A Time-Series Signal Classification Algorithm and Its Application to Nanopore Ionic Current Signal Identification★

doi:10.6023/A23040113

Acta Chimica Sinica ›› 2023, Vol. 81 ›› Issue (8): 912-919.DOI: 10.6023/A23040113 Previous Articles Next Articles

Special Issue: 庆祝《化学学报》创刊90周年合辑

Article

一种时序信号分类算法在纳米孔道离子电流信号识别中的应用^★

倪雪^a, 辛凯莉^b, 胡正利^b^,^*(), 蒋翠玲^a^,^*(), 万永菁^a, 应佚伦^b, 龙亿涛^b

a 华东理工大学信息科学与工程学院上海 200237
b 南京大学化学化工学院分子传感与成像中心南京 210023

投稿日期:2023-04-03 发布日期:2023-09-14
作者简介:
^★庆祝《化学学报》创刊90周年.
† 共同第一作者
基金资助:
项目受科技部重点研发计划(2022YFA1304604); 国家自然科学基金(22106066); 国家自然科学基金(22027806)

A Time-Series Signal Classification Algorithm and Its Application to Nanopore Ionic Current Signal Identification^★

Xue Ni^a, Kaili Xin^b, Zhengli Hu^b(), Cuiling Jiang^a(), Yongjing Wan^a, Yi-Lun Ying^b, Yi-Tao Long^b

a School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237
b School of Chemistry and Chemical Engineering, Molecular Sensing and Imaging Center (MSIC), Nanjing University, Nanjing 210023

Received:2023-04-03 Published:2023-09-14
Contact: *E-mail: zhenglihu@nju.edu.cn; cuilingjiang@ecust.edu.cn
About author:
^★Dedicated to the 90th anniversary of Acta Chimica Sinica.
† These authors contributed equally to this work.
Supported by:
Ministry of Science and Technology Key R&D Program of China(2022YFA1304604); National Natural Science Foundation of China(22106066); National Natural Science Foundation of China(22027806)

1. .pdf(1166KB)

Abstract

Nanopore-based single molecular analysis technique usually uses time-domain features such as time-current scatter plots of blocking currents for event recognition. However, as the time-domain features overlap with each other, the substances with extremely similar molecular structures are difficult to be accurately discriminated using traditional nanopore recognition methods. The differences in the deep feature representations need fully explored to obtain credible recognition results, thus improving the recognition accuracy of nanopore ionic current signals. Here, a time-series signal classification algorithm is proposed in this paper: firstly, the original signal is framed with overlapping sliding windows to generate sub-signals and extract their shallow feature information; then a time-series signal classification network based on Emphasized Channel Attention, Propagation and Aggregation in time delay neural network (ECAPA-TDNN) is proposed to develop a multi-branch inter-layer feature fusion model for deep feature extraction, where the multi-branch multi-level attention module of this model (RepVGG-SE-Res2Block, RSR-Block) obtains multi-scale features by constructing a feature pyramid structure within each residual block, reduces the inference speed based on structural reparameterization techniques while ensuring the model performance, and introduces Adaptively Spatial Feature Fusion (ASFF) to fuse the features of different layers in the network; finally, a credible statistical prediction strategy is used to obtain reliable classification results by counting the classification probabilities of sub-signals. The experimental results show that for the peptide sequences N'-DDFFIFFDD-C' (DF_I) and N'-DDFFLFFDD- C' (DF_L) containing only the different amino acids I (isoleucine) and L (leucine), which are isomers of each other, the algorithm achieves a recognition accuracy of 99.00%, obviously improving the sensing capability of nanopores for single molecules with similar or even identical molecular weights.

Key words: nanopore analysis, time-series signal, deep feature extraction, inter-layer feature fusion, credible statistical predictions

Cite this article

Xue Ni, Kaili Xin, Zhengli Hu, Cuiling Jiang, Yongjing Wan, Yi-Lun Ying, Yi-Tao Long. A Time-Series Signal Classification Algorithm and Its Application to Nanopore Ionic Current Signal Identification^★[J]. Acta Chimica Sinica, 2023, 81(8): 912-919.

Export EndNote|Reference Manager|ProCite|BibTeX|RefWorks

share this article

Fig. & Tab. 6

Figure 1. (a) Mutant aerolysin nanopore detection of single peptides. The sequences of DF_L and DF_I peptides are N'-DDFFLFFDD-C' and N'-DDFFIFFDD-C', respectively. (b) Ionic current signals, and (c) time-current scatter plot of different peptide substances. Herein, I/I0 indicates the degree of residual current generated by a single peptide molecule entering the nanopore channel, where I0 is the opening current generated by a single Aerolysin pore, I is the residual current after the molecule enters the pore, and τoff represents the residence time of a single peptide molecule in the pore. (d) Flowchart of a nanopore ionic current signal recognition algorithm based on multi-branch interlayer feature fusion networks

Figure 2. Structural diagram of multi-branch interlayer feature fusion network

l	r	ACC/%
256	1/4	89.00
256	1/2	90.18
256	3/4	91.61
192	3/4	90.89
128	3/4	90.17

Table 1. Effect of sub-signal segmentation parameters on experimental results

Models	Subsignal results				Statistical results
Models	Recall/%	Precision/%	F1/%	ACC/%	Recall/%	Precision/%	F1/%	ACC/%
Backbone	90.18	90.37	90.25	90.29	98.00	98.00	98.00	98.00
Backbone with RepVGG	91.09	91.27	91.16	91.19	98.00	98.00	98.00	98.00
Backbone with ASFF	91.39	91.36	91.37	91.39	99.00	99.02	98.99	99.00
This work	91.61	91.58	91.59	91.61	99.00	99.02	98.99	99.00

Table 2. Results of ablation experiments

Figure 3. ROC curves of ablation experiment

Figure 4. Visualization of t-SNE feature distribution

References 32

[1]	Afshar Bakshloo M.; Kasianowicz J. J.; Pastoriza-Gallego M.; Mathé J.; Daniel R.; Piguet F.; Oukhaled A. J. Am. Chem. Soc. 2022, 144, 2716. doi: 10.1021/jacs.1c11758
[2]	Derrington I. M.; Butler T. Z.; Collins M. D.; Manrao E.; Pavlenok M.; Niederweis M.; Gundlach J. H. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 16060. doi: 10.1073/pnas.1001831107
[3]	Hu Z.-L.; Huo M.-Z.; Ying Y.-L.; Long Y.-T. Angew. Chem., Int. Ed. 2021, 60, 14738. doi: 10.1002/anie.v60.27
[4]	Pratanwanich P. N.; Yao F.; Chen Y.; Koh C. W.; Wan Y. K.; Hendra C.; Poon P.; Goh Y. T.; Yap P. M.; Chooi J. Y. Nat. Biotechnol. 2021, 39, 1394. doi: 10.1038/s41587-021-00949-w
[5]	Goenka S. D.; Gorzynski J. E.; Shafin K.; Fisk D. G.; Pesout T.; Jensen T. D.; Monlong J.; Chang P. C.; Baid G.; Bernstein J. A. Nat. Biotechnol. 2022, 40, 1035. doi: 10.1038/s41587-022-01221-5
[6]	Sheng Y.; Zhou K.; Liu L.; Wu H.-C. Angew. Chem., Int. Ed. 2022, 61, e202200866. doi: 10.1002/anie.v61.20
[7]	Ju Y.; Pu M.; Sun K.; Song G.; Geng J. Chem. - Asian J. 2022, 17, e202200774. doi: 10.1002/asia.v17.22
[8]	Zhang Z.; Li T.; Sheng Y.; Liu L.; Wu H.-C. Small 2019, 15, 1804078. doi: 10.1002/smll.v15.2
[9]	Tsutsui M.; Yokota K.; Yoshida T.; Hotehama C.; Kowada H.; Esaki Y.; Taniguchi M.; Washio T.; Kawai T. ACS Sens. 2019, 4, 748. doi: 10.1021/acssensors.9b00113
[10]	Tanimoto I. M. F.; Cressiot B.; Greive S. J.; Le Pioufle B.; Bacri L.; Pelta J. Nano Res. 2022, 15, 9906. doi: 10.1007/s12274-022-4379-2
[11]	Wu X. Y.; Ying Y. L.; Long Y. T. Chem. J. Chin. Univ. 2019, 40, 1825. (in Chinese)
	( 武雪原, 应佚伦, 龙亿涛, 高等学校化学学报, 2019, 40, 1825.)
[12]	Wang L. Y.; Wang H. W.; Lu S. M.; Long Y. T. Chin. J. Anal. Chem. 2021, 49, 1166. (in Chinese)
	( 王凌远, 王浩炜, 芦思珉, 龙亿涛, 分析化学, 2021, 49, 1166.)
[13]	Lu Y.; Hu Z. L.; Ying Y. L.; Long Y. T. J. Instrum. Anal. 2019, 38, 129. (in Chinese)
	( 路瑶, 胡正利, 应佚伦, 龙亿涛, 分析测试学报, 2019, 38, 129.)
[14]	Chen Z.; Wang Z.; Xu Y.; Zhang X.; Tian B.; Bai J. Chem. Sci. 2021, 12, 15750. doi: 10.1039/D1SC04342K
[15]	Zernia S.; van der Heide N. J.; Galenkamp N. S.; Gouridis G.; Maglia G. ACS Nano 2020, 14, 2296. doi: 10.1021/acsnano.9b09434
[16]	Niu H. Y.; Hu Z. L.; Ying Y. L.; Long Y. T. Acta Chim. Sinica 2019, 77, 989. (in Chinese) doi: 10.6023/A19060230
	( 牛红艳, 胡正利, 应佚伦, 龙亿涛, 化学学报, 2019, 77, 989.)
[17]	Li M. Y.; Ying Y. L.; Long Y. T. Acta Chim. Sinica 2019, 77, 984. (in Chinese) doi: 10.6023/A19060202
	( 李孟寅, 应佚伦, 龙亿涛, 化学学报, 2019, 77, 984.)
[18]	Huo M.-Z.; Li M.-Y.; Ying Y.-L.; Long Y.-T. Anal. Chem. 2021, 93, 11364. doi: 10.1021/acs.analchem.1c00851
[19]	Ouldali H.; Sarthak K.; Ensslen T.; Piguet F.; Manivet P.; Pelta J.; Behrends J. C.; Aksimentiev A.; Oukhaled A. Nat. Biotechnol. 2020, 38, 176. doi: 10.1038/s41587-019-0345-2
[20]	Xin K.-L.; Hu Z.-L.; Liu S.-C.; Li X.; Li J.-G.; Niu H.; Ying Y.-L.; Long Y.-T. Angew. Chem., Int. Ed. 2022, 61, e202209970. doi: 10.1002/anie.v61.44
[21]	Hu R.; Rodrigues J. V.; Waduge P.; Yamazaki H.; Cressiot B.; Chishti Y.; Makowski L.; Yu D.; Shakhnovich E.; Zhao Q. ACS Nano 2018, 12, 4494. doi: 10.1021/acsnano.8b00734
[22]	Liu Y.; Zhang S.; Wang Y.; Wang L.; Cao Z.; Sun W.; Fan P.; Zhang P.; Chen H. Y.; Huang S. J. Am. Chem. Soc. 2022, 144, 13717. doi: 10.1021/jacs.2c04595
[23]	Li S. J.; Li X.; Wan Y.-J.; Ying Y.-L.; Yu R.-J.; Long Y.-T. Chem. - Asian J. 2023, 18, e202201144. doi: 10.1002/asia.v18.3
[24]	Liu S.-C.; Li M.-X.; Li M.-Y.; Wang Y.-Q.; Ying Y.-L.; Wan Y.-J.; Long Y.-T. Faraday Discuss. 2018, 210, 87. doi: 10.1039/C8FD00023A
[25]	Li X.; Ying Y.-L.; Fu X.-X.; Wan Y.-J.; Long Y.-T. Angew. Chem., Int. Ed. 2021, 60, 24582. doi: 10.1002/anie.v60.46
[26]	Desplanques B.; Thienpondt J.; Demuynck K.In 21st Annual Conference of the International Speech Communication Association (INTERSPEECH 2020), Shanghai, 2020, pp. 3830-3834.
[27]	Morlet J.; Arens G.; Fourgeau E.; Giard D. Geophysics 1982, 47, 222. doi: 10.1190/1.1441329
[28]	Niu H.; Li M.-Y.; Ying Y.-L.; Long Y.-T. Chem. Sci. 2022, 13, 2456. doi: 10.1039/D1SC06459B
[29]	Cao C.; Li M.-Y.; Cirauqui N.; Wang Y.-Q.; Dal Peraro M.; Tian H.; Long Y.-T. Nat. Commun. 2018, 9, 2823. doi: 10.1038/s41467-018-05108-5
[30]	Fawcett T. Pattern Recognit. Lett. 2006, 27, 861. doi: 10.1016/j.patrec.2005.10.010
[31]	Van der Maaten L.; Hinton G. J. Mach. Learn. Res. 2008, 9, 2579.
[32]	Yang C. Y.; Gu Z.; Hu Z. L.; Ying Y. L.; Long Y. T. J. Electrochem. 2019, 25, 312. (in Chinese)
	( 杨铖宇, 顾震, 胡正利, 应佚伦, 龙亿涛, 电化学, 2019, 25, 312.)

一种时序信号分类算法在纳米孔道离子电流信号识别中的应用^★

A Time-Series Signal Classification Algorithm and Its Application to Nanopore Ionic Current Signal Identification^★

RichHTML

PDF

Supporting Info.

Knowledge

Abstract

Cite this article

share this article

Fig. & Tab. 6

References 32

Related Articles 0

Recommended Articles

Metrics

Comments

一种时序信号分类算法在纳米孔道离子电流信号识别中的应用★

A Time-Series Signal Classification Algorithm and Its Application to Nanopore Ionic Current Signal Identification★

RichHTML

PDF

Supporting Info.

Knowledge

Abstract

Cite this article

share this article

Fig. & Tab. 6

References 32

Related Articles 0

Recommended Articles

Metrics

Comments

一种时序信号分类算法在纳米孔道离子电流信号识别中的应用^★

A Time-Series Signal Classification Algorithm and Its Application to Nanopore Ionic Current Signal Identification^★