Defect detection in atomic-resolution images via unsupervised learning with translational invariance
Abstract
Abstract Crystallographic defects can now be routinely imaged at atomic resolution with aberration-corrected scanning transmission electron microscopy (STEM) at high speed, with the potential for vast volumes of data to be acquired in relatively short times or through autonomous experiments that can continue over very long periods. Automatic detection and classification of defects in the STEM images are needed in order to handle the data in an efficient way. However, like many other tasks related to object detection and identification in artificial intelligence, it is challenging to detect and identify defects from STEM images. Furthermore, it is difficult to deal with crystal structures that have many atoms and low symmetries. Previous methods used for defect detection and classification were based on supervised learning, which requires human-labeled data. In this work, we develop an approach for defect detection with unsupervised machine learning based on a one-class support vector machine (OCSVM). We introduce two schemes of image segmentation and data preprocessing, both of which involve taking the Patterson function of each segment as inputs. We demonstrate that this method can be applied to various defects, such as point and line defects in 2D materials and twin boundaries in 3D nanocrystals.
- Authors:
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1829523
- Alternate Identifier(s):
- OSTI ID: 1831665
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Published Article
- Journal Name:
- npj Computational Materials
- Additional Journal Information:
- Journal Name: npj Computational Materials Journal Volume: 7 Journal Issue: 1; Journal ID: ISSN 2057-3960
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE
Citation Formats
Guo, Yueming, Kalinin, Sergei V., Cai, Hui, Xiao, Kai, Krylyuk, Sergiy, Davydov, Albert V., Guo, Qianying, and Lupini, Andrew R. Defect detection in atomic-resolution images via unsupervised learning with translational invariance. United Kingdom: N. p., 2021.
Web. doi:10.1038/s41524-021-00642-1.
Guo, Yueming, Kalinin, Sergei V., Cai, Hui, Xiao, Kai, Krylyuk, Sergiy, Davydov, Albert V., Guo, Qianying, & Lupini, Andrew R. Defect detection in atomic-resolution images via unsupervised learning with translational invariance. United Kingdom. https://doi.org/10.1038/s41524-021-00642-1
Guo, Yueming, Kalinin, Sergei V., Cai, Hui, Xiao, Kai, Krylyuk, Sergiy, Davydov, Albert V., Guo, Qianying, and Lupini, Andrew R. Tue .
"Defect detection in atomic-resolution images via unsupervised learning with translational invariance". United Kingdom. https://doi.org/10.1038/s41524-021-00642-1.
@article{osti_1829523,
title = {Defect detection in atomic-resolution images via unsupervised learning with translational invariance},
author = {Guo, Yueming and Kalinin, Sergei V. and Cai, Hui and Xiao, Kai and Krylyuk, Sergiy and Davydov, Albert V. and Guo, Qianying and Lupini, Andrew R.},
abstractNote = {Abstract Crystallographic defects can now be routinely imaged at atomic resolution with aberration-corrected scanning transmission electron microscopy (STEM) at high speed, with the potential for vast volumes of data to be acquired in relatively short times or through autonomous experiments that can continue over very long periods. Automatic detection and classification of defects in the STEM images are needed in order to handle the data in an efficient way. However, like many other tasks related to object detection and identification in artificial intelligence, it is challenging to detect and identify defects from STEM images. Furthermore, it is difficult to deal with crystal structures that have many atoms and low symmetries. Previous methods used for defect detection and classification were based on supervised learning, which requires human-labeled data. In this work, we develop an approach for defect detection with unsupervised machine learning based on a one-class support vector machine (OCSVM). We introduce two schemes of image segmentation and data preprocessing, both of which involve taking the Patterson function of each segment as inputs. We demonstrate that this method can be applied to various defects, such as point and line defects in 2D materials and twin boundaries in 3D nanocrystals.},
doi = {10.1038/s41524-021-00642-1},
journal = {npj Computational Materials},
number = 1,
volume = 7,
place = {United Kingdom},
year = {2021},
month = {11}
}
https://doi.org/10.1038/s41524-021-00642-1
Works referenced in this record:
Automatic detection of crystallographic defects in STEM images by unsupervised learning with translational invariance
journal, July 2021
- Guo, Yueming; Lupini, Andrew R.; Cai, Hui
- Microscopy and Microanalysis, Vol. 27, Issue S1
In-situ formation and evolution of atomic defects in monolayer WSe 2 under electron irradiation
journal, September 2020
- Leiter, Robert; Li, Yueliang; Kaiser, Ute
- Nanotechnology, Vol. 31, Issue 49
Super-compression of large electron microscopy time series by deep compressive sensing learning
journal, July 2021
- Zheng, Siming; Wang, Chunyang; Yuan, Xin
- Patterns, Vol. 2, Issue 7
Mapping mesoscopic phase evolution during E-beam induced transformations via deep learning of atomically resolved images
journal, June 2018
- Vasudevan, Rama K.; Laanait, Nouamane; Ferragut, Erik M.
- npj Computational Materials, Vol. 4, Issue 1
Deep Learning Enabled Strain Mapping of Single-Atom Defects in Two-Dimensional Transition Metal Dichalcogenides with Sub-Picometer Precision
journal, April 2020
- Lee, Chia-Hao; Khan, Abid; Luo, Di
- Nano Letters, Vol. 20, Issue 5
Are Dislocations Present in Nanoparticles?: Fourier Filtering of Images Obtained From In-Situ TEM Nanoindentation
journal, July 2009
- Carlton, C.; Ferreira, Pj
- Microscopy and Microanalysis, Vol. 15, Issue S2
In Situ TEM Study of Catalytic Nanoparticle Reactions in Atmospheric Pressure Gas Environment
journal, September 2013
- Xin, Huolin L.; Niu, Kaiyang; Alsem, Daan Hein
- Microscopy and Microanalysis, Vol. 19, Issue 6
In situ atomistic insight into the growth mechanisms of single layer 2D transition metal carbides
journal, June 2018
- Sang, Xiahan; Xie, Yu; Yilmaz, Dundar E.
- Nature Communications, Vol. 9, Issue 1
Direct evidence for atomic defects in graphene layers
journal, August 2004
- Hashimoto, Ayako; Suenaga, Kazu; Gloter, Alexandre
- Nature, Vol. 430, Issue 7002
Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations
journal, October 2016
- Ziatdinov, Maxim; Dyck, Ondrej; Maksov, Artem
- ACS Nano, Vol. 11, Issue 12
TEMImageNet training library and AtomSegNet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images
journal, March 2021
- Lin, Ruoqian; Zhang, Rui; Wang, Chunyang
- Scientific Reports, Vol. 11, Issue 1
Support Vector Data Description
journal, January 2004
- Tax, David M. J.; Duin, Robert P. W.
- Machine Learning, Vol. 54, Issue 1
The crystal structure of baddeleyite (monoclinic ZrO2)
journal, July 1959
- McCullough, J. D.; Trueblood, K. N.
- Acta Crystallographica, Vol. 12, Issue 7
Detection of defects in atomic-resolution images of materials using cycle analysis
journal, March 2020
- Ovchinnikov, Oleg S.; O’Hara, Andrew; Jesse, Stephen
- Advanced Structural and Chemical Imaging, Vol. 6, Issue 1
Estimating the Support of a High-Dimensional Distribution
journal, July 2001
- Schölkopf, Bernhard; Platt, John C.; Shawe-Taylor, John
- Neural Computation, Vol. 13, Issue 7
Deep learning analysis of defect and phase evolution during electron beam-induced transformations in WS2
journal, February 2019
- Maksov, Artem; Dyck, Ondrej; Wang, Kai
- npj Computational Materials, Vol. 5, Issue 1
A performance evaluation of local descriptors
journal, October 2005
- Mikolajczyk, K.; Schmid, C.
- IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 27, Issue 10
A joint deep learning model to recover information and reduce artifacts in missing-wedge sinograms for electron tomography and beyond
journal, September 2019
- Ding, Guanglei; Liu, Yitong; Zhang, Rui
- Scientific Reports, Vol. 9, Issue 1
Manipulating low-dimensional materials down to the level of single atoms with electron irradiation
journal, September 2017
- Susi, Toma; Meyer, Jannik C.; Kotakoski, Jani
- Ultramicroscopy, Vol. 180
Fire up the atom forge
journal, November 2016
- Kalinin, Sergei V.; Borisevich, Albina; Jesse, Stephen
- Nature, Vol. 539, Issue 7630
Automated defect analysis in electron microscopic images
journal, July 2018
- Li, Wei; Field, Kevin G.; Morgan, Dane
- npj Computational Materials, Vol. 4, Issue 1
A Fourier Series Method for the Determination of the Components of Interatomic Distances in Crystals
journal, September 1934
- Patterson, A. L.
- Physical Review, Vol. 46, Issue 5
Investigating phase transitions from local crystallographic analysis based on statistical learning of atomic environments in 2D MoS 2 -ReS 2
journal, March 2021
- Vasudevan, Rama K.; Ziatdinov, Maxim; Sharma, Vinit
- Applied Physics Reviews, Vol. 8, Issue 1
LIBSVM: A library for support vector machines
journal, April 2011
- Chang, Chih-Chung; Lin, Chih-Jen
- ACM Transactions on Intelligent Systems and Technology, Vol. 2, Issue 3
Efficient Unsupervised Parameter Estimation for One-Class Support Vector Machines
journal, October 2018
- Ghafoori, Zahra; Erfani, Sarah M.; Rajasegarar, Sutharshan
- IEEE Transactions on Neural Networks and Learning Systems, Vol. 29, Issue 10
Quantitative measurement of displacement and strain fields from HREM micrographs
journal, August 1998
- Hÿtch, M. J.; Snoeck, E.; Kilaas, R.
- Ultramicroscopy, Vol. 74, Issue 3, p. 131-146
Visualization and quantification of transition metal atomic mixing in Mo1−xWxS2 single layers
journal, January 2013
- Dumcenco, Dumitru O.; Kobayashi, Haruka; Liu, Zheng
- Nature Communications, Vol. 4, Article No. 1351
0.7 Å Resolution Electron Tomography Enabled by Deep‐Learning‐Aided Information Recovery
journal, September 2020
- Wang, Chunyang; Ding, Guanglei; Liu, Yitong
- Advanced Intelligent Systems, Vol. 2, Issue 12
Band Gap Engineering and Layer-by-Layer Mapping of Selenium-Doped Molybdenum Disulfide
journal, December 2013
- Gong, Yongji; Liu, Zheng; Lupini, Andrew R.
- Nano Letters, Vol. 14, Issue 2
Dynamic scan control in STEM: spiral scans
journal, June 2016
- Sang, Xiahan; Lupini, Andrew R.; Unocic, Raymond R.
- Advanced Structural and Chemical Imaging, Vol. 2, Issue 1