN) models were trained, one for each abbreviation, to disambiguate abbreviation senses. A reverse substitution (of long forms with short forms) method from a previous study was used on clinical narratives from Cleveland Clinic, USA, to auto-generate training data. Accuracy of the CNN and traditional Support Vector Machine (SVM) models were studied using: (a) 5-fold cross validation on the auto-generated training data; (b) a manually created, set-aside gold standard; and (c) 10-fold cross validation on a publicly available dataset from a previous study. RESULTS: CNN improved accuracy by 1-4 percentage points on all the three datasets compared to SVM, and the improvement was the most for the set-aside dataset. The improvement was statistically significant at p < 0.05 on the auto-generated dataset. We found that for some common abbreviations, sense distributions mismatch between the test and auto generated training data, and mitigating the mismatch significantly improved the model accuracy. CONCLUSION: The neural network models work well in disambiguating abbreviations in clinical narratives, and they are robust across datasets. This avoids feature-engineering for each dataset. Coupled with an enhanced auto-training data generation, neural networks can simplify development of a practical abbreviation disambiguation system.