QuipuNet: Convolutional Neural Network for Single-Molecule Nanopore Sensing

Nano Letters
Karolis MisiunasUlrich F Keyser

Abstract

Nanopore sensing is a versatile technique for the analysis of molecules on the single-molecule level. However, extracting information from data with established algorithms usually requires time-consuming checks by an experienced researcher due to inherent variability of solid-state nanopores. Here, we develop a convolutional neural network (CNN) for the fully automated extraction of information from the time-series signals obtained by nanopore sensors. In our demonstration, we use a previously published data set on multiplexed single-molecule protein sensing. The neural network learns to classify translocation events with greater accuracy than previously possible, while also increasing the number of analyzable events by a factor of 5. Our results demonstrate that deep learning can achieve significant improvements in single molecule nanopore detection with potential applications in rapid diagnostics.

References

Mar 13, 2012·Nature Nanotechnology·Ruoshan WeiUlrich Rant
Feb 7, 2013·Physical Review Letters·Mirna MihovilovicDerek Stein
Feb 5, 2015·Nanotechnology·Calin Plesa, Cees Dekker
Jun 16, 2015·Nature Methods·Nicholas J LomanJared T Simpson
Apr 5, 2016·Nature Nanotechnology·Nicholas A W Bell, Ulrich F Keyser
Nov 1, 2016·Nature Nanotechnology·Calin PlesaCees Dekker
Nov 1, 2016·Analytical Chemistry·Jacob H ForstaterArvind Balijepalli
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Aug 2, 2017·Nanotechnology·Tim AlbrechtS M Masudur R Al-Arif

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Citations

Nov 28, 2018·Chemical Communications : Chem Comm·Liang WangXiyun Guan
Jul 17, 2019·Nature Nanotechnology·Morteza ArameshJános Vörös
May 31, 2019·PLoS Computational Biology·Shilo OhayonAmit Meller
Aug 25, 2020·Nanoscale·Eric BeamishMichel Godin
Jan 12, 2020·Communications Biology·Numan CelikRichard Barrett-Jolley
Dec 2, 2020·Small·Rachel E ArmstrongPeter Zijlstra
Jan 31, 2021·The Journal of Chemical Physics·Ángel Díaz CarralMaria Fyta
Sep 12, 2019·Journal of the American Chemical Society·Yi-Lun Ying, Yi-Tao Long
Dec 27, 2018·Nano Letters·Kaikai ChenUlrich F Keyser
Apr 1, 2020·Nano Letters·Kaikai ChenUlrich F Keyser
Mar 18, 2020·Analytical Chemistry·Si-Min LuYi-Tao Long
Sep 30, 2021·ACS Nano·Dario DemattiesShi-Li Zhang
Oct 5, 2021·ACS Sensors·Chenyu WenShi-Li Zhang
Dec 4, 2021·Analytical Chemistry·Iat Wai LeongMasateru Taniguchi

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Methods Mentioned

BETA
feature extraction

Software Mentioned

Inca
QuipuNet

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