An approach for medical event detection in Chinese clinical notes of electronic health records.
Background: Medical event detection in narrative clinical notes of electronic health records (EHRs) is a task designed for reading text and extracting information. Most of the previous work of medical event detection treats the task as extracting concepts at word granularity, which omits the overall...
| Published in: | BMC Medical Informatics & Decision Making Vol. 19 |
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| Main Authors: | , , , , |
| Format: | research Journal Article |
| Published: |
BioMed Central
4/9/2019 Supplement 2
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=135796234&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 135796234 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 14726947 1CI0 jtl: BMC Medical Informatics & Decision Making issn: 14726947 maglogo: N pubinfo: dt: 4/9/2019 Supplement 2 vid: 19 pid: 24147 pub: BioMed Central artinfo: ui: 135796234 135796234 NLM30961587 135796234 10.1186/s12911-019-0756-5 NLM30961587 135796234 ppct: 1 formats: tig: atl: An approach for medical event detection in Chinese clinical notes of electronic health records. aug: au: Zhou, Xuesi Xiong, Haoqi Zeng, Sihan Fu, Xiangling Wu, Ji affil: Department of Electronic Engineering, Tsinghua University, Beijing, China sug: ab: Background: Medical event detection in narrative clinical notes of electronic health records (EHRs) is a task designed for reading text and extracting information. Most of the previous work of medical event detection treats the task as extracting concepts at word granularity, which omits the overall structural information of the clinical notes. In this work, we treat each clinical note as a sequence of short sentences and propose an end-to-end deep neural network framework.Methods: We redefined the task as a sequence labelling task at short sentence granularity, and proposed a novel tag system correspondingly. The dataset were derived from a third-level grade-A hospital, consisting of 2000 annotated clinical notes according to our proposed tag system. The proposed end-to-end deep neural network framework consists of a feature extractor and a sequence labeller, and we explored different implementations respectively. We additionally proposed a smoothed Viterbi decoder as sequence labeller without additional parameter training, which can be a good alternative to conditional random field (CRF) when computing resources are limited.Results: Our sequence labelling models were compared to four baselines which treat the task as text classification of short sentences. Experimental results showed that our approach significantly outperforms the baselines. The best result was obtained by using the convolutional neural networks (CNNs) feature extractor and the sequential CRF sequence labeller, achieving an accuracy of 92.6%. Our proposed smoothed Viterbi decoder achieved a comparable accuracy of 90.07% with reduced training parameters, and brought more balanced performance across all categories, which means better generalization ability.Conclusions: Evaluated on our annotated dataset, the comparison results demonstrated the effectiveness of our approach for medical event detection in Chinese clinical notes of EHRs. The best feature extractor is the CNNs feature extractor, and the best sequence labeller is the sequential CRF decoder. And it was empirically verified that our proposed smoothed Viterbi decoder could bring better generalization ability while achieving comparable performance to the sequential CRF decoder. pubtype: Academic Journal doctype: research Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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