A Bayesian nonparametric model for textural pattern heterogeneity

Cancer radiomics is an emerging discipline promising to elucidate lesion phenotypes and tumor heterogeneity through patterns of enhancement, texture, morphology, and shape. The prevailing technique for image texture analysis relies on the construction and synthesis of Gray-Level Co-occurrence Matrices (GLCM). Practice currently reduces the structured count data of a GLCM to reductive and redundant summary statistics for which analysis requires variable selection and multiple comparisons for each application, thus limiting reproducibility. In this article, we develop a Bayesian multivariate probabilistic framework for the analysis and unsupervised clustering of a sample of GLCM objects. By appropriately accounting for skewness and zero-inflation of the observed counts and simultaneously adjusting for existing spatial autocorrelation at nearby cells, the methodology facilitates estimation of texture pattern distributions within the GLCM lattice itself. The techniques are applied to cluster images of adrenal lesions obtained from CT scans with and without administration of contrast. We further assess whether the resultant subtypes are clinically oriented by investigating their correspondence with pathological diagnoses. Additionally, we compare performance to a class of machine-learning approaches currently used in cancer radiomics with simulation studies.

[1]  Weisheng Wang,et al.  A Study for Texture Feature Extraction of High-Resolution Satellite Images Based on a Direction Measure and Gray Level Co-Occurrence Matrix Fusion Algorithm , 2017, Sensors.

[2]  Irène Buvat,et al.  Tumor Texture Analysis in PET: Where Do We Stand? , 2015, The Journal of Nuclear Medicine.

[3]  Jeffrey W. Miller,et al.  Mixture Models With a Prior on the Number of Components , 2015, Journal of the American Statistical Association.

[4]  L E Quint,et al.  Delayed enhanced CT for differentiation of benign from malignant adrenal masses. , 1996, Radiology.

[5]  Vishwa Parekh,et al.  Radiomics: a new application from established techniques , 2016, Expert review of precision medicine and drug development.

[6]  Ruijiang Li,et al.  Robust Intratumor Partitioning to Identify High-Risk Subregions in Lung Cancer: A Pilot Study. , 2016, International journal of radiation oncology, biology, physics.

[7]  Payel Ghosh,et al.  Utility of Intermediate-Delay Washout CT Images for Differentiation of Malignant and Benign Adrenal Lesions: A Multivariate Analysis. , 2018, AJR. American journal of roentgenology.

[8]  D. B. Dahl Bayesian Inference for Gene Expression and Proteomics: Model-Based Clustering for Expression Data via a Dirichlet Process Mixture Model , 2006 .

[9]  Hui Ye,et al.  Diagnostic performance of 18-F-FDG-PET–CT in adrenal lesions using histopathology as reference standard , 2017, Abdominal Radiology.

[10]  M. Newton,et al.  Multiple Hypothesis Testing by Clustering Treatment Effects , 2007 .

[11]  Patrick Granton,et al.  Radiomics: extracting more information from medical images using advanced feature analysis. , 2012, European journal of cancer.

[12]  Payel Ghosh,et al.  Differentiation of Malignant and Benign Adrenal Lesions With Delayed CT: Multivariate Analysis and Predictive Models. , 2018, AJR. American journal of roentgenology.

[13]  Benjamin Haibe-Kains,et al.  Radiomic feature clusters and Prognostic Signatures specific for Lung and Head & Neck cancer , 2015, Scientific Reports.

[14]  Antonio Canale,et al.  Robustifying Bayesian nonparametric mixtures for count data , 2017, Biometrics.

[15]  Paul Nikolaidis,et al.  Adrenal imaging: a comprehensive review. , 2012, Radiologic clinics of North America.

[16]  Kim-Anh Do,et al.  An Efficient Nonparametric Estimate for Spatially Correlated Functional Data , 2019, Statistics in Biosciences.

[17]  P. Lambin,et al.  Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach , 2014, Nature Communications.

[18]  Mario Castro,et al.  Quantitative computed tomographic imaging–based clustering differentiates asthmatic subgroups with distinctive clinical phenotypes , 2017, The Journal of allergy and clinical immunology.

[19]  W. Gilks,et al.  Adaptive Rejection Metropolis Sampling Within Gibbs Sampling , 1995 .

[20]  By W. R. GILKSt,et al.  Adaptive Rejection Sampling for Gibbs Sampling , 2010 .

[21]  Sw. Banerjee,et al.  Hierarchical Modeling and Analysis for Spatial Data , 2003 .

[22]  J. Besag Spatial Interaction and the Statistical Analysis of Lattice Systems , 1974 .

[23]  P R Mueller,et al.  Adrenal masses: characterization with delayed contrast-enhanced CT. , 1997, Radiology.

[24]  Mario Medvedovic,et al.  Bayesian infinite mixture model based clustering of gene expression profiles , 2002, Bioinform..

[25]  P. Müller,et al.  Bayesian inference for gene expression and proteomics , 2006 .

[26]  Fionn Murtagh,et al.  Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion? , 2011, Journal of Classification.

[27]  S. MacEachern,et al.  Bayesian Nonparametric Spatial Modeling With Dirichlet Process Mixing , 2005 .

[28]  Peter Müller,et al.  A Bayesian semiparametric approach for the differential analysis of sequence counts data , 2014, Journal of the Royal Statistical Society. Series C, Applied statistics.

[29]  Jang Ho Yoon,et al.  The washout rate on the delayed CT image as a diagnostic tool for adrenal adenoma verified by pathology: a multicenter study , 2012, International Urology and Nephrology.

[30]  R. Kanthan,et al.  Diagnostic and prognostic features in adrenocortical carcinoma: a single institution case series and review of the literature , 2015, World Journal of Surgical Oncology.

[31]  Earl W Duncan,et al.  Comparing Bayesian spatial models: Goodness-of-smoothing criteria for assessing under- and over-smoothing , 2020, PloS one.

[32]  Boris Sepesi,et al.  Development of an Immune-Pathology Informed Radiomics Model for Non-Small Cell Lung Cancer , 2018, Scientific Reports.

[33]  Fernando A. Quintana,et al.  Bayesian Nonparametric Longitudinal Data Analysis , 2016, Journal of the American Statistical Association.

[34]  David B. Dunson,et al.  Bayesian inference on quasi-sparse count data , 2016, Biometrika.

[35]  H. Aerts,et al.  Applications and limitations of radiomics , 2016, Physics in medicine and biology.

[36]  M. Escobar,et al.  Bayesian Density Estimation and Inference Using Mixtures , 1995 .

[37]  Marina Vannucci,et al.  A spatiotemporal nonparametric Bayesian model of multi-subject fMRI data , 2016 .

[38]  Antonio Canale,et al.  Bayesian Kernel Mixtures for Counts , 2011, Journal of the American Statistical Association.

[39]  Andre Dekker,et al.  Radiomics: the process and the challenges. , 2012, Magnetic resonance imaging.

[40]  M. He,et al.  Anterior segment imaging-based subdivision of subjects with primary angle-closure glaucoma , 2017, Eye.

[41]  Duncan Lee,et al.  CARBayes: An R Package for Bayesian Spatial Modeling with Conditional Autoregressive Priors , 2013 .

[42]  Ajay Jasra,et al.  Markov Chain Monte Carlo Methods and the Label Switching Problem in Bayesian Mixture Modeling , 2005 .

[43]  J. H. Ward Hierarchical Grouping to Optimize an Objective Function , 1963 .

[44]  Vicky Goh,et al.  Radiomics in PET: principles and applications , 2014, Clinical and Translational Imaging.

[45]  Zoubin Ghahramani,et al.  Bayesian Cluster Analysis: Point Estimation and Credible Balls (with Discussion) , 2015, Bayesian Analysis.

[46]  A. Trister,et al.  Assessing the scale of tumor heterogeneity by complete hierarchical segmentation of MRI , 2015, Physics in medicine and biology.

[47]  Robert M. Haralick,et al.  Textural Features for Image Classification , 1973, IEEE Trans. Syst. Man Cybern..

[48]  P. Müller,et al.  10 Model-Based Clustering for Expression Data via a Dirichlet Process Mixture Model , 2006 .

[49]  A. Azzalini,et al.  Statistical applications of the multivariate skew normal distribution , 2009, 0911.2093.

[50]  Paul Kinahan,et al.  Radiomics: Images Are More than Pictures, They Are Data , 2015, Radiology.

[51]  Sylvia Richardson,et al.  Sampling from Dirichlet process mixture models with unknown concentration parameter: mixing issues in large data implementations , 2013, Statistics and Computing.

[52]  K. Yeom,et al.  Radiomics in Brain Tumor: Image Assessment, Quantitative Feature Descriptors, and Machine-Learning Approaches , 2017, American Journal of Neuroradiology.

[53]  Antonio Canale,et al.  Non‐parametric spatial models for clustered ordered periodontal data , 2016, Journal of the Royal Statistical Society. Series C, Applied statistics.

[54]  Marina Vannucci,et al.  A Bayesian Nonparametric Approach for Functional Data Classification with Application to Hepatic Tissue Characterization , 2015, Cancer informatics.

[55]  D. Karlis,et al.  Mixed Poisson Distributions , 2005 .

[56]  W. Krzanowski,et al.  A Criterion for Determining the Number of Groups in a Data Set Using Sum-of-Squares Clustering , 1988 .

[57]  Xiao Li,et al.  Spatial Bayesian modeling of GLCM with application to malignant lesion characterization , 2019, Journal of applied statistics.

[58]  Jianhua Hu,et al.  A functional model for classifying metastatic lesions integrating scans and biomarkers , 2020, Statistical methods in medical research.

[59]  Nial Friel,et al.  Optimal Bayesian estimators for latent variable cluster models , 2016, Statistics and Computing.

[60]  Payel Ghosh,et al.  Combining Washout and Noncontrast Data From Adrenal Protocol CT: Improving Diagnostic Performance. , 2018, Academic radiology.