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McAuliffe TP, Dye D, Britton TB. Spherical-angular dark field imaging and sensitive microstructural phase clustering with unsupervised machine learning. Ultramicroscopy 2020; 219:113132. [PMID: 33053461 DOI: 10.1016/j.ultramic.2020.113132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 11/18/2022]
Abstract
Electron backscatter diffraction is a widely used technique for nano- to micro-scale analysis of crystal structure and orientation. Backscatter patterns produced by an alloy solid solution matrix and its ordered superlattice exhibit only extremely subtle differences, due to the inelastic scattering that precedes coherent diffraction. We show that unsupervised machine learning (with principal component analysis, non-negative matrix factorisation, and an autoencoder neural network) is well suited to fine feature extraction and superlattice/matrix classification. Remapping cluster average patterns onto the diffraction sphere lets us compare Kikuchi band profiles to dynamical simulations, confirm the superlattice stoichiometry, and facilitate virtual imaging with a spherical solid angle aperture. This pipeline now enables unparalleled mapping of exquisite crystallographic detail from a wide range of materials within the scanning electron microscope.
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Affiliation(s)
- T P McAuliffe
- Department of Materials, Imperial College London, Prince Consort Road, London, UK.
| | - D Dye
- Department of Materials, Imperial College London, Prince Consort Road, London, UK
| | - T B Britton
- Department of Materials, Imperial College London, Prince Consort Road, London, UK
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2
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An B, Zhang B. Logistic regression with image covariates via the combination of L1 and Sobolev regularizations. PLoS One 2020; 15:e0234975. [PMID: 32589677 PMCID: PMC7319310 DOI: 10.1371/journal.pone.0234975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 06/06/2020] [Indexed: 11/19/2022] Open
Abstract
The use of image covariates to build a classification model has lots of impact in various fields, such as computer science, medicine, and so on. The aim of this paper is to develop an estimation method for logistic regression model with image covariates. We propose a novel regularized estimation approach, where the regularization is a combination of L1 regularization and Sobolev norm regularization. The L1 penalty can perform variable selection, while the Sobolev norm penalty can capture the shape edges information of image data. We develop an efficient algorithm for the optimization problem. We also establish a nonasymptotic error bound on parameter estimation. Simulated studies and a real data application demonstrate that our proposed method performs very well.
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Affiliation(s)
- Baiguo An
- School of Statistics, Capital University of Economics and Business, Beijing, China
| | - Beibei Zhang
- School of Statistics, Capital University of Economics and Business, Beijing, China
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Affiliation(s)
- Fei Xue
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA
| | - Annie Qu
- Department of Statistics, University of California Irvine, Irvine, CA
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Feng CM, Xu Y, Liu JX, Gao YL, Zheng CH. Supervised Discriminative Sparse PCA for Com-Characteristic Gene Selection and Tumor Classification on Multiview Biological Data. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2019; 30:2926-2937. [PMID: 30802874 DOI: 10.1109/tnnls.2019.2893190] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Principal component analysis (PCA) has been used to study the pathogenesis of diseases. To enhance the interpretability of classical PCA, various improved PCA methods have been proposed to date. Among these, a typical method is the so-called sparse PCA, which focuses on seeking sparse loadings. However, the performance of these methods is still far from satisfactory due to their limitation of using unsupervised learning methods; moreover, the class ambiguity within the sample is high. To overcome this problem, this paper developed a new PCA method, which is named the supervised discriminative sparse PCA (SDSPCA). The main innovation of this method is the incorporation of discriminative information and sparsity into the PCA model. Specifically, in contrast to the traditional sparse PCA, which imposes sparsity on the loadings, here, sparse components are obtained to represent the data. Furthermore, via the linear transformation, the sparse components approximate the given label information. On the one hand, sparse components improve interpretability over the traditional PCA, while on the other hand, they are have discriminative abilities suitable for classification purposes. A simple algorithm is developed, and its convergence proof is provided. SDSPCA has been applied to the common-characteristic gene selection and tumor classification on multiview biological data. The sparsity and classification performance of SDSPCA are empirically verified via abundant, reasonable, and effective experiments, and the obtained results demonstrate that SDSPCA outperforms other state-of-the-art methods.
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de Pierrefeu A, Lofstedt T, Hadj-Selem F, Dubois M, Jardri R, Fovet T, Ciuciu P, Frouin V, Duchesnay E. Structured Sparse Principal Components Analysis With the TV-Elastic Net Penalty. IEEE TRANSACTIONS ON MEDICAL IMAGING 2018; 37:396-407. [PMID: 28880163 DOI: 10.1109/tmi.2017.2749140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Principal component analysis (PCA) is an exploratory tool widely used in data analysis to uncover the dominant patterns of variability within a population. Despite its ability to represent a data set in a low-dimensional space, PCA's interpretability remains limited. Indeed, the components produced by PCA are often noisy or exhibit no visually meaningful patterns. Furthermore, the fact that the components are usually non-sparse may also impede interpretation, unless arbitrary thresholding is applied. However, in neuroimaging, it is essential to uncover clinically interpretable phenotypic markers that would account for the main variability in the brain images of a population. Recently, some alternatives to the standard PCA approach, such as sparse PCA (SPCA), have been proposed, their aim being to limit the density of the components. Nonetheless, sparsity alone does not entirely solve the interpretability problem in neuroimaging, since it may yield scattered and unstable components. We hypothesized that the incorporation of prior information regarding the structure of the data may lead to improved relevance and interpretability of brain patterns. We therefore present a simple extension of the popular PCA framework that adds structured sparsity penalties on the loading vectors in order to identify the few stable regions in the brain images that capture most of the variability. Such structured sparsity can be obtained by combining, e.g., and total variation (TV) penalties, where the TV regularization encodes information on the underlying structure of the data. This paper presents the structured SPCA (denoted SPCA-TV) optimization framework and its resolution. We demonstrate SPCA-TV's effectiveness and versatility on three different data sets. It can be applied to any kind of structured data, such as, e.g., -dimensional array images or meshes of cortical surfaces. The gains of SPCA-TV over unstructured approaches (such as SPCA and ElasticNet PCA) or structured approach (such as GraphNet PCA) are significant, since SPCA-TV reveals the variability within a data set in the form of intelligible brain patterns that are easier to interpret and more stable across different samples.
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Affiliation(s)
- Xin Zhang
- Department of Statistics, Florida State University, Tallahassee, FL
| | - Lexin Li
- Division of Biostatistics, University of California, Berkeley, CA
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Yang F, Hamit M, Yan CB, Yao J, Kutluk A, Kong XM, Zhang SX. Feature Extraction and Classification on Esophageal X-Ray Images of Xinjiang Kazak Nationality. JOURNAL OF HEALTHCARE ENGINEERING 2017; 2017:4620732. [PMID: 29065605 PMCID: PMC5394892 DOI: 10.1155/2017/4620732] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/09/2017] [Accepted: 02/06/2017] [Indexed: 01/06/2023]
Abstract
Esophageal cancer is one of the fastest rising types of cancers in China. The Kazak nationality is the highest-risk group in Xinjiang. In this work, an effective computer-aided diagnostic system is developed to assist physicians in interpreting digital X-ray image features and improving the quality of diagnosis. The modules of the proposed system include image preprocessing, feature extraction, feature selection, image classification, and performance evaluation. 300 original esophageal X-ray images were resized to a region of interest and then enhanced by the median filter and histogram equalization method. 37 features from textural, frequency, and complexity domains were extracted. Both sequential forward selection and principal component analysis methods were employed to select the discriminative features for classification. Then, support vector machine and K-nearest neighbors were applied to classify the esophageal cancer images with respect to their specific types. The classification performance was evaluated in terms of the area under the receiver operating characteristic curve, accuracy, precision, and recall, respectively. Experimental results show that the classification performance of the proposed system outperforms the conventional visual inspection approaches in terms of diagnostic quality and processing time. Therefore, the proposed computer-aided diagnostic system is promising for the diagnostics of esophageal cancer.
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Affiliation(s)
- Fang Yang
- Department of Medical Engineering, The Affiliated Tumor Hospital, Xinjiang Medical University, Urumqi 830011, China
| | - Murat Hamit
- College of Medical Engineering Technology, Xinjiang Medical University, Urumqi 830011, China
| | - Chuan B. Yan
- College of Medical Engineering Technology, Xinjiang Medical University, Urumqi 830011, China
| | - Juan Yao
- Department of Radiology, The First Affiliated Hospital, Xinjiang Medical University, Urumqi 830054, China
| | - Abdugheni Kutluk
- College of Medical Engineering Technology, Xinjiang Medical University, Urumqi 830011, China
| | - Xi M. Kong
- College of Medical Engineering Technology, Xinjiang Medical University, Urumqi 830011, China
| | - Sui X. Zhang
- College of Medical Engineering Technology, Xinjiang Medical University, Urumqi 830011, China
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Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Green RC, Harvey D, Jack CR, Jagust W, Morris JC, Petersen RC, Saykin AJ, Shaw LM, Toga AW, Trojanowski JQ. Recent publications from the Alzheimer's Disease Neuroimaging Initiative: Reviewing progress toward improved AD clinical trials. Alzheimers Dement 2017; 13:e1-e85. [PMID: 28342697 DOI: 10.1016/j.jalz.2016.11.007] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/21/2016] [Accepted: 11/28/2016] [Indexed: 01/31/2023]
Abstract
INTRODUCTION The Alzheimer's Disease Neuroimaging Initiative (ADNI) has continued development and standardization of methodologies for biomarkers and has provided an increased depth and breadth of data available to qualified researchers. This review summarizes the over 400 publications using ADNI data during 2014 and 2015. METHODS We used standard searches to find publications using ADNI data. RESULTS (1) Structural and functional changes, including subtle changes to hippocampal shape and texture, atrophy in areas outside of hippocampus, and disruption to functional networks, are detectable in presymptomatic subjects before hippocampal atrophy; (2) In subjects with abnormal β-amyloid deposition (Aβ+), biomarkers become abnormal in the order predicted by the amyloid cascade hypothesis; (3) Cognitive decline is more closely linked to tau than Aβ deposition; (4) Cerebrovascular risk factors may interact with Aβ to increase white-matter (WM) abnormalities which may accelerate Alzheimer's disease (AD) progression in conjunction with tau abnormalities; (5) Different patterns of atrophy are associated with impairment of memory and executive function and may underlie psychiatric symptoms; (6) Structural, functional, and metabolic network connectivities are disrupted as AD progresses. Models of prion-like spreading of Aβ pathology along WM tracts predict known patterns of cortical Aβ deposition and declines in glucose metabolism; (7) New AD risk and protective gene loci have been identified using biologically informed approaches; (8) Cognitively normal and mild cognitive impairment (MCI) subjects are heterogeneous and include groups typified not only by "classic" AD pathology but also by normal biomarkers, accelerated decline, and suspected non-Alzheimer's pathology; (9) Selection of subjects at risk of imminent decline on the basis of one or more pathologies improves the power of clinical trials; (10) Sensitivity of cognitive outcome measures to early changes in cognition has been improved and surrogate outcome measures using longitudinal structural magnetic resonance imaging may further reduce clinical trial cost and duration; (11) Advances in machine learning techniques such as neural networks have improved diagnostic and prognostic accuracy especially in challenges involving MCI subjects; and (12) Network connectivity measures and genetic variants show promise in multimodal classification and some classifiers using single modalities are rivaling multimodal classifiers. DISCUSSION Taken together, these studies fundamentally deepen our understanding of AD progression and its underlying genetic basis, which in turn informs and improves clinical trial design.
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Affiliation(s)
- Michael W Weiner
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA; Department of Radiology, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, CA, USA.
| | - Dallas P Veitch
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA
| | - Paul S Aisen
- Alzheimer's Therapeutic Research Institute, University of Southern California, San Diego, CA, USA
| | - Laurel A Beckett
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Nigel J Cairns
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, Saint Louis, MO, USA; Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Danielle Harvey
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | | | - William Jagust
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - John C Morris
- Alzheimer's Therapeutic Research Institute, University of Southern California, San Diego, CA, USA
| | | | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, Institute of Neuroimaging and Informatics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Alzheimer's Disease Core Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Udall Parkinson's Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Zhu H, Shen D, Peng X, Liu LY. MWPCR: Multiscale Weighted Principal Component Regression for High-dimensional Prediction. J Am Stat Assoc 2016; 112:1009-1021. [PMID: 29151657 DOI: 10.1080/01621459.2016.1261710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We propose a multiscale weighted principal component regression (MWPCR) framework for the use of high dimensional features with strong spatial features (e.g., smoothness and correlation) to predict an outcome variable, such as disease status. This development is motivated by identifying imaging biomarkers that could potentially aid detection, diagnosis, assessment of prognosis, prediction of response to treatment, and monitoring of disease status, among many others. The MWPCR can be regarded as a novel integration of principal components analysis (PCA), kernel methods, and regression models. In MWPCR, we introduce various weight matrices to prewhitten high dimensional feature vectors, perform matrix decomposition for both dimension reduction and feature extraction, and build a prediction model by using the extracted features. Examples of such weight matrices include an importance score weight matrix for the selection of individual features at each location and a spatial weight matrix for the incorporation of the spatial pattern of feature vectors. We integrate the importance score weights with the spatial weights in order to recover the low dimensional structure of high dimensional features. We demonstrate the utility of our methods through extensive simulations and real data analyses of the Alzheimer's disease neuroimaging initiative (ADNI) data set.
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Affiliation(s)
- Hongtu Zhu
- Professor of Biostatistics, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77230, and University of North Carolina, Chapel Hill, NC, 27599
| | - Dan Shen
- Assistant Professor in Interdisciplinary Data Sciences Consortium and Department of Mathematics and Statistics, University of South Florida, Tampa, FL 33620
| | | | - Leo Yufeng Liu
- Doctoral student under the supervision of Dr. Hongtu Zhu
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