Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform

Kannan, R.; Ievlev, A. V.; Laanait, N.; Ziatdinov, M. A.; Vasudevan, R. K.; Jesse, S.; Kalinin, S. V.

doi:10.1186/s40679-018-0055-8

Title: Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform

Journal Article · Mon Apr 30 00:00:00 EDT 2018 · Advanced Structural and Chemical Imaging

DOI:https://doi.org/10.1186/s40679-018-0055-8· OSTI ID:1435364

; Ievlev, A. V.; Laanait, N.; Ziatdinov, M. A.; Vasudevan, R. K.; Jesse, S.; Kalinin, S. V.

Abstract Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear. Here, we present a tutorial paper targeted at domain scientists to introduce linear unmixing techniques, to facilitate greater understanding of spectroscopic imaging data. We detail a matrix factorization framework that can incorporate different domain information through various parameters of the matrix factorization method. We demonstrate many domain-specific examples to explain the expressivity of the matrix factorization framework and show how the appropriate use of domain-specific constraints such as non-negativity and sum-to-one abundance result in physically meaningful spectral decompositions that are more readily interpretable. Our aim is not only to explain the off-the-shelf available tools, but to add additional constraints when ready-made algorithms are unavailable for the task. All examples use the scalable open source implementation from https://github.com/ramkikannan/nmflibrary that can run from small laptops to supercomputers, creating a user-wide platform for rapid dissemination and adoption across scientific disciplines.

View Journal Article

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1435364

Alternate ID(s):: OSTI ID: 1474632

Journal Information:: Advanced Structural and Chemical Imaging, Journal Name: Advanced Structural and Chemical Imaging Vol. 4 Journal Issue: 1; ISSN 2198-0926

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: Germany

Language:: English

References (67)

Dynamic piezoresponse force microscopy: Spatially resolved probing of polarization dynamics in time and voltage domains Kumar, A.; Ehara, Y.; Wada, A. Journal of Applied Physics, Vol. 112, Issue 5 https://doi.org/10.1063/1.4746080	journal	September 2012
Microscopy: Hasten high resolution Pennycook, Stephen J.; Kalinin, Sergei V. Nature, Vol. 515, Issue 7528 https://doi.org/10.1038/515487a	journal	November 2014
STEM-EELS imaging of complex oxides and interfaces Varela, Maria; Gazquez, Jaume; Pennycook, Stephen J. MRS Bulletin, Vol. 37, Issue 01, p. 29-35 https://doi.org/10.1557/mrs.2011.330	journal	January 2012
Multivariate statistical methods for the analysis of microscope image series: applications in materials science Bonnet, N. Journal of Microscopy, Vol. 190, Issue 1‐2 https://doi.org/10.1046/j.1365-2818.1998.3250876.x	journal	April 1998
Principal component and spatial correlation analysis of spectroscopic-imaging data in scanning probe microscopy Jesse, Stephen; Kalinin, Sergei V. Nanotechnology, Vol. 20, Issue 8 https://doi.org/10.1088/0957-4484/20/8/085714	journal	February 2009
‘All models are wrong...’: an introduction to model uncertainty Wit, Ernst; Heuvel, Edwin van den; Romeijn, Jan-Willem Statistica Neerlandica, Vol. 66, Issue 3 https://doi.org/10.1111/j.1467-9574.2012.00530.x	journal	July 2012
Exact matrix completion via convex optimization Candès, Emmanuel; Recht, Benjamin Communications of the ACM, Vol. 55, Issue 6 https://doi.org/10.1145/2184319.2184343	journal	June 2012
Quantitative 3D-KPFM imaging with simultaneous electrostatic force and force gradient detection Collins, L.; Okatan, M. B.; Li, Q. Nanotechnology, Vol. 26, Issue 17 https://doi.org/10.1088/0957-4484/26/17/175707	journal	April 2015
LIII. On lines and planes of closest fit to systems of points in space Pearson, Karl The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, Vol. 2, Issue 11 https://doi.org/10.1080/14786440109462720	journal	November 1901
Direct Mapping of Ion Diffusion Times on LiCoO2 Surfaces with Nanometer Resolution Guo, S.; Jesse, S.; Kalnaus, S. Journal of The Electrochemical Society, Vol. 158, Issue 8 https://doi.org/10.1149/1.3604759	journal	January 2011
MPI-FAUN: An MPI-Based Framework for Alternating-Updating Nonnegative Matrix Factorization Kannan, Ramakrishnan; Ballard, Grey; Park, Haesun IEEE Transactions on Knowledge and Data Engineering, Vol. 30, Issue 3 https://doi.org/10.1109/TKDE.2017.2767592	journal	March 2018
Direct evidence of mesoscopic dynamic heterogeneities at the surfaces of ergodic ferroelectric relaxors Kalinin, S. V.; Rodriguez, B. J.; Budai, J. D. Physical Review B, Vol. 81, Issue 6 https://doi.org/10.1103/PhysRevB.81.064107	journal	February 2010
Matrix Factorization for Automatic Chemical Mapping from Electron Microscopic Spectral Imaging Datasets Shiga, Motoki; Muto, Shunsuke; Tatsumi, Kazuyoshi Transactions of the Materials Research Society of Japan, Vol. 41, Issue 4 https://doi.org/10.14723/tmrsj.41.333	journal	January 2016
Full-field X-ray reflection microscopy of epitaxial thin-films Laanait, Nouamane; Zhang, Zhan; Schlepütz, Christian M. Journal of Synchrotron Radiation, Vol. 21, Issue 6 https://doi.org/10.1107/S1600577514016555	journal	October 2014
Document clustering based on non-negative matrix factorization Xu, Wei; Liu, Xin; Gong, Yihong Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval - SIGIR '03 https://doi.org/10.1145/860435.860485	conference	January 2003
Hyperspectral coherent Raman imaging - principle, theory, instrumentation, and applications to life sciences: Hyperspectral coherent Raman imaging Kano, Hideaki; Segawa, Hiroki; Okuno, Masanari Journal of Raman Spectroscopy, Vol. 47, Issue 1 https://doi.org/10.1002/jrs.4853	journal	December 2015
Hyperspectral surface-enhanced Raman imaging of labeled silver nanoparticles in single cells Wabuyele, Musundi B.; Yan, Fei; Griffin, Guy D. Review of Scientific Instruments, Vol. 76, Issue 6 https://doi.org/10.1063/1.1938667	journal	June 2005
Structure, physical properties, and applications of ${SrRuO}_{3}$ thin films Koster, Gertjan; Klein, Lior; Siemons, Wolter Reviews of Modern Physics, Vol. 84, Issue 1 https://doi.org/10.1103/RevModPhys.84.253	journal	March 2012
TEM and EELS measurements of interface roughness in epitaxial Fe/MgO/Fe magnetic tunnel junctions Serin, V.; Andrieu, S.; Serra, R. Physical Review B, Vol. 79, Issue 14 https://doi.org/10.1103/PhysRevB.79.144413	journal	April 2009
Disorder Identification in Hysteresis Data: Recognition Analysis of the Random-Bond–Random-Field Ising Model Ovchinnikov, O. S.; Jesse, S.; Bintacchit, P. Physical Review Letters, Vol. 103, Issue 15 https://doi.org/10.1103/PhysRevLett.103.157203	journal	October 2009
Chemical State Evolution in Ferroelectric Films during Tip-Induced Polarization and Electroresistive Switching Ievlev, Anton V.; Maksymovych, Petro; Trassin, Morgan ACS Applied Materials & Interfaces, Vol. 8, Issue 43 https://doi.org/10.1021/acsami.6b10784	journal	October 2016
Joint Bayesian Endmember Extraction and Linear Unmixing for Hyperspectral Imagery Dobigeon, N.; Moussaoui, S.; Coulon, M. IEEE Transactions on Signal Processing, Vol. 57, Issue 11 https://doi.org/10.1109/TSP.2009.2025797	journal	November 2009
VisIRR: Visual analytics for information retrieval and recommendation with large-scale document data Choo, Jaegul; Lee, Changhyun; Kim, Hannah 2014 IEEE Conference on Visual Analytics Science and Technology (VAST) https://doi.org/10.1109/VAST.2014.7042511	conference	October 2014
Spectral unmixing Keshava, N.; Mustard, J. F. IEEE Signal Processing Magazine, Vol. 19, Issue 1 https://doi.org/10.1109/79.974727	journal	January 2002
Imaging nanoscale lattice variations by machine learning of x-ray diffraction microscopy data Laanait, Nouamane; Zhang, Zhan; Schlepütz, Christian M. Nanotechnology, Vol. 27, Issue 37 https://doi.org/10.1088/0957-4484/27/37/374002	journal	August 2016
Electronic Properties of Isosymmetric Phase Boundaries in Highly Strained Ca-Doped BiFeO ₃ Seidel, Jan; Trassin, Morgan; Zhang, Yi Advanced Materials, Vol. 26, Issue 25 https://doi.org/10.1002/adma.201400557	journal	April 2014
Learning the parts of objects by non-negative matrix factorization Lee, Daniel D.; Seung, H. Sebastian Nature, Vol. 401, Issue 6755 https://doi.org/10.1038/44565	journal	October 1999
Better Catalysts through Microscopy: Mesoscale M1/M2 Intergrowth in Molybdenum–Vanadium Based Complex Oxide Catalysts for Propane Ammoxidation He, Qian; Woo, Jungwon; Belianinov, Alexei ACS Nano, Vol. 9, Issue 4 https://doi.org/10.1021/acsnano.5b00271	journal	February 2015
Memory Efficient Principal Component Analysis for the Dimensionality Reduction of Large Mass Spectrometry Imaging Data Sets Race, Alan M.; Steven, Rory T.; Palmer, Andrew D. Analytical Chemistry, Vol. 85, Issue 6 https://doi.org/10.1021/ac302528v	journal	March 2013
Spatial distribution of relaxation behavior on the surface of a ferroelectric relaxor in the ergodic phase Kalinin, S. V.; Rodriguez, B. J.; Jesse, S. Applied Physics Letters, Vol. 95, Issue 14 https://doi.org/10.1063/1.3242011	journal	October 2009
Principal Component Analysis of TOF-SIMS Images of Organic Monolayers Biesinger, Mark C.; Paepegaey, Pierre-Yves; McIntyre, N. Stewart Analytical Chemistry, Vol. 74, Issue 22 https://doi.org/10.1021/ac020311n	journal	November 2002
Fast rank-2 nonnegative matrix factorization for hierarchical document clustering Kuang, Da; Park, Haesun Proceedings of the 19th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '13 https://doi.org/10.1145/2487575.2487606	conference	January 2013
Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data Ievlev, Anton V.; Belianinov, Alexei; Jesse, Stephen Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-17049-y	journal	December 2017
Matrix Factorization Techniques for Recommender Systems Koren, Yehuda; Bell, Robert; Volinsky, Chris Computer, Vol. 42, Issue 8 https://doi.org/10.1109/MC.2009.263	journal	August 2009
Nanoscale Hard X-Ray Microscopy Methods for Materials Studies Holt, Martin; Harder, Ross; Winarski, Robert Annual Review of Materials Research, Vol. 43, Issue 1 https://doi.org/10.1146/annurev-matsci-071312-121654	journal	July 2013
Imaging Local Polarization in Ferroelectric Thin Films by Coherent X-Ray Bragg Projection Ptychography Hruszkewycz, S. O.; Highland, M. J.; Holt, M. V. Physical Review Letters, Vol. 110, Issue 17, Article No. 177601 https://doi.org/10.1103/PhysRevLett.110.177601	journal	April 2013
Algorithms for nonnegative matrix and tensor factorizations: a unified view based on block coordinate descent framework Kim, Jingu; He, Yunlong; Park, Haesun Journal of Global Optimization, Vol. 58, Issue 2 https://doi.org/10.1007/s10898-013-0035-4	journal	March 2013
Hyperopt: A Python Library for Optimizing the Hyperparameters of Machine Learning Algorithms Bergstra, James; Yamins, Dan; Cox, David Proceedings of the Python in Science Conference https://doi.org/10.25080/Majora-8b375195-003	conference	January 2013
Numerical Methods for Least Squares Problems Björck, Åke Society for Industrial and Applied Mathematics https://doi.org/10.1137/1.9781611971484	book	January 1996
Sparse modeling of EELS and EDX spectral imaging data by nonnegative matrix factorization Shiga, Motoki; Tatsumi, Kazuyoshi; Muto, Shunsuke Ultramicroscopy, Vol. 170 https://doi.org/10.1016/j.ultramic.2016.08.006	journal	November 2016
Atomic-resolution spectroscopic imaging: past, present and future Pennycook, S. J.; Varela, M.; Lupini, A. R. Journal of Electron Microscopy, Vol. 58, Issue 3 https://doi.org/10.1093/jmicro/dfn030	journal	January 2009
X-ray micro-beam characterization of lattice rotations and distortions due to an individual dislocation Hofmann, Felix; Abbey, Brian; Liu, Wenjun Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3774	journal	November 2013
Spatial resolution, information limit, and contrast transfer in piezoresponse force microscopy Kalinin, S. V.; Jesse, S.; Rodriguez, B. J. Nanotechnology, Vol. 17, Issue 14 https://doi.org/10.1088/0957-4484/17/14/010	journal	June 2006
Near-Field Hyperspectral Optical Imaging Bouillard, Jean-Sebastien G.; Dickson, Wayne; Wurtz, Gregory A. ChemPhysChem, Vol. 15, Issue 4 https://doi.org/10.1002/cphc.201300826	journal	February 2014
Effect of molybdenum $4 d$ hole substitution in BaFe $_{2}$ As $_{2}$ Sefat, Athena S.; Marty, Karol; Christianson, Andrew D. Physical Review B, Vol. 85, Issue 2 https://doi.org/10.1103/PhysRevB.85.024503	journal	January 2012
Phases and Interfaces from Real Space Atomically Resolved Data: Physics-Based Deep Data Image Analysis Vasudevan, Rama K.; Ziatdinov, Maxim; Jesse, Stephen Nano Letters, Vol. 16, Issue 9 https://doi.org/10.1021/acs.nanolett.6b02130	journal	August 2016
Data mining graphene: correlative analysis of structure and electronic degrees of freedom in graphenic monolayers with defects Ziatdinov, Maxim; Fujii, Shintaro; Kiguchi, Manabu Nanotechnology, Vol. 27, Issue 49 https://doi.org/10.1088/0957-4484/27/49/495703	journal	November 2016
Imaging with Mass Spectrometry Pacholski, M. L.; Winograd, N. Chemical Reviews, Vol. 99, Issue 10 https://doi.org/10.1021/cr980137w	journal	October 1999
Direct Determination of the Chemical Bonding of Individual Impurities in Graphene Zhou, Wu; Kapetanakis, Myron D.; Prange, Micah P. Physical Review Letters, Vol. 109, Issue 20 https://doi.org/10.1103/PhysRevLett.109.206803	journal	November 2012
Imaging mass spectrometry McDonnell, Liam A.; Heeren, Ron M. A. Mass Spectrometry Reviews, Vol. 26, Issue 4 https://doi.org/10.1002/mas.20124	journal	January 2007
Graph Regularized Nonnegative Matrix Factorization for Data Representation IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 33, Issue 8 https://doi.org/10.1109/TPAMI.2010.231	journal	August 2011
Deep data mining in a real space: separation of intertwined electronic responses in a lightly doped BaFe ₂ As ₂ Ziatdinov, Maxim; Maksov, Artem; Li, Li Nanotechnology, Vol. 27, Issue 47 https://doi.org/10.1088/0957-4484/27/47/475706	journal	October 2016
Mapping chemical and bonding information using multivariate analysis of electron energy-loss spectrum images Bosman, M.; Watanabe, M.; Alexander, D. T. L. Ultramicroscopy, Vol. 106, Issue 11-12, p. 1024-1032 https://doi.org/10.1016/j.ultramic.2006.04.016	journal	October 2006
Bounded matrix factorization for recommender system Kannan, Ramakrishnan; Ishteva, Mariya; Park, Haesun Knowledge and Information Systems, Vol. 39, Issue 3 https://doi.org/10.1007/s10115-013-0710-2	journal	December 2013
Hyperspectral Imaging with Stimulated Raman Scattering by Chirped Femtosecond Lasers Fu, Dan; Holtom, Gary; Freudiger, Christian The Journal of Physical Chemistry B, Vol. 117, Issue 16 https://doi.org/10.1021/jp308938t	journal	November 2012
Three-dimensional X-ray structural microscopy with submicrometre resolution Larson, B. C.; Yang, Wenge; Ice, G. E. Nature, Vol. 415, p. 887-890 https://doi.org/10.1038/415887a	journal	February 2002
Direct Mapping of Ionic Transport in a Si Anode on the Nanoscale: Time Domain Electrochemical Strain Spectroscopy Study Jesse, Stephen; Balke, Nina; Eliseev, Eugene ACS Nano, Vol. 5, Issue 12 https://doi.org/10.1021/nn203141g	journal	November 2011
Spatially Inhomogeneous Metal-Insulator Transition in Doped Manganites Fäth, M. Science, Vol. 285, Issue 5433 https://doi.org/10.1126/science.285.5433.1540	journal	September 1999
Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space Collins, Liam; Belianinov, Alex; Somnath, Suhas Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep30557	journal	August 2016
Misfit strain relaxation by dislocations in SrRuO3/SrTiO3 (001) heteroepitaxy Oh, Sang Ho; Park, Chan Gyung Journal of Applied Physics, Vol. 95, Issue 9 https://doi.org/10.1063/1.1690484	journal	May 2004
Atom-by-atom spectroscopy at graphene edge Suenaga, Kazu; Koshino, Masanori Nature, Vol. 468, Issue 7327 https://doi.org/10.1038/nature09664	journal	December 2010
Reconstruction of surface potential from Kelvin probe force microscopy images Cohen, G.; Halpern, E.; Nanayakkara, S. U. Nanotechnology, Vol. 24, Issue 29 https://doi.org/10.1088/0957-4484/24/29/295702	journal	June 2013
The Race to X-ray Microbeam and Nanobeam Science Ice, G. E.; Budai, J. D.; Pang, J. W. L. Science, Vol. 334, Issue 6060 https://doi.org/10.1126/science.1202366	journal	December 2011
On the Equivalence of Nonnegative Matrix Factorization and Spectral Clustering Ding, Chris; He, Xiaofeng; Simon, Horst D. Proceedings of the 2005 SIAM International Conference on Data Mining https://doi.org/10.1137/1.9781611972757.70	conference	January 2014
3D Chemical Image using TOF-SIMS Revealing the Biopolymer Component Spatial and Lateral Distributions in Biomass Jung, Seokwon; Foston, Marcus; Kalluri, Udaya C. Angewandte Chemie International Edition, Vol. 51, Issue 48 https://doi.org/10.1002/anie.201205243	journal	October 2012
Hyperspectral optical imaging of human iris in vivo: characteristics of reflectance spectra Medina, José M.; Pereira, Luís M.; Correia, Hélder T. Journal of Biomedical Optics, Vol. 16, Issue 7 https://doi.org/10.1117/1.3595710	journal	January 2011
Li-ion dynamics and reactivity on the nanoscale Kalinin, Sergei; Balke, Nina; Jesse, Stephen Materials Today, Vol. 14, Issue 11 https://doi.org/10.1016/S1369-7021(11)70280-2	journal	November 2011

Similar Records

Distributed deep reinforcement learning for simulation control

Journal Article · Wed Apr 14 00:00:00 EDT 2021 · Machine Learning: Science and Technology · OSTI ID:1435364

Pawar, Suraj; Maulik, Romit

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment

Journal Article · Thu Dec 07 00:00:00 EST 2023 · Algorithms for Molecular Biology · OSTI ID:1435364

Shen, Chengze; Liu, Baqiao; Williams, Kelly P.; +1 more

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

Journal Article · Tue Feb 12 00:00:00 EST 2019 · mSystems · OSTI ID:1435364

Martino, Cameron; Morton, James T.; Marotz, Clarisse A.; +5 more

Related Subjects

97 MATHEMATICS AND COMPUTING
47 OTHER INSTRUMENTATION
Unmixing
Image segmentation
Scanning probe microscopy
Matrix factorization
Big data
High performance

Title: Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform

Citation Formats

References (67)

Similar Records

Related Subjects