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基于DNA链置换的赢家通吃神经网络

王宾 李亚 赵宏伟

王宾, 李亚, 赵宏伟. 基于DNA链置换的赢家通吃神经网络[J]. 电子与信息学报, 2021, 43(8): 2430-2438. doi: 10.11999/JEIT200579
引用本文: 王宾, 李亚, 赵宏伟. 基于DNA链置换的赢家通吃神经网络[J]. 电子与信息学报, 2021, 43(8): 2430-2438. doi: 10.11999/JEIT200579
Bin WANG, Ya LI, Hongwei ZHAO. The Winner-Take-All Neural Network Based on DNA Strand Displacement[J]. Journal of Electronics & Information Technology, 2021, 43(8): 2430-2438. doi: 10.11999/JEIT200579
Citation: Bin WANG, Ya LI, Hongwei ZHAO. The Winner-Take-All Neural Network Based on DNA Strand Displacement[J]. Journal of Electronics & Information Technology, 2021, 43(8): 2430-2438. doi: 10.11999/JEIT200579

基于DNA链置换的赢家通吃神经网络

doi: 10.11999/JEIT200579
基金项目: 国家重点研发计划重大专项项目(2018YFC0910500),国家自然科学基金(61425002, 61751203, 61772100, 61972266, 61802040, 61672121),辽宁省自认科学基金(20180551241, 2019-ZD-0567)
详细信息
    作者简介:

    王宾:男,1983年生,副教授,研究方向为DNA计算、信息安全、智能计算

    李亚:女,1994年生,硕士生,研究方向为DNA计算

    赵宏伟:男,1974年生,副教授,研究方向为模式识别和机器学习

    通讯作者:

    王宾 wangbin@dlu.edu.cn

  • 中图分类号: TN911.7; TP391

The Winner-Take-All Neural Network Based on DNA Strand Displacement

Funds: The National Key R&D Program of China (2018YFC0910500), The National Natural Science Foundation of China (61425002, 61751203, 61772100, 61972266, 61802040, 61672121), The Natural Science Foundation of Liaoning of Province (20180551241, 2019-ZD-0567)
  • 摘要: DNA链置换技术广泛用于生物计算中,在计算能力和信息处理方面表现出色。但是,在信号的放大、恢复与比较等一些计算中使用DNA链置换技术,不仅增加DNA链的数量,还会带来额外的计算成本。因此,为了减少DNA链的使用数量,该文构建了一个基于DNA链置换实现的赢家通吃(WTA)神经网络。首先,通过神经元实现逻辑运算AND, NAND和OR,将其级联成WTA神经网络解决了线性不可分问题。通过与别人结果的比较,证明该文采用方法的有效性,并在Visual DSD(DNA链置换)中获得了稳定而直观的结果。然后,为了检验神经元级联的可扩展性,设计了一个3人表决器,并对科学家进行分类,该文展示了分子系统如何表现出与大脑具有类似行为的思考能力,最后证明获得的准确率高于其他方法。
  • 图  1  神经元结构图

    图  2  实现AND的过程

    图  3  神经元实现逻辑运算AND

    图  4  WTA实现XOR的仿真图

    图  5  采用AND和OR实现的双轨XOR

    图  6  WTA神经网络实现XOR

    图  7  3人表决器的WTA简化结构图

    图  8  3人表决器的仿真图

    图  9  分类电路的结构

    图  10  WTA神经网络的DNA实现

    图  11  湮灭方法实现科学家模拟图

  • [1] ADLEMAN L M. Molecular computation of solutions to combinatorial problems[J]. Science, 1994, 266(5187): 1021–1024. doi: 10.1126/science.7973651
    [2] LI Wei, YANG Yang, YAN Hao, et al. Three-input majority logic gate and multiple input logic circuit based on DNA strand displacement[J]. Nano Letters, 2013, 13(6): 2980–2988. doi: 10.1021/nl4016107
    [3] THUBAGERE A J, THACHUK C, BERLEANT J, et al. Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components[J]. Nature Communications, 2017, 8: 14373. doi: 10.1038/ncomms14373
    [4] GREEN S J, LUBRICH D, and TURBERFIELD A J. DNA hairpins: fuel for autonomous DNA devices[J]. Biophysical Journal, 2006, 91(8): 2966–2975. doi: 10.1529/biophysj.106.084681
    [5] ZHAO Yunbin, LIU Yuan, ZHENG Xuedong, et al. Half adder and half subtractor logic gates based on nicking enzymes[J]. Molecular Systems Design & Engineering, 2019, 4(6): 1103–1113. doi: 10.1039/C9ME00090A
    [6] 殷志祥, 唐震, 张强, 等. 基于DNA折纸基底的与非门计算模型[J]. 电子与信息学报, 2020, 42(6): 1355–1364. doi: 10.11999/JEIT190825

    YIN Zhixiang, TANG Zhen, ZHANG Qiang, et al. NAND gate computational model based on the DNA origami template[J]. Journal of Electronics &Information Technology, 2020, 42(6): 1355–1364. doi: 10.11999/JEIT190825
    [7] 孙军伟, 李智, 王延峰. 基于DNA链置换的三级联组合分子逻辑电路设计[J]. 电子与信息学报, 2020, 42(6): 1401–1409. doi: 10.11999/JEIT190847

    SUN Junwei, LI Zhi, and WANG Yanfeng. Design of three-cascade combinatorial molecular logic circuit based on DNA strand displacement[J]. Journal of Electronics &Information Technology, 2020, 42(6): 1401–1409. doi: 10.11999/JEIT190847
    [8] LILIENTHAL S, KLEIN M, ORBACH R, et al. Continuous variables logic via coupled automata using a DNAzyme cascade with feedback[J]. Chemical Science, 2017, 8(3): 2161–2168. doi: 10.1039/C6SC03892A
    [9] WANG Bin, XIE Yingjie, ZHOU Shihua, et al. Correcting errors in image encryption based on DNA coding[J]. Molecules, 2018, 23(8): 1878. doi: 10.3390/molecules23081878
    [10] WANG Bin, ZHANG Qiang, and WEI Xiaopeng. Tabu variable neighborhood search for designing DNA barcodes[J]. IEEE Transactions on NanoBioscience, 2020, 19(1): 127–131. doi: 10.1109/TNB.2019.2942036
    [11] SONG Tianqi, GOPALKRISHNAN N, ESHRA A, et al. Improving the performance of DNA strand displacement circuits by shadow cancellation[J]. ACS Nano, 2018, 12(11): 11689–11697. doi: 10.1021/acsnano.8b07394
    [12] 许鹏, 方刚, 石晓龙, 等. DNA存储及其研究进展[J]. 电子与信息学报, 2020, 42(6): 1326–1331. doi: 10.11999/JEIT190863

    XU Peng, FANG Gang, SHI Xiaolong, et al. DNA storage and its research progress[J]. Journal of Electronics &Information Technology, 2020, 42(6): 1326–1331. doi: 10.11999/JEIT190863
    [13] SEELIG G, SOLOVEICHIK D, ZHANG D Y, et al. Enzyme-free nucleic acid logic circuits[J]. Science, 2006, 314(5805): 1585–1588. doi: 10.1126/science.1132493
    [14] ZHANG D Y, TURBERFIELD A J, YURKE B, et al. Engineering entropy-driven reactions and networks catalyzed by DNA[J]. Science, 2007, 318(5853): 1121–1125. doi: 10.1126/science.1148532
    [15] LAKIN M R and STEFANOVIC D. Supervised learning in adaptive DNA strand displacement networks[J]. ACS Synthetic Biology, 2016, 5(8): 885–897. doi: 10.1021/acssynbio.6b00009
    [16] SONG Tianqi, GARG S, MOKHTAR R, et al. Analog computation by DNA strand displacement circuits[J]. ACS Synthetic Biology, 2016, 5(8): 898–912. doi: 10.1021/acssynbio.6b00144
    [17] QIAN Lulu, WINFREE E, and BRUCK J. Neural network computation with DNA strand displacement cascades[J]. Nature, 2011, 475(7356): 368–372. doi: 10.1038/nature10262
    [18] GENOT A J, FUJII T, and RONDELEZ Y. Scaling down DNA circuits with competitive neural networks[J]. Journal of the Royal Society Interface, 2013, 10(85): 20130212. doi: 10.1098/rsif.2013.0212
    [19] SHI Xiaolong, WANG Zhiyu, DENG Chenyan, et al. A novel bio-sensor based on DNA strand displacement[J]. PLoS One, 2014, 9(10): e108856. doi: 10.1371/journal.pone.0108856
    [20] CHERRY K M and QIAN Lulu. Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks[J]. Nature, 2018, 559(7714): 370–376. doi: 10.1038/s41586-018-0289-6
    [21] LAKIN M R, YOUSSEF S, POLO F, et al. Visual DSD: A design and analysis tool for DNA strand displacement systems[J]. Bioinformatics, 2011, 27(22): 3211–3213. doi: 10.1093/bioinformatics/btr543
    [22] WANG Yanfeng, ZHANG Wenwen, LI Xing, et al. Molecular logic gates based on localized DNA strand displacement[J]. Journal of Computational and Theoretical Nanoscience, 2016, 13(6): 3948–3952. doi: 10.1166/jctn.2016.5231
    [23] SONG Tianqi, GARG S, MOKHTAR R, et al. Design and analysis of compact DNA strand displacement circuits for analog computation using autocatalytic amplifiers[J]. ACS Synthetic Biology, 2018, 7(1): 46–53. doi: 10.1021/acssynbio.6b00390
    [24] YANG Jing, WU Ranfeng, LI Yifan, et al. Entropy-driven DNA logic circuits regulated by DNAzyme[J]. Nucleic Acids Research, 2018, 46(16): 8532–8541. doi: 10.1093/nar/gky663
    [25] ESHRA A, SHAH S, SONG Tianqi, et al. Renewable DNA hairpin-based logic circuits[J]. IEEE Transactions on Nanotechnology, 2019, 18: 252–259. doi: 10.1109/TNANO.2019.2896189
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出版历程
  • 收稿日期:  2020-07-15
  • 修回日期:  2020-11-10
  • 网络出版日期:  2020-11-23
  • 刊出日期:  2021-08-10

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