ArticleJournal of the American Medical Informatics Association : JAMIA
Automated concept-level information extraction to reduce the need for custom software and rules development.
Article in Journal of the American Medical Informatics Association : JAMIA. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 of them syntheses that pooled it.
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Who cites it
24 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Clinical Decision Support and Natural Language Processing in Medicine: Systematic Literature Review.Journal of medical Internet research · 2024Pooled it
- Natural Language Processing Applications in the Clinical Neurosciences: A Machine Learning Augmented Systematic Review.Acta neurochirurgica. Supplement · 2022Pooled it
- Translational NLP: A New Paradigm and General Principles for Natural Language Processing Research.Proceedings of the conference. Association for Computational Linguistics. North American Chapter. Meeting · 2021Article
- Natural Language Processing and Machine Learning for Identifying Incident Stroke From Electronic Health Records: Algorithm Development and Validation.Journal of medical Internet research · 2021Article
- Interactive NLP in Clinical Care: Identifying Incidental Findings in Radiology Reports.Applied clinical informatics · 2019Article
- CogStack - experiences of deploying integrated information retrieval and extraction services in a large National Health Service Foundation Trust hospital.BMC medical informatics and decision making · 2018Article
- NLPReViz: an interactive tool for natural language processing on clinical text.Journal of the American Medical Informatics Association : JAMIA · 2018Article
- Institutional variation in surgical care for early-stage breast cancer at community hospitals.The Journal of surgical research · 2017Article
- A computational framework for converting textual clinical diagnostic criteria into the quality data model.Journal of biomedical informatics · 2016Article
- Automating the generation of lexical patterns for processing free text in clinical documents.Journal of the American Medical Informatics Association : JAMIA · 2015Article
- Comparison of a semi-automatic annotation tool and a natural language processing application for the generation of clinical statement entries.Journal of the American Medical Informatics Association : JAMIA · 2015Article
- Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2014Article
- TextHunter--A User Friendly Tool for Extracting Generic Concepts from Free Text in Clinical Research.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2014Article
- Automatically Detecting Acute Myocardial Infarction Events from EHR Text: A Preliminary Study.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2014Article
- Electronic health records-driven phenotyping: challenges, recent advances, and perspectives.Journal of the American Medical Informatics Association : JAMIA · 2013Article
- Pharmacovigilance using clinical notes.Clinical pharmacology and therapeutics · 2013Article
- Using the electronic medical record to identify community-acquired pneumonia: toward a replicable automated strategy.PloS one · 2013Article
- Learning signals of adverse drug-drug interactions from the unstructured text of electronic health records.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2013Article
- Using natural language processing on the free text of clinical documents to screen for evidence of homelessness among US veterans.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2013Article
- Mining the pharmacogenomics literature--a survey of the state of the art.Briefings in bioinformatics · 2012Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
objectiveDespite at least 40 years of promising empirical performance, very few clinical natural language processing (NLP) or information extraction systems currently contribute to medical science or care. The authors address this gap by reducing the need for custom software and rules development with a graphical user interface-driven, highly generalizable approach to concept-level retrieval. MATERIALS AND
methodsA 'learn by example' approach combines features derived from open-source NLP pipelines with open-source machine learning classifiers to automatically and iteratively evaluate top-performing configurations. The Fourth i2b2/VA Shared Task Challenge's concept extraction task provided the data sets and metrics used to evaluate performance.
resultsTop F-measure scores for each of the tasks were medical problems (0.83), treatments (0.82), and tests (0.83). Recall lagged precision in all experiments. Precision was near or above 0.90 in all tasks. Discussion With no customization for the tasks and less than 5 min of end-user time to configure and launch each experiment, the average F-measure was 0.83, one point behind the mean F-measure of the 22 entrants in the competition. Strong precision scores indicate the potential of applying the approach for more specific clinical information extraction tasks. There was not one best configuration, supporting an iterative approach to model creation.
conclusionAcceptable levels of performance can be achieved using fully automated and generalizable approaches to concept-level information extraction. The described implementation and related documentation is available for download.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.