Evidence map›Paper›PMID 37196988›Full record

ArticleJournal of biomedical informatics2023

A deep learning approach for medication disposition and corresponding attributes extraction.

Qiwei Gan, Mengke Hu, Kelly S Peterson, Hannah Eyre, Patrick R Alba, Annie E Bowles, Johnathan C Stanley, Scott L DuVall, Jianlin Shi

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of biomedical informatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Review
  2. AI-Based Automation for Medication Reconciliation: Scoping Review.Journal of medical Internet research · 2026
    Article
  3. Clinical natural language processing for secondary uses.Journal of biomedical informatics · 2024
    Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Qiwei GanVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA.
Mengke HuVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA.
Kelly S PetersonDivision of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA; Veterans Health Administration Office of Analytics and Performance Integration, 500, Foothill Boulevard, Salt Lake City 84148, USA.
Hannah EyreVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA.
Patrick R AlbaVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA.
Annie E BowlesVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA.
Johnathan C StanleyVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA.
Scott L DuVallVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA.
Jianlin ShiVA Salt Lake City Health Care System, 500, Foothill Boulevard, Salt Lake City 84148, USA; Division of Epidemiology, University of Utah, 295 Chipeta Way, Salt Lake City 84132, USA. Electronic address: jianlin.shi@utah.edu.

Funding

From genomics to natural language processing: A protected environment for research computing in the health scienceS10OD021644 · OD · UNIVERSITY OF UTAH · PI CHEATHAM, THOMAS E. · 2017 to 2017
$494k
NIH HHS S10 OD021644
6 · The paper itself

Abstract

objectiveThis article summarizes our approach to extracting medication and corresponding attributes from clinical notes, which is the focus of track 1 of the 2022 National Natural Language Processing (NLP) Clinical Challenges(n2c2) shared task.

methodsThe dataset was prepared using Contextualized Medication Event Dataset (CMED), including 500 notes from 296 patients. Our system consisted of three components: medication named entity recognition (NER), event classification (EC), and context classification (CC). These three components were built using transformer models with slightly different architecture and input text engineering. A zero-shot learning solution for CC was also explored.

resultsOur best performance systems achieved micro-average F1 scores of 0.973, 0.911, and 0.909 for the NER, EC, and CC, respectively.

conclusionIn this study, we implemented a deep learning-based NLP system and demonstrated that our approach of (1) utilizing special tokens helps our model to distinguish multiple medications mentions in the same context; (2) aggregating multiple events of a single medication into multiple labels improves our model's performance.

Indexed as

Deep LearningHumansNatural Language ProcessingClinical natural language processingConcept-attribute relation classificationMedication information extraction

Identifiers

PMID37196988
PMCPMC10527481

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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.