中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
Helix Matrix Transformation Combined With Convolutional Neural Network Algorithm for Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Bacterial Identification

文献类型:期刊论文

作者Ling, Jin1,2; Li, Gaomin1,2; Shao, Hong1,2; Wang, Hong1,2; Yin, Hongrui1,2; Zhou, Hu3; Song, Yufei4; Chen, Gang1,2
刊名FRONTIERS IN MICROBIOLOGY
出版日期2020-11-12
卷号11页码:10
ISSN号1664-302X
关键词matrix-assisted laser desorption ionization-time of flight mass spectrometry bacterial identification helix matrix transformation convolutional neural network algorithm study
DOI10.3389/fmicb.2020.565434
通讯作者Song, Yufei(517582445@qq.com) ; Chen, Gang(ggangchen@139.com)
英文摘要Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis is a rapid and reliable method for bacterial identification. Classification algorithms, as a critical part of the MALDI-TOF MS analysis approach, have been developed using both traditional algorithms and machine learning algorithms. In this study, a method that combined helix matrix transformation with a convolutional neural network (CNN) algorithm was presented for bacterial identification. A total of 14 bacterial species including 58 strains were selected to create an in-house MALDI-TOF MS spectrum dataset. The 1D array-type MALDI-TOF MS spectrum data were transformed through a helix matrix transformation into matrix-type data, which was fitted during the CNN training. Through the parameter optimization, the threshold for binarization was set as 16 and the final size of a matrix-type data was set as 25 x 25 to obtain a clean dataset with a small size. A CNN model with three convolutional layers was well trained using the dataset to predict bacterial species. The filter sizes for the three convolutional layers were 4, 8, and 16. The kernel size was three and the activation function was the rectified linear unit (ReLU). A back propagation neural network (BPNN) model was created without helix matrix transformation and a convolution layer to demonstrate whether the helix matrix transformation combined with CNN algorithm works better. The areas under the receiver operating characteristic (ROC) curve of the CNN and BPNN models were 0.98 and 0.87, respectively. The accuracies of the CNN and BPNN models were 97.78 +/- 0.08 and 86.50 +/- 0.01, respectively, with a significant statistical difference (p < 0.001). The results suggested that helix matrix transformation combined with the CNN algorithm enabled the feature extraction of the bacterial MALDI-TOF MS spectrum, which might be a proposed solution to identify bacterial species.
资助项目Pharmacopeia Committee Project[2020S06] ; Zhejiang Province Public Welfare Technology Application Research Project[LGF19H030008]
WOS研究方向Microbiology
语种英语
出版者FRONTIERS MEDIA SA
WOS记录号WOS:000592210700001
源URL[http://119.78.100.183/handle/2S10ELR8/292613]  
专题中国科学院上海药物研究所
通讯作者Song, Yufei; Chen, Gang
作者单位1.Shanghai Inst Food & Drug Control, NMPA Key Lab Qual Control Therapeut Monoclonal An, Shanghai, Peoples R China
2.Shanghai Inst Food & Drug Control, Dept Biochem Drugs & Biol Prod, Shanghai, Peoples R China
3.Chinese Acad Sci, Shanghai Inst Mat Med, Dept Analyt Chem, Shanghai, Peoples R China
4.Lihuili Hosp, Ningbo Med Ctr, Dept Gastroenterol, Ningbo, Peoples R China
推荐引用方式
GB/T 7714
Ling, Jin,Li, Gaomin,Shao, Hong,et al. Helix Matrix Transformation Combined With Convolutional Neural Network Algorithm for Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Bacterial Identification[J]. FRONTIERS IN MICROBIOLOGY,2020,11:10.
APA Ling, Jin.,Li, Gaomin.,Shao, Hong.,Wang, Hong.,Yin, Hongrui.,...&Chen, Gang.(2020).Helix Matrix Transformation Combined With Convolutional Neural Network Algorithm for Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Bacterial Identification.FRONTIERS IN MICROBIOLOGY,11,10.
MLA Ling, Jin,et al."Helix Matrix Transformation Combined With Convolutional Neural Network Algorithm for Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Bacterial Identification".FRONTIERS IN MICROBIOLOGY 11(2020):10.

入库方式: OAI收割

来源:上海药物研究所

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