Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

Untapped Potential of Clinical Text for Opioid Surveillance

Accurate surveillance is needed to combat the growing opioid epidemic. To investigate the potential volume of missed opioid overdoses, we compare overdose encounters identified by ICD-10-CM codes and an NLP pipeline from two different medical systems. Our results show that the NLP pipeline identified a larger percentage of OOD encounters than ICD-10-CM codes. Thus, incorporating sophisticated NLP techniques into current diagnostic methods has the potential to improve surveillance on the incidence of opioid overdoses

Assessing mortality prediction through different representation models based on concepts extracted from clinical notes

Recent years have seen particular interest in using electronic medical records (EMRs) for secondary purposes to enhance the quality and safety of healthcare delivery. EMRs tend to contain large amounts of valuable clinical notes. Learning of embedding is a method for converting notes into a format that makes them comparable. Transformer-based representation models have recently made a great leap forward. These models are pre-trained on large online datasets to understand natural language texts effectively. The quality of a learning embedding is influenced by how clinical notes are used as input to representation models. A clinical note has several sections with different levels of information value. It is also common for healthcare providers to use different expressions for the same concept. Existing methods use clinical notes directly or with an initial preprocessing as input to representation models. However, to learn a good embedding, we identified the most essential clinical notes section. We then mapped the extracted concepts from selected sections to the standard names in the Unified Medical Language System (UMLS). We used the standard phrases corresponding to the unique concepts as input for clinical models. We performed experiments to measure the usefulness of the learned embedding vectors in the task of hospital mortality prediction on a subset of the publicly available Medical Information Mart for Intensive Care (MIMIC-III) dataset. According to the experiments, clinical transformer-based representation models produced better results with getting input generated by standard names of extracted unique concepts compared to other input formats. The best-performing models were BioBERT, PubMedBERT, and UmlsBERT, respectively

GNTeam at 2018 n2c2:Feature-augmented BiLSTM-CRF for drug-related entity recognition in hospital discharge summaries

Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency, dosage, strength, form, duration, and adverse events) from hospital discharge summaries through deep learning that relies on various representations for clinical named entity recognition. This work was officially part of the 2018 n2c2 shared task, and we use the data supplied as part of the task. We developed two deep learning architecture based on recurrent neural networks and pre-trained language models. We also explore the effect of augmenting word representations with semantic features for clinical named entity recognition. Our feature-augmented BiLSTM-CRF model performed with F1-score of 92.67% and ranked 4th for entity extraction sub-task among submitted systems to n2c2 challenge. The recurrent neural networks that use the pre-trained domain-specific word embeddings and a CRF layer for label optimization perform drug, adverse event and related entities extraction with micro-averaged F1-score of over 91%. The augmentation of word vectors with semantic features extracted using available clinical NLP toolkits can further improve the performance. Word embeddings that are pre-trained on a large unannotated corpus of relevant documents and further fine-tuned to the task perform rather well. However, the augmentation of word embeddings with semantic features can help improve the performance (primarily by boosting precision) of drug-related named entity recognition from electronic health records

Mining and Representing Unstructured Nicotine Use Data in a Structured Format for Secondary Use

The objective of this study was to use rules, NLP and machine learning for addressing the problem of clinical data interoperability across healthcare providers. Addressing this problem has the potential to make clinical data comparable, retrievable and exchangeable between healthcare providers. Our focus was in giving structure to unstructured patient smoking information. We collected our data from the MIMIC-III database. We wrote rules for annotating the data, then trained a CRF sequence classifier. We obtained an f-measure of 86%, 72%, 69%, 80%, and 12% for substance smoked, frequency, amount, temporal, and duration respectively. Amount smoked yielded a small value due to scarcity of related data. Then for smoking status we obtained an f-measure of 94.8% for non-smoker class, 83.0% for current-smoker, and 65.7% for past-smoker. We created a FHIR profile for mapping the extracted data based on openEHR reference models, however in future we will explore mapping to CIMI models