Accelerated training of bootstrap aggregation-based deep information extraction systems from cancer pathology reports.
Objective: In machine learning, it is evident that the classification of the task performance increases if bootstrap aggregation (bagging) is applied. However, the bagging of deep neural networks takes tremendous amounts of computational resources and training time. The research question that we aim...
| Publicado en: | Journal of Biomedical Informatics Vol. 110 |
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| Autores principales: | , , , , , , , , , , , , |
| Formato: | research Journal Article |
| Publicado: |
Academic Press Inc.
Oct2020
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=146481893&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 146481893 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 15320464 OMB jtl: Journal of Biomedical Informatics issn: 15320464 maglogo: N pubinfo: dt: Oct2020 vid: 110 pid: 735 pub: Academic Press Inc. place: Burlington, Massachusetts artinfo: ui: 146481893 146481893 NLM32919043 146481893 10.1016/j.jbi.2020.103564 NLM32919043 146481893 ppct: 1 formats: tig: atl: Accelerated training of bootstrap aggregation-based deep information extraction systems from cancer pathology reports. aug: au: Yoon, Hong-Jun Klasky, Hilda B. Gounley, John P. Alawad, Mohammed Gao, Shang Durbin, Eric B. Wu, Xiao-Cheng Stroup, Antoinette Doherty, Jennifer Coyle, Linda Penberthy, Lynne Blair Christian, J. Tourassi, Georgia D. affil: Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States of America sug: subj: Neoplasms Information Retrieval Human Computing Methodologies Comparative Studies Multicenter Studies Evaluation Research Validation Studies Funding Source ab: Objective: In machine learning, it is evident that the classification of the task performance increases if bootstrap aggregation (bagging) is applied. However, the bagging of deep neural networks takes tremendous amounts of computational resources and training time. The research question that we aimed to answer in this research is whether we could achieve higher task performance scores and accelerate the training by dividing a problem into sub-problems.Materials and Methods: The data used in this study consist of free text from electronic cancer pathology reports. We applied bagging and partitioned data training using Multi-Task Convolutional Neural Network (MT-CNN) and Multi-Task Hierarchical Convolutional Attention Network (MT-HCAN) classifiers. We split a big problem into 20 sub-problems, resampled the training cases 2,000 times, and trained the deep learning model for each bootstrap sample and each sub-problem-thus, generating up to 40,000 models. We performed the training of many models concurrently in a high-performance computing environment at Oak Ridge National Laboratory (ORNL).Results: We demonstrated that aggregation of the models improves task performance compared with the single-model approach, which is consistent with other research studies; and we demonstrated that the two proposed partitioned bagging methods achieved higher classification accuracy scores on four tasks. Notably, the improvements were significant for the extraction of cancer histology data, which had more than 500 class labels in the task; these results show that data partition may alleviate the complexity of the task. On the contrary, the methods did not achieve superior scores for the tasks of site and subsite classification. Intrinsically, since data partitioning was based on the primary cancer site, the accuracy depended on the determination of the partitions, which needs further investigation and improvement.Conclusion: Results in this research demonstrate that 1. The data partitioning and bagging strategy achieved higher performance scores. 2. We achieved faster training leveraged by the high-performance Summit supercomputer at ORNL. pubtype: Academic Journal doctype: research Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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