Inferring ADR causality by predicting the Naranjo Score from Clinical Notes.

Clinical judgment studies are an integral part of drug safety surveillance and pharmacovigilance frameworks. They help quantify the causal relationship between medication and its adverse drug reactions (ADRs). To conduct such studies, physicians need to review patients' charts manually to answer Naranjo questionnaire.

Calibrating Structured Output Predictors for Natural Language Processing.

We address the problem of calibrating prediction confidence for output entities of interest in natural language processing (NLP) applications. It is important that NLP applications such as named entity recognition and question answering produce calibrated confidence scores for their predictions, especially if the applications are to be deployed in a safety-critical domain such as healthcare. However, the output space of such structured prediction models is often too large to adapt binary or multi-class calibration methods directly.

Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0).

Introduction: This work describes the Medication and Adverse Drug Events from Electronic Health Records (MADE 1.0) corpus and provides an overview of the MADE 1.0 2018 challenge for extracting medication, indication, and adverse drug events (ADEs) from electronic health record (EHR) notes.

Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach.

Background: Medical terms are a major obstacle for patients to comprehend their electronic health record (EHR) notes. Clinical natural language processing (NLP) systems that link EHR terms to lay terms or definitions allow patients to easily access helpful information when reading through their EHR notes, and have shown to improve patient EHR comprehension. However, high-quality lay language resources for EHR terms are very limited in the public domain.

Structured prediction models for RNN based sequence labeling in clinical text.

Sequence labeling is a widely used method for named entity recognition and information extraction from unstructured natural language data. In clinical domain one major application of sequence labeling involves extraction of medical entities such as medication, indication, and side-effects from Electronic Health Record narratives. Sequence labeling in this domain, presents its own set of challenges and objectives.

Bidirectional RNN for Medical Event Detection in Electronic Health Records.

Sequence labeling for extraction of medical events and their attributes from unstructured text in Electronic Health Record (EHR) notes is a key step towards semantic understanding of EHRs. It has important applications in health informatics including pharmacovigilance and drug surveillance. The state of the art supervised machine learning models in this domain are based on Conditional Random Fields (CRFs) with features calculated from fixed context windows.