The Technome - A Predictive Internal Calibration Approach for Quantitative Imaging Biomarker Research

The goal of radiomics is to convert medical images into a minable data space by extraction of quantitative imaging features for clinically relevant analyses, e.g. survival time prediction of a patient. One problem of radiomics from computed tomography is the impact of technical variation such as reconstruction kernel variation within a study. Additionally, what is often neglected is the impact of inter-patient technical variation, resulting from patient characteristics, even when scan and reconstruction parameters are constant. In our approach, measurements within 3D regions-of-interests (ROI) are calibrated by further ROIs such as air, adipose tissue, liver, etc. that are used as control regions (CR). Our goal is to derive general rules for an automated internal calibration that enhance prediction, based on the analysed features and a set of CRs. We define qualification criteria motivated by status-quo radiomics stability analysis techniques to only collect information from the CRs which is relevant given a respective task. These criteria are used in an optimisation to automatically derive a suitable internal calibration for prediction tasks based on the CRs. Our calibration enhanced the performance for centrilobular emphysema prediction in a COPD study and prediction of patients’ one-year-survival in an oncological study.

[1]  Chris H. Q. Ding,et al.  Minimum redundancy feature selection from microarray gene expression data , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[2]  S. Armato,et al.  Role of the Quantitative Imaging Biomarker Alliance in optimizing CT for the evaluation of lung cancer screen-detected nodules. , 2015, Journal of the American College of Radiology : JACR.

[3]  Martin Pelikan,et al.  Bayesian Optimization Algorithm , 2005 .

[4]  D. Goldberg,et al.  BOA: the Bayesian optimization algorithm , 1999 .

[5]  Geoffrey G. Zhang,et al.  Intrinsic dependencies of CT radiomic features on voxel size and number of gray levels , 2017, Medical physics.

[6]  Verónica Bolón-Canedo,et al.  Fast‐mRMR: Fast Minimum Redundancy Maximum Relevance Algorithm for High‐Dimensional Big Data , 2017, Int. J. Intell. Syst..

[7]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[8]  David M. Simcha,et al.  Tackling the widespread and critical impact of batch effects in high-throughput data , 2010, Nature Reviews Genetics.

[9]  Michael Sühling,et al.  General purpose radiomics for multi-modal clinical research , 2019, Medical Imaging.

[10]  Horst-Michael Gross,et al.  Predicting Lesion Growth and Patient Survival in Colorectal Cancer Patients using Deep Neural Networks , 2018 .

[11]  Rolf W. Günther,et al.  Semi-Automated Quantification of Hepatic Lesions in a Phantom , 2009, Investigative radiology.

[12]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[13]  Diana Adler,et al.  Using Multivariate Statistics , 2016 .

[14]  Heinz-Otto Peitgen,et al.  Morphological segmentation and partial volume analysis for volumetry of solid pulmonary lesions in thoracic CT scans , 2006, IEEE Transactions on Medical Imaging.

[15]  Shouhao Zhou,et al.  Comprehensive Investigation on Controlling for CT Imaging Variabilities in Radiomics Studies , 2018, Scientific Reports.

[16]  Ruben Martinez-Cantin,et al.  BayesOpt: a Bayesian optimization library for nonlinear optimization, experimental design and bandits , 2014, J. Mach. Learn. Res..

[17]  Heinz-Otto Peitgen,et al.  Advanced Segmentation Techniques for Lung Nodules, Liver Metastases, and Enlarged Lymph Nodes in CT Scans , 2009, IEEE Journal of Selected Topics in Signal Processing.

[18]  Lawrence H. Schwartz,et al.  Assessing Agreement between Radiomic Features Computed for Multiple CT Imaging Settings , 2016, PloS one.

[19]  E. Moros,et al.  Precision of quantitative computed tomography texture analysis using image filtering , 2017, Medicine.

[20]  Xia Sheng,et al.  Bayesian design of synthetic biological systems , 2011, Proceedings of the National Academy of Sciences.

[21]  Andriy Fedorov,et al.  Computational Radiomics System to Decode the Radiographic Phenotype. , 2017, Cancer research.

[22]  O. Matsui,et al.  Correlation between the blood supply and grade of malignancy of hepatocellular nodules associated with liver cirrhosis: evaluation by CT during intraarterial injection of contrast medium. , 1999, AJR. American journal of roentgenology.

[23]  Russell T. Shinohara,et al.  Removing inter-subject technical variability in magnetic resonance imaging studies , 2016, NeuroImage.

[24]  Steffen Löck,et al.  Image biomarker standardisation initiative , 2016 .

[25]  Fanny Orlhac,et al.  Validation of A Method to Compensate Multicenter Effects Affecting CT Radiomics. , 2019, Radiology.

[26]  Philippe Lambin,et al.  4DCT imaging to assess radiomics feature stability: An investigation for thoracic cancers. , 2017, Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology.

[27]  M. Baker 1,500 scientists lift the lid on reproducibility , 2016, Nature.

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

[29]  Sang Joon Park,et al.  Impact of Reconstruction Algorithms on CT Radiomic Features of Pulmonary Tumors: Analysis of Intra- and Inter-Reader Variability and Inter-Reconstruction Algorithm Variability , 2016, PloS one.

[30]  Willi A. Kalender,et al.  Computed tomography : fundamentals, system technology, image quality, applications , 2000 .

[31]  David J. Kriegman,et al.  Eigenfaces vs. Fisherfaces: Recognition Using Class Specific Linear Projection , 1996, ECCV.

[32]  Christopher. Simons,et al.  Machine learning with Python , 2017 .

[33]  Gianluca Bontempi,et al.  A comprehensive overview of Infinium HumanMethylation450 data processing , 2013, Briefings Bioinform..

[34]  Hyeongmin Jin,et al.  Deep learning-enabled scan parameter normalization of imaging biomarkers in low-dose lung CT , 2018, 2018 International Workshop on Advanced Image Technology (IWAIT).

[35]  Klaus Engelke,et al.  Three-dimensional Distribution of Muscle and Adipose Tissue of the Thigh at CT: Association with Acute Hip Fracture. , 2019, Radiology.

[36]  M. Kalra,et al.  Techniques and applications of automatic tube current modulation for CT. , 2004, Radiology.

[37]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[38]  W. Kalender,et al.  The European Spine Phantom--a tool for standardization and quality control in spinal bone mineral measurements by DXA and QCT. , 1995, European journal of radiology.

[39]  Daguang Xu,et al.  Automatic Liver Segmentation Using an Adversarial Image-to-Image Network , 2017, MICCAI.

[40]  K. Hansen,et al.  Functional normalization of 450k methylation array data improves replication in large cancer studies , 2014, Genome Biology.

[41]  Dorin Comaniciu,et al.  Hierarchical parsing and semantic navigation of full body CT data , 2009, Medical Imaging.

[42]  David J. Kriegman,et al.  Recognition using class specific linear projection , 1997 .

[43]  E. Regan,et al.  Genetic Epidemiology of COPD (COPDGene) Study Design , 2011, COPD.