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Wang R, Guo W, Wang Y, Zhou X, Leung JC, Yan S, Cui L. Hybrid multimodal fusion for graph learning in disease prediction. Methods 2024; 229:41-48. [PMID: 38880433 DOI: 10.1016/j.ymeth.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024] Open
Abstract
Graph neural networks (GNNs) have gained significant attention in disease prediction where the latent embeddings of patients are modeled as nodes and the similarities among patients are represented through edges. The graph structure, which determines how information is aggregated and propagated, plays a crucial role in graph learning. Recent approaches typically create graphs based on patients' latent embeddings, which may not accurately reflect their real-world closeness. Our analysis reveals that raw data, such as demographic attributes and laboratory results, offers a wealth of information for assessing patient similarities and can serve as a compensatory measure for graphs constructed exclusively from latent embeddings. In this study, we first construct adaptive graphs from both latent representations and raw data respectively, and then merge these graphs via weighted summation. Given that the graphs may contain extraneous and noisy connections, we apply degree-sensitive edge pruning and kNN sparsification techniques to selectively sparsify and prune these edges. We conducted intensive experiments on two diagnostic prediction datasets, and the results demonstrate that our proposed method surpasses current state-of-the-art techniques.
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Affiliation(s)
| | - Wei Guo
- Shandong University, Jinan, 250210, China.
| | | | - Xin Zhou
- Nanyang Technological University, Singapore.
| | | | - Shuo Yan
- Shandong University, Jinan, 250210, China.
| | - Lizhen Cui
- Shandong University, Jinan, 250210, China.
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Nazari E, Biviji R, Roshandel D, Pour R, Shahriari MH, Mehrabian A, Tabesh H. Decision fusion in healthcare and medicine: a narrative review. Mhealth 2022; 8:8. [PMID: 35178439 PMCID: PMC8800206 DOI: 10.21037/mhealth-21-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/02/2021] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE To provide an overview of the decision fusion (DF) technique and describe the applications of the technique in healthcare and medicine at prevention, diagnosis, treatment and administrative levels. BACKGROUND The rapid development of technology over the past 20 years has led to an explosion in data growth in various industries, like healthcare. Big data analysis within the healthcare systems is essential for arriving to a value-based decision over a period of time. Diversity and uncertainty in big data analytics have made it impossible to analyze data by using conventional data mining techniques and thus alternative solutions are required. DF is a form of data fusion techniques that could increase the accuracy of diagnosis and facilitate interpretation, summarization and sharing of information. METHODS We conducted a review of articles published between January 1980 and December 2020 from various databases such as Google Scholar, IEEE, PubMed, Science Direct, Scopus and web of science using the keywords decision fusion (DF), information fusion, healthcare, medicine and big data. A total of 141 articles were included in this narrative review. CONCLUSIONS Given the importance of big data analysis in reducing costs and improving the quality of healthcare; along with the potential role of DF in big data analysis, it is recommended to know the full potential of this technique including the advantages, challenges and applications of the technique before its use. Future studies should focus on describing the methodology and types of data used for its applications within the healthcare sector.
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Affiliation(s)
- Elham Nazari
- Department of Medical Informatics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rizwana Biviji
- Science of Healthcare Delivery, College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Danial Roshandel
- Centre for Ophthalmology and Visual Science (affiliated with the Lions Eye Institute), The University of Western Australia, Perth, Western Australia, Australia
| | - Reza Pour
- Department of Computer Engineering, Azad University, Mashhad, Iran
| | - Mohammad Hasan Shahriari
- Department of Health Information Technology and Management, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amin Mehrabian
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Hamed Tabesh
- Department of Medical Informatics, Mashhad University of Medical Sciences, Mashhad, Iran
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3
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Understanding breast cancer heterogeneity through non-genetic heterogeneity. Breast Cancer 2021; 28:777-791. [PMID: 33723745 DOI: 10.1007/s12282-021-01237-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/04/2021] [Indexed: 01/01/2023]
Abstract
Intricacy in treatment and diagnosis of breast cancer has been an obstacle due to genotype and phenotype heterogeneity. Understanding of non-genetic heterogeneity mechanisms along with considering role of genetic heterogeneity may fill the gaps in landscape painting of heterogeneity. The main factors contribute to non-genetic heterogeneity including: transcriptional pulsing/bursting or discontinuous transcriptions, stochastic partitioning of components at cell division and various signal transduction from tumor ecosystem. Throughout this review, we desired to provide a conceptual framework focused on non-genetic heterogeneity, which has been intended to offer insight into prediction, diagnosis and treatment of breast cancer.
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Gokcay D, Eken A, Baltaci S. Binary Classification Using Neural and Clinical Features: An Application in Fibromyalgia With Likelihood-Based Decision Level Fusion. IEEE J Biomed Health Inform 2019; 23:1490-1498. [DOI: 10.1109/jbhi.2018.2844300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Viswanath SE, Tiwari P, Lee G, Madabhushi A. Dimensionality reduction-based fusion approaches for imaging and non-imaging biomedical data: concepts, workflow, and use-cases. BMC Med Imaging 2017; 17:2. [PMID: 28056889 PMCID: PMC5217665 DOI: 10.1186/s12880-016-0172-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/09/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND With a wide array of multi-modal, multi-protocol, and multi-scale biomedical data being routinely acquired for disease characterization, there is a pressing need for quantitative tools to combine these varied channels of information. The goal of these integrated predictors is to combine these varied sources of information, while improving on the predictive ability of any individual modality. A number of application-specific data fusion methods have been previously proposed in the literature which have attempted to reconcile the differences in dimensionalities and length scales across different modalities. Our objective in this paper was to help identify metholodological choices that need to be made in order to build a data fusion technique, as it is not always clear which strategy is optimal for a particular problem. As a comprehensive review of all possible data fusion methods was outside the scope of this paper, we have focused on fusion approaches that employ dimensionality reduction (DR). METHODS In this work, we quantitatively evaluate 4 non-overlapping existing instantiations of DR-based data fusion, within 3 different biomedical applications comprising over 100 studies. These instantiations utilized different knowledge representation and knowledge fusion methods, allowing us to examine the interplay of these modules in the context of data fusion. The use cases considered in this work involve the integration of (a) radiomics features from T2w MRI with peak area features from MR spectroscopy for identification of prostate cancer in vivo, (b) histomorphometric features (quantitative features extracted from histopathology) with protein mass spectrometry features for predicting 5 year biochemical recurrence in prostate cancer patients, and (c) volumetric measurements on T1w MRI with protein expression features to discriminate between patients with and without Alzheimers' Disease. RESULTS AND CONCLUSIONS Our preliminary results in these specific use cases indicated that the use of kernel representations in conjunction with DR-based fusion may be most effective, as a weighted multi-kernel-based DR approach resulted in the highest area under the ROC curve of over 0.8. By contrast non-optimized DR-based representation and fusion methods yielded the worst predictive performance across all 3 applications. Our results suggest that when the individual modalities demonstrate relatively poor discriminability, many of the data fusion methods may not yield accurate, discriminatory representations either. In summary, to outperform the predictive ability of individual modalities, methodological choices for data fusion must explicitly account for the sparsity of and noise in the feature space.
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Affiliation(s)
- Satish E Viswanath
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave, Wickenden 523, Cleveland, OH, USA.
| | - Pallavi Tiwari
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave, Wickenden 523, Cleveland, OH, USA
| | - George Lee
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave, Wickenden 523, Cleveland, OH, USA
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave, Wickenden 523, Cleveland, OH, USA
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Choi JY. A generalized multiple classifier system for improving computer-aided classification of breast masses in mammography. Biomed Eng Lett 2016. [DOI: 10.1007/s13534-015-0191-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Choi JY, Kim DH, Plataniotis KN, Ro YM. Computer-aided detection (CAD) of breast masses in mammography: combined detection and ensemble classification. Phys Med Biol 2014; 59:3697-719. [DOI: 10.1088/0031-9155/59/14/3697] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Integration of high-volume molecular and imaging data for composite biomarker discovery in the study of melanoma. BIOMED RESEARCH INTERNATIONAL 2014; 2014:145243. [PMID: 24527435 PMCID: PMC3914284 DOI: 10.1155/2014/145243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 09/28/2013] [Accepted: 10/12/2013] [Indexed: 12/19/2022]
Abstract
In this work the effects of simple imputations are studied, regarding the integration of multimodal data originating from different patients. Two separate datasets of cutaneous melanoma are used, an image analysis (dermoscopy) dataset together with a transcriptomic one, specifically DNA microarrays. Each modality is related to a different set of patients, and four imputation methods are employed to the formation of a unified, integrative dataset. The application of backward selection together with ensemble classifiers (random forests), followed by principal components analysis and linear discriminant analysis, illustrates the implication of the imputations on feature selection and dimensionality reduction methods. The results suggest that the expansion of the feature space through the data integration, achieved by the exploitation of imputation schemes in general, aids the classification task, imparting stability as regards the derivation of putative classifiers. In particular, although the biased imputation methods increase significantly the predictive performance and the class discrimination of the datasets, they still contribute to the study of prominent features and their relations. The fusion of separate datasets, which provide a multimodal description of the same pathology, represents an innovative, promising avenue, enhancing robust composite biomarker derivation and promoting the interpretation of the biomedical problem studied.
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Alagoz O, Chhatwal J, Burnside ES. Optimal Policies for Reducing Unnecessary Follow-up Mammography Exams in Breast Cancer Diagnosis. DECISION ANALYSIS 2013; 10:200-224. [PMID: 24501588 PMCID: PMC3910299 DOI: 10.1287/deca.2013.0272] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mammography is the most effective screening tool for early diagnosis of breast cancer. Based on the mammography findings, radiologists need to choose from one of the following three alternatives: 1) take immediate diagnostic actions including prompt biopsy to confirm breast cancer; 2) recommend a follow-up mammogram; 3) recommend routine annual mammography. There are no validated structured guidelines based on a decision-analytical framework to aid radiologists in making such patient management decisions. Surprisingly, only 15-45% of the breast biopsies and less than 1% of short-interval follow-up recommendations are found to be malignant, resulting in unnecessary tests and patient-anxiety. We develop a finite-horizon discrete-time Markov decision process (MDP) model that may help radiologists make patient-management decisions to maximize a patient's total expected quality-adjusted life years. We use clinical data to find the policies recommended by the MDP model and also compare them to decisions made by radiologists at a large mammography practice. We also derive the structural properties of the MDP model, including sufficiency conditions that ensure the existence of a double control-limit type policy.
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Affiliation(s)
- Oguzhan Alagoz
- Department of Industrial and Systems Engineering, University of Wisconsin-Madison, 1513 University Avenue, Madison, WI, 53705,
| | - Jagpreet Chhatwal
- Department of Health Policy and Management and Industrial Engineering, University of Pittsburgh, 130 De Soto Street Pittsburgh, PA, 15261,
| | - Elizabeth S Burnside
- Department of Radiology, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792,
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Belle A, Kon MA, Najarian K. Biomedical informatics for computer-aided decision support systems: a survey. ScientificWorldJournal 2013; 2013:769639. [PMID: 23431259 PMCID: PMC3575619 DOI: 10.1155/2013/769639] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/09/2013] [Indexed: 11/18/2022] Open
Abstract
The volumes of current patient data as well as their complexity make clinical decision making more challenging than ever for physicians and other care givers. This situation calls for the use of biomedical informatics methods to process data and form recommendations and/or predictions to assist such decision makers. The design, implementation, and use of biomedical informatics systems in the form of computer-aided decision support have become essential and widely used over the last two decades. This paper provides a brief review of such systems, their application protocols and methodologies, and the future challenges and directions they suggest.
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Affiliation(s)
- Ashwin Belle
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Mark A. Kon
- Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA
| | - Kayvan Najarian
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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Kozikowski RT, Smith SE, Lee JA, Castleman WL, Sorg BS, Hahn DW. Comparative evaluation of differential laser-induced perturbation spectroscopy as a technique to discriminate emerging skin pathology. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:067002. [PMID: 22734780 DOI: 10.1117/1.jbo.17.6.067002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fluorescence spectroscopy has been widely investigated as a technique for identifying pathological tissue; however, unrelated subject-to-subject variations in spectra complicate data analysis and interpretation. We describe and evaluate a new biosensing technique, differential laser-induced perturbation spectroscopy (DLIPS), based on deep ultraviolet (UV) photochemical perturbation in combination with difference spectroscopy. This technique combines sequential fluorescence probing (pre- and post-perturbation) with sub-ablative UV perturbation and difference spectroscopy to provide a new spectral dimension, facilitating two improvements over fluorescence spectroscopy. First, the differential technique eliminates significant variations in absolute fluorescence response within subject populations. Second, UV perturbations alter the extracellular matrix (ECM), directly coupling the DLIPS response to the biological structure. Improved biosensing with DLIPS is demonstrated in vivo in a murine model of chemically induced skin lesion development. Component loading analysis of the data indicates that the DLIPS technique couples to structural proteins in the ECM. Analysis of variance shows that DLIPS has a significant response to emerging pathology as opposed to other population differences. An optimal likelihood ratio classifier for the DLIPS dataset shows that this technique holds promise for improved diagnosis of epithelial pathology. Results further indicate that DLIPS may improve diagnosis of tissue by augmenting fluorescence spectra (i.e. orthogonal sensing).
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Affiliation(s)
- Raymond T Kozikowski
- University of Florida, J. Crayton Pruitt Department of Biomedical Engineering, Gainesville, Florida 32611, USA
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Velikova M, Lucas PJ, Samulski M, Karssemeijer N. A probabilistic framework for image information fusion with an application to mammographic analysis. Med Image Anal 2012; 16:865-75. [DOI: 10.1016/j.media.2012.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 11/20/2011] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
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Tiwari P, Kurhanewicz J, Viswanath S, Sridhar A, Madabhushi A. Multimodal wavelet embedding representation for data combination (MaWERiC): integrating magnetic resonance imaging and spectroscopy for prostate cancer detection. NMR IN BIOMEDICINE 2012; 25:607-619. [PMID: 21960175 PMCID: PMC3298634 DOI: 10.1002/nbm.1777] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 05/28/2023]
Abstract
Recently, both Magnetic Resonance (MR) Imaging (MRI) and Spectroscopy (MRS) have emerged as promising tools for detection of prostate cancer (CaP). However, due to the inherent dimensionality differences in MR imaging and spectral information, quantitative integration of T(2) weighted MRI (T(2)w MRI) and MRS for improved CaP detection has been a major challenge. In this paper, we present a novel computerized decision support system called multimodal wavelet embedding representation for data combination (MaWERiC) that employs, (i) wavelet theory to extract 171 Haar wavelet features from MRS and 54 Gabor features from T(2)w MRI, (ii) dimensionality reduction to individually project wavelet features from MRS and T(2)w MRI into a common reduced Eigen vector space, and (iii), a random forest classifier for automated prostate cancer detection on a per voxel basis from combined 1.5 T in vivo MRI and MRS. A total of 36 1.5 T endorectal in vivo T(2)w MRI and MRS patient studies were evaluated per voxel by MaWERiC using a three-fold cross validation approach over 25 iterations. Ground truth for evaluation of results was obtained by an expert radiologist annotations of prostate cancer on a per voxel basis who compared each MRI section with corresponding ex vivo wholemount histology sections with the disease extent mapped out on histology. Results suggest that MaWERiC based MRS T(2)w meta-classifier (mean AUC, μ = 0.89 ± 0.02) significantly outperformed (i) a T(2)w MRI (using wavelet texture features) classifier (μ = 0.55 ± 0.02), (ii) a MRS (using metabolite ratios) classifier (μ = 0.77 ± 0.03), (iii) a decision fusion classifier obtained by combining individual T(2)w MRI and MRS classifier outputs (μ = 0.85 ± 0.03), and (iv) a data combination method involving a combination of metabolic MRS and MR signal intensity features (μ = 0.66 ± 0.02).
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Affiliation(s)
- Pallavi Tiwari
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854
| | - John Kurhanewicz
- University of California, Department of Radiology, San Francisco, CA, 94143
| | - Satish Viswanath
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854
| | - Akshay Sridhar
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854
| | - Anant Madabhushi
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854
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Modeling Paradigms for Medical Diagnostic Decision Support: A Survey and Future Directions. J Med Syst 2011; 36:3029-49. [PMID: 21964969 DOI: 10.1007/s10916-011-9780-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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Madabhushi A, Agner S, Basavanhally A, Doyle S, Lee G. Computer-aided prognosis: predicting patient and disease outcome via quantitative fusion of multi-scale, multi-modal data. Comput Med Imaging Graph 2011; 35:506-14. [PMID: 21333490 DOI: 10.1016/j.compmedimag.2011.01.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 12/16/2010] [Accepted: 01/10/2011] [Indexed: 12/31/2022]
Abstract
Computer-aided prognosis (CAP) is a new and exciting complement to the field of computer-aided diagnosis (CAD) and involves developing and applying computerized image analysis and multi-modal data fusion algorithms to digitized patient data (e.g. imaging, tissue, genomic) for helping physicians predict disease outcome and patient survival. While a number of data channels, ranging from the macro (e.g. MRI) to the nano-scales (proteins, genes) are now being routinely acquired for disease characterization, one of the challenges in predicting patient outcome and treatment response has been in our inability to quantitatively fuse these disparate, heterogeneous data sources. At the Laboratory for Computational Imaging and Bioinformatics (LCIB)(1) at Rutgers University, our team has been developing computerized algorithms for high dimensional data and image analysis for predicting disease outcome from multiple modalities including MRI, digital pathology, and protein expression. Additionally, we have been developing novel data fusion algorithms based on non-linear dimensionality reduction methods (such as Graph Embedding) to quantitatively integrate information from multiple data sources and modalities with the overarching goal of optimizing meta-classifiers for making prognostic predictions. In this paper, we briefly describe 4 representative and ongoing CAP projects at LCIB. These projects include (1) an Image-based Risk Score (IbRiS) algorithm for predicting outcome of Estrogen receptor positive breast cancer patients based on quantitative image analysis of digitized breast cancer biopsy specimens alone, (2) segmenting and determining extent of lymphocytic infiltration (identified as a possible prognostic marker for outcome in human epidermal growth factor amplified breast cancers) from digitized histopathology, (3) distinguishing patients with different Gleason grades of prostate cancer (grade being known to be correlated to outcome) from digitized needle biopsy specimens, and (4) integrating protein expression measurements obtained from mass spectrometry with quantitative image features derived from digitized histopathology for distinguishing between prostate cancer patients at low and high risk of disease recurrence following radical prostatectomy.
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Affiliation(s)
- Anant Madabhushi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, USA.
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Chhatwal J, Alagoz O, Burnside ES. Optimal Breast Biopsy Decision-Making Based on Mammographic Features and Demographic Factors. OPERATIONS RESEARCH 2010; 58:1577-1591. [PMID: 21415931 PMCID: PMC3057079 DOI: 10.1287/opre.1100.0877] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Breast cancer is the most common non-skin cancer affecting women in the United States, where every year more than 20 million mammograms are performed. Breast biopsy is commonly performed on the suspicious findings on mammograms to confirm the presence of cancer. Currently, 700,000 biopsies are performed annually in the U.S.; 55%-85% of these biopsies ultimately are found to be benign breast lesions, resulting in unnecessary treatments, patient anxiety, and expenditures. This paper addresses the decision problem faced by radiologists: When should a woman be sent for biopsy based on her mammographic features and demographic factors? This problem is formulated as a finite-horizon discrete-time Markov decision process. The optimal policy of our model shows that the decision to biopsy should take the age of patient into account; particularly, an older patient's risk threshold for biopsy should be higher than that of a younger patient. When applied to the clinical data, our model outperforms radiologists in the biopsy decision-making problem. This study also derives structural properties of the model, including sufficiency conditions that ensure the existence of a control-limit type policy and nondecreasing control-limits with age.
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Affiliation(s)
- Jagpreet Chhatwal
- Health Economic Statistics, Merck Research Laboratories, North Wales, Pennsylvania 19454,
| | - Oguzhan Alagoz
- Department of Industrial and Systems Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706,
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Singh S, Maxwell J, Baker JA, Nicholas JL, Lo JY. Computer-aided classification of breast masses: performance and interobserver variability of expert radiologists versus residents. Radiology 2010; 258:73-80. [PMID: 20971779 DOI: 10.1148/radiol.10081308] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PURPOSE To evaluate the interobserver variability in descriptions of breast masses by dedicated breast imagers and radiology residents and determine how any differences in lesion description affect the performance of a computer-aided diagnosis (CAD) computer classification system. MATERIALS AND METHODS Institutional review board approval was obtained for this HIPAA-compliant study, and the requirement to obtain informed consent was waived. Images of 50 breast lesions were individually interpreted by seven dedicated breast imagers and 10 radiology residents, yielding 850 lesion interpretations. Lesions were described with use of 11 descriptors from the Breast Imaging Reporting and Data System, and interobserver variability was calculated with the Cohen κ statistic. Those 11 features were selected, along with patient age, and merged together by a linear discriminant analysis (LDA) classification model trained by using 1005 previously existing cases. Variability in the recommendations of the computer model for different observers was also calculated with the Cohen κ statistic. RESULTS A significant difference was observed for six lesion features, and radiology residents had greater interobserver variability in their selection of five of the six features than did dedicated breast imagers. The LDA model accurately classified lesions for both sets of observers (area under the receiver operating characteristic curve = 0.94 for residents and 0.96 for dedicated imagers). Sensitivity was maintained at 100% for residents and improved from 98% to 100% for dedicated breast imagers. For residents, the computer model could potentially improve the specificity from 20% to 40% (P < .01) and the κ value from 0.09 to 0.53 (P < .001). For dedicated breast imagers, the computer model could increase the specificity from 34% to 43% (P = .16) and the κ value from 0.21 to 0.61 (P < .001). CONCLUSION Among findings showing a significant difference, there was greater interobserver variability in lesion descriptions among residents; however, an LDA model using data from either dedicated breast imagers or residents yielded a consistently high performance in the differentiation of benign from malignant breast lesions, demonstrating potential for improving specificity and decreasing interobserver variability in biopsy recommendations.
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Affiliation(s)
- Swatee Singh
- Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, 2424 Erwin Rd, Ste 302, Durham, NC 27705, USA.
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Cao Y, Hao X, Zhu X, Xia S. An adaptive region growing algorithm for breast masses in mammograms. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11460-010-0017-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Chawla AS, Lo JY, Baker JA, Samei E. Optimized image acquisition for breast tomosynthesis in projection and reconstruction space. Med Phys 2010; 36:4859-69. [PMID: 19994493 DOI: 10.1118/1.3231814] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Breast tomosynthesis has been an exciting new development in the field of breast imaging. While the diagnostic improvement via tomosynthesis is notable, the full potential of tomosynthesis has not yet been realized. This may be attributed to the dependency of the diagnostic quality of tomosynthesis on multiple variables, each of which needs to be optimized. Those include dose, number of angular projections, and the total angular span of those projections. In this study, the authors investigated the effects of these acquisition parameters on the overall diagnostic image quality of breast tomosynthesis in both the projection and reconstruction space. Five mastectomy specimens were imaged using a prototype tomosynthesis system. 25 angular projections of each specimen were acquired at 6.2 times typical single-view clinical dose level. Images at lower dose levels were then simulated using a noise modification routine. Each projection image was supplemented with 84 simulated 3 mm 3D lesions embedded at the center of 84 nonoverlapping ROIs. The projection images were then reconstructed using a filtered backprojection algorithm at different combinations of acquisition parameters to investigate which of the many possible combinations maximizes the performance. Performance was evaluated in terms of a Laguerre-Gauss channelized Hotelling observer model-based measure of lesion detectability. The analysis was also performed without reconstruction by combining the model results from projection images using Bayesian decision fusion algorithm. The effect of acquisition parameters on projection images and reconstructed slices were then compared to derive an optimization rule for tomosynthesis. The results indicated that projection images yield comparable but higher performance than reconstructed images. Both modes, however, offered similar trends: Performance improved with an increase in the total acquisition dose level and the angular span. Using a constant dose level and angular span, the performance rolled off beyond a certain number of projections, indicating that simply increasing the number of projections in tomosynthesis may not necessarily improve its performance. The best performance for both projection images and tomosynthesis slices was obtained for 15-17 projections spanning an angular are of approximately 45 degrees--the maximum tested in our study, and for an acquisition dose equal to single-view mammography. The optimization framework developed in this framework is applicable to other reconstruction techniques and other multiprojection systems.
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Affiliation(s)
- Amarpreet S Chawla
- Department of Radiology, Duke Advanced Imaging Laboratories, Duke University, Durham, North Carolina 27705, USA.
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Barr RC, Nolte LW, Pollard AE. Bayesian quantitative electrophysiology and its multiple applications in bioengineering. IEEE Rev Biomed Eng 2010; 3:155-68. [PMID: 22275206 PMCID: PMC3935245 DOI: 10.1109/rbme.2010.2089375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bayesian interpretation of observations began in the early 1700s, and scientific electrophysiology began in the late 1700s. For two centuries these two fields developed mostly separately. In part that was because quantitative Bayesian interpretation, in principle a powerful method of relating measurements to their underlying sources, often required too many steps to be feasible with hand calculation in real applications. As computer power became widespread in the later 1900s, Bayesian models and interpretation moved rapidly but unevenly from the domain of mathematical statistics into applications. Use of Bayesian models now is growing rapidly in electrophysiology. Bayesian models are well suited to the electrophysiological environment, allowing a direct and natural way to express what is known (and unknown) and to evaluate which one of many alternatives is most likely the source of the observations, and the closely related receiver operating characteristic (ROC) curve is a powerful tool in making decisions. Yet, in general, many people would ask what such models are for, in electrophysiology, and what particular advantages such models provide. So to examine this question in particular, this review identifies a number of electrophysiological papers in bioengineering arising from questions in several organ systems to see where Bayesian electrophysiological models or ROC curves were important to the results that were achieved.
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Affiliation(s)
- Roger C. Barr
- Departments of Biomedical Engineering and Pediatrics, Duke University, Durham, NC 27708 USA
| | - Loren W. Nolte
- Department of Electrical and Computer Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
| | - Andrew E. Pollard
- Departments of Biomedical Engineering and Pediatrics, Duke University, Durham, NC 27708 USA
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Mazurowski MA, Zurada JM, Tourassi GD. An adaptive incremental approach to constructing ensemble classifiers: application in an information-theoretic computer-aided decision system for detection of masses in mammograms. Med Phys 2009; 36:2976-84. [PMID: 19673196 PMCID: PMC2832038 DOI: 10.1118/1.3132304] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 04/18/2009] [Accepted: 04/20/2009] [Indexed: 11/07/2022] Open
Abstract
Ensemble classifiers have been shown efficient in multiple applications. In this article, the authors explore the effectiveness of ensemble classifiers in a case-based computer-aided diagnosis system for detection of masses in mammograms. They evaluate two general ways of constructing subclassifiers by resampling of the available development dataset: Random division and random selection. Furthermore, they discuss the problem of selecting the ensemble size and propose two adaptive incremental techniques that automatically select the size for the problem at hand. All the techniques are evaluated with respect to a previously proposed information-theoretic CAD system (IT-CAD). The experimental results show that the examined ensemble techniques provide a statistically significant improvement (AUC = 0.905 +/- 0.024) in performance as compared to the original IT-CAD system (AUC = 0.865 +/- 0.029). Some of the techniques allow for a notable reduction in the total number of examples stored in the case base (to 1.3% of the original size), which, in turn, results in lower storage requirements and a shorter response time of the system. Among the methods examined in this article, the two proposed adaptive techniques are by far the most effective for this purpose. Furthermore, the authors provide some discussion and guidance for choosing the ensemble parameters.
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Affiliation(s)
- Maciej A Mazurowski
- Department of Radiology, Carl E. Ravin Advanced Imaging Laboratories, Duke University Medical Center, Durham, North Carolina 27705, USA.
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Chawla AS, Saunders RS, Singh S, Lo JY, Samei E. Towards optimized acquisition scheme for multiprojection correlation imaging of breast cancer. Acad Radiol 2009; 16:456-63. [PMID: 19268858 DOI: 10.1016/j.acra.2008.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 09/22/2008] [Accepted: 09/23/2008] [Indexed: 11/19/2022]
Abstract
RATIONALE AND OBJECTIVES Correlation imaging (CI) is a form of multiprojection imaging in which multiple images of a patient are acquired from slightly different angles. Information from these images is combined to make the final diagnosis. A critical factor affecting the performance of CI is its data acquisition scheme, because nonoptimized acquisition may distort pathologic indicators. The authors describe a computer-aided detection (CADe) methodology to optimize the acquisition scheme of CI for superior diagnostic accuracy. MATERIALS AND METHODS Images from 106 subjects were used. For each subject, 25 angular projections of a single breast were acquired. Projection images were supplemented with a simulated 3-mm three-dimensional lesion. Each projection was then processed using a traditional CADe algorithm at high sensitivity, followed by the reduction of false-positives by combining the geometric correlation information available from the multiple images. The performance of the CI system was determined in terms of free-response receiver-operating characteristic curves and the areas under receiver-operating characteristic curves. For optimization, the components of acquisition, such as the number of projections and their angular span, were systematically changed to investigate which of the many possible combinations maximized the obtainable CADe sensitivity and specificity. RESULTS The performance of the CI system was improved by increasing the angular span. Increasing the number of angular projections beyond a certain number did not improve performance. Maximum performance was obtained between 7 and 10 projections spanning a maximum angular arc of 45 degrees . CONCLUSION The findings suggest the existence of an optimum acquisition scheme for CI of the breast. CADe results confirmed earlier predictions on the basis of observer models. An optimized CI system may be an important diagnostic tool for improved breast cancer detection.
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Affiliation(s)
- Amarpreet S Chawla
- Department of Radiology, Duke Advanced Imaging Laboratories, Duke University, Durham, NC 27705, USA.
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Park SC, Pu J, Zheng B. Improving performance of computer-aided detection scheme by combining results from two machine learning classifiers. Acad Radiol 2009; 16:266-74. [PMID: 19201355 DOI: 10.1016/j.acra.2008.08.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 08/15/2008] [Accepted: 08/16/2008] [Indexed: 10/21/2022]
Abstract
RATIONALE AND OBJECTIVES Global data-based and local instance-based machine-learning methods and classifiers have been widely used to optimize computer-aided detection and diagnosis (CAD) schemes to classify between true-positive and false-positive detections. In this study, the correlation between these two types of classifiers was investigated using a new independent testing data set, and the potential improvement of a CAD scheme's performance by combining the results of the two classifiers in detecting breast masses was assessed. MATERIALS AND METHODS The CAD scheme first used image filtering and a multilayer topographic region growth algorithm to detect and segment suspicious mass regions. The scheme then used an image feature-based classifier to classify these regions into true-positive and false-positive regions. Two classifiers were used in this study. One was a global data-based machine-learning classifier, an artificial neural network (ANN), and the other was a local instance-based machine-learning classifier, a k-nearest neighbor (KNN) algorithm. An independent image database including 400 mammographic examinations was used in this study. Of these, 200 were cancer cases and 200 were negative cases. The preoptimized CAD scheme was applied twice to the database using the two different classifiers. The correlation between the two sets of classification results was analyzed. Three sets of CAD performance results using the ANN, KNN, and average detection scores from both classifiers were assessed and compared using the free-response receiver-operating characteristic method. RESULTS The results showed that the ANN achieved higher performance than the KNN algorithm, with a normalized area under the performance curve (AUC) of 0.891 versus 0.845. The correlation coefficients between the detection scores generated by the two classifiers were 0.436 and 0.161 for the true-positive and false-positive detections, respectively. The average detection scores of the two classifiers improved CAD performance and reliability by increasing the AUC to 0.912 and reducing the standard error of the estimated AUC by 14.4%. The detection sensitivity was also increased from 75.8% (ANN) and 65.9% (KNN) to 80.3% at a false-positive detection rate of 0.3 per image. CONCLUSIONS This study demonstrates that two global data-based and local data-based machine-learning classifiers (ANN and KNN) generated low correlated detection results and that combining the detection scores of these two classifiers significantly improved overall CAD performance (P < .01) and reduced standard error in CAD performance assessment.
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Chawla AS, Samei E, Saunders RS, Lo JY, Baker JA. A mathematical model platform for optimizing a multiprojection breast imaging system. Med Phys 2008; 35:1337-45. [PMID: 18491528 DOI: 10.1118/1.2885367] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Multiprojection imaging is a technique in which a plurality of digital radiographic images of the same patient are acquired within a short interval of time from slightly different angles. Information from each image is combined to determine the final diagnosis. Projection data are either reconstructed into slices as in the case of tomosynthesis or analyzed directly as in the case of multiprojection correlation imaging technique, thereby avoiding reconstruction artifacts. In this study, the authors investigated the optimum geometry of acquisitions of a multiprojection breast correlation imaging system in terms of the number of projections and their total angular span that yield maximum performance in a task that models clinical decision. Twenty-five angular projections of each breast from 82 human subjects in our breast tomosynthesis database were each supplemented with a simulated 3 mm mass. An approach based on Laguerre-Gauss channelized Hotelling observer was developed to assess the detectability of the mass in terms of receiver operating characteristic (ROC) curves. Two methodologies were developed to integrate results from individual projections into one combined ROC curve as the overall figure of merit. To optimize the acquisition geometry, different components of acquisitions were changed to investigate which one of the many possible configurations maximized the area under the combined ROC curve. Optimization was investigated under two acquisition dose conditions corresponding to a fixed total dose delivered to the patient and a variable dose condition, based on the number of projections used. In either case, the detectability was dependent on the number of projections used, the total angular span of those projections, and the acquisition dose level. In the first case, the detectability approximately followed a bell curve as a function of the number of projections with the maximum between 8 and 16 projections spanning angular arcs of about 23 degrees-45 degrees, respectively. In the second case, the detectability increased with the number of projections approaching an asymptote at 11-17 projections for an angular span of about 45 degrees. These results indicate the inherent information content of the multi-projection image data reflecting the relative role of quantum and anatomical noise in multiprojection breast imaging. The optimization scheme presented here may be applied to any multiprojection imaging modalities and may be extended by including reconstruction in the case of digital breast tomosynthesis and breast computed tomography.
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Affiliation(s)
- Amarpreet S Chawla
- Duke Advanced Imaging Laboratories, Department of Radiology, Duke University, Durham, North Carolina 27705, USA.
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Shi J, Sahiner B, Chan HP, Ge J, Hadjiiski L, Helvie MA, Nees A, Wu YT, Wei J, Zhou C, Zhang Y, Cui J. Characterization of mammographic masses based on level set segmentation with new image features and patient information. Med Phys 2008; 35:280-90. [PMID: 18293583 DOI: 10.1118/1.2820630] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Computer-aided diagnosis (CAD) for characterization of mammographic masses as malignant or benign has the potential to assist radiologists in reducing the biopsy rate without increasing false negatives. The purpose of this study was to develop an automated method for mammographic mass segmentation and explore new image based features in combination with patient information in order to improve the performance of mass characterization. The authors' previous CAD system, which used the active contour segmentation, and morphological, textural, and spiculation features, has achieved promising results in mass characterization. The new CAD system is based on the level set method and includes two new types of image features related to the presence of microcalcifications with the mass and abruptness of the mass margin, and patient age. A linear discriminant analysis (LDA) classifier with stepwise feature selection was used to merge the extracted features into a classification score. The classification accuracy was evaluated using the area under the receiver operating characteristic curve. The authors' primary data set consisted of 427 biopsy-proven masses (200 malignant and 227 benign) in 909 regions of interest (ROIs) (451 malignant and 458 benign) from multiple mammographic views. Leave-one-case-out resampling was used for training and testing. The new CAD system based on the level set segmentation and the new mammographic feature space achieved a view-based Az value of 0.83 +/- 0.01. The improvement compared to the previous CAD system was statistically significant (p = 0.02). When patient age was included in the new CAD system, view-based and case-based Az values were 0.85 +/- 0.01 and 0.87 +/- 0.02, respectively. The study also demonstrated the consistency of the newly developed CAD system by evaluating the statistics of the weights of the LDA classifiers in leave-one-case-out classification. Finally, an independent test on the publicly available digital database for screening mammography with 132 benign and 197 malignant ROIs containing masses achieved a view-based Az value of 0.84 +/- 0.02.
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Affiliation(s)
- Jiazheng Shi
- Department of Radiology, The University of Michigan, Ann Arbor, Michigan 48109-0904, USA.
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