142 research outputs found

    A Survey on Deep Learning in Medical Image Analysis

    Full text link
    Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

    Cancer diagnosis using deep learning: A bibliographic review

    Get PDF
    In this paper, we first describe the basics of the field of cancer diagnosis, which includes steps of cancer diagnosis followed by the typical classification methods used by doctors, providing a historical idea of cancer classification techniques to the readers. These methods include Asymmetry, Border, Color and Diameter (ABCD) method, seven-point detection method, Menzies method, and pattern analysis. They are used regularly by doctors for cancer diagnosis, although they are not considered very efficient for obtaining better performance. Moreover, considering all types of audience, the basic evaluation criteria are also discussed. The criteria include the receiver operating characteristic curve (ROC curve), Area under the ROC curve (AUC), F1 score, accuracy, specificity, sensitivity, precision, dice-coefficient, average accuracy, and Jaccard index. Previously used methods are considered inefficient, asking for better and smarter methods for cancer diagnosis. Artificial intelligence and cancer diagnosis are gaining attention as a way to define better diagnostic tools. In particular, deep neural networks can be successfully used for intelligent image analysis. The basic framework of how this machine learning works on medical imaging is provided in this study, i.e., pre-processing, image segmentation and post-processing. The second part of this manuscript describes the different deep learning techniques, such as convolutional neural networks (CNNs), generative adversarial models (GANs), deep autoencoders (DANs), restricted Boltzmann’s machine (RBM), stacked autoencoders (SAE), convolutional autoencoders (CAE), recurrent neural networks (RNNs), long short-term memory (LTSM), multi-scale convolutional neural network (M-CNN), multi-instance learning convolutional neural network (MIL-CNN). For each technique, we provide Python codes, to allow interested readers to experiment with the cited algorithms on their own diagnostic problems. The third part of this manuscript compiles the successfully applied deep learning models for different types of cancers. Considering the length of the manuscript, we restrict ourselves to the discussion of breast cancer, lung cancer, brain cancer, and skin cancer. The purpose of this bibliographic review is to provide researchers opting to work in implementing deep learning and artificial neural networks for cancer diagnosis a knowledge from scratch of the state-of-the-art achievements

    Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions

    Full text link
    Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020. Breast imaging plays a significant role in early diagnosis and intervention to improve the outcome of breast cancer patients. In the past decade, deep learning has shown remarkable progress in breast cancer imaging analysis, holding great promise in interpreting the rich information and complex context of breast imaging modalities. Considering the rapid improvement in the deep learning technology and the increasing severity of breast cancer, it is critical to summarize past progress and identify future challenges to be addressed. In this paper, we provide an extensive survey of deep learning-based breast cancer imaging research, covering studies on mammogram, ultrasound, magnetic resonance imaging, and digital pathology images over the past decade. The major deep learning methods, publicly available datasets, and applications on imaging-based screening, diagnosis, treatment response prediction, and prognosis are described in detail. Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging.Comment: Survey, 41 page

    Computer-aided Detection of Breast Cancer in Digital Tomosynthesis Imaging Using Deep and Multiple Instance Learning

    Get PDF
    Breast cancer is the most common cancer among women in the world. Nevertheless, early detection of breast cancer improves the chance of successful treatment. Digital breast tomosynthesis (DBT) as a new tomographic technique was developed to minimize the limitations of conventional digital mammography screening. A DBT is a quasi-three-dimensional image that is reconstructed from a small number of two-dimensional (2D) low-dose X-ray images. The 2D X-ray images are acquired over a limited angular around the breast. Our research aims to introduce computer-aided detection (CAD) frameworks to detect early signs of breast cancer in DBTs. In this thesis, we propose three CAD frameworks for detection of breast cancer in DBTs. The first CAD framework is based on hand-crafted feature extraction. Concerning early signs of breast cancer: mass, micro-calcifications, and bilateral asymmetry between left and right breast, the system includes three separate channels to detect each sign. Next two CAD frameworks automatically learn complex patterns of 2D slices using the deep convolutional neural network and the deep cardinality-restricted Boltzmann machines. Finally, the CAD frameworks employ a multiple-instance learning approach with randomized trees algorithm to classify DBT images based on extracted information from 2D slices. The frameworks operate on 2D slices which are generated from DBT volumes. These frameworks are developed and evaluated using 5,040 2D image slices obtained from 87 DBT volumes. We demonstrate the validation and usefulness of the proposed CAD frameworks within empirical experiments for detecting breast cancer in DBTs

    Deep-Learning-Based Computer- Aided Systems for Breast Cancer Imaging: A Critical Review

    Full text link
    [EN] This paper provides a critical review of the literature on deep learning applications in breast tumor diagnosis using ultrasound and mammography images. It also summarizes recent advances in computer-aided diagnosis/detection (CAD) systems, which make use of new deep learning methods to automatically recognize breast images and improve the accuracy of diagnoses made by radiologists. This review is based upon published literature in the past decade (January 2010-January 2020), where we obtained around 250 research articles, and after an eligibility process, 59 articles were presented in more detail. The main findings in the classification process revealed that new DL-CAD methods are useful and effective screening tools for breast cancer, thus reducing the need for manual feature extraction. The breast tumor research community can utilize this survey as a basis for their current and future studies.This project has been co-financed by the Spanish Government Grant PID2019-107790RB-C22, "Software development for a continuous PET crystal systems applied to breast cancer".Jiménez-Gaona, Y.; Rodríguez Álvarez, MJ.; Lakshminarayanan, V. (2020). Deep-Learning-Based Computer- Aided Systems for Breast Cancer Imaging: A Critical Review. Applied Sciences. 10(22):1-29. https://doi.org/10.3390/app10228298S1291022Jemal, A., Bray, F., Center, M. M., Ferlay, J., Ward, E., & Forman, D. (2011). Global cancer statistics. CA: A Cancer Journal for Clinicians, 61(2), 69-90. doi:10.3322/caac.20107Gao, F., Chia, K.-S., Ng, F.-C., Ng, E.-H., & Machin, D. (2002). Interval cancers following breast cancer screening in Singaporean women. International Journal of Cancer, 101(5), 475-479. doi:10.1002/ijc.10636Munir, K., Elahi, H., Ayub, A., Frezza, F., & Rizzi, A. (2019). Cancer Diagnosis Using Deep Learning: A Bibliographic Review. Cancers, 11(9), 1235. doi:10.3390/cancers11091235Nahid, A.-A., & Kong, Y. (2017). Involvement of Machine Learning for Breast Cancer Image Classification: A Survey. Computational and Mathematical Methods in Medicine, 2017, 1-29. doi:10.1155/2017/3781951Ramadan, S. Z. (2020). Methods Used in Computer-Aided Diagnosis for Breast Cancer Detection Using Mammograms: A Review. Journal of Healthcare Engineering, 2020, 1-21. doi:10.1155/2020/9162464CHAN, H.-P., DOI, K., VYBRONY, C. J., SCHMIDT, R. A., METZ, C. E., LAM, K. L., … MACMAHON, H. (1990). Improvement in Radiologists?? Detection of Clustered Microcalcifications on Mammograms. Investigative Radiology, 25(10), 1102-1110. doi:10.1097/00004424-199010000-00006Olsen, O., & Gøtzsche, P. C. (2001). Cochrane review on screening for breast cancer with mammography. The Lancet, 358(9290), 1340-1342. doi:10.1016/s0140-6736(01)06449-2Mann, R. M., Kuhl, C. K., Kinkel, K., & Boetes, C. (2008). Breast MRI: guidelines from the European Society of Breast Imaging. European Radiology, 18(7), 1307-1318. doi:10.1007/s00330-008-0863-7Jalalian, A., Mashohor, S. B. T., Mahmud, H. R., Saripan, M. I. B., Ramli, A. R. B., & Karasfi, B. (2013). Computer-aided detection/diagnosis of breast cancer in mammography and ultrasound: a review. Clinical Imaging, 37(3), 420-426. doi:10.1016/j.clinimag.2012.09.024Sarno, A., Mettivier, G., & Russo, P. (2015). Dedicated breast computed tomography: Basic aspects. Medical Physics, 42(6Part1), 2786-2804. doi:10.1118/1.4919441Njor, S., Nyström, L., Moss, S., Paci, E., Broeders, M., Segnan, N., & Lynge, E. (2012). Breast Cancer Mortality in Mammographic Screening in Europe: A Review of Incidence-Based Mortality Studies. Journal of Medical Screening, 19(1_suppl), 33-41. doi:10.1258/jms.2012.012080Morrell, S., Taylor, R., Roder, D., & Dobson, A. (2012). Mammography screening and breast cancer mortality in Australia: an aggregate cohort study. Journal of Medical Screening, 19(1), 26-34. doi:10.1258/jms.2012.011127Marmot, M. G., Altman, D. G., Cameron, D. A., Dewar, J. A., Thompson, S. G., & Wilcox, M. (2013). The benefits and harms of breast cancer screening: an independent review. British Journal of Cancer, 108(11), 2205-2240. doi:10.1038/bjc.2013.177Pisano, E. D., Gatsonis, C., Hendrick, E., Yaffe, M., Baum, J. K., Acharyya, S., … Rebner, M. (2005). Diagnostic Performance of Digital versus Film Mammography for Breast-Cancer Screening. New England Journal of Medicine, 353(17), 1773-1783. doi:10.1056/nejmoa052911Carney, P. A., Miglioretti, D. L., Yankaskas, B. C., Kerlikowske, K., Rosenberg, R., Rutter, C. M., … Ballard-Barbash, R. (2003). Individual and Combined Effects of Age, Breast Density, and Hormone Replacement Therapy Use on the Accuracy of Screening Mammography. Annals of Internal Medicine, 138(3), 168. doi:10.7326/0003-4819-138-3-200302040-00008Woodard, D. B., Gelfand, A. E., Barlow, W. E., & Elmore, J. G. (2007). Performance assessment for radiologists interpreting screening mammography. Statistics in Medicine, 26(7), 1532-1551. doi:10.1002/sim.2633Cole, E. B., Pisano, E. D., Kistner, E. O., Muller, K. E., Brown, M. E., Feig, S. A., … Braeuning, M. P. (2003). Diagnostic Accuracy of Digital Mammography in Patients with Dense Breasts Who Underwent Problem-solving Mammography: Effects of Image Processing and Lesion Type. Radiology, 226(1), 153-160. doi:10.1148/radiol.2261012024Boyd, N. F., Guo, H., Martin, L. J., Sun, L., Stone, J., Fishell, E., … Yaffe, M. J. (2007). Mammographic Density and the Risk and Detection of Breast Cancer. New England Journal of Medicine, 356(3), 227-236. doi:10.1056/nejmoa062790Bird, R. E., Wallace, T. W., & Yankaskas, B. C. (1992). Analysis of cancers missed at screening mammography. Radiology, 184(3), 613-617. doi:10.1148/radiology.184.3.1509041Kerlikowske, K. (2000). Performance of Screening Mammography among Women with and without a First-Degree Relative with Breast Cancer. Annals of Internal Medicine, 133(11), 855. doi:10.7326/0003-4819-133-11-200012050-00009Nunes, F. L. S., Schiabel, H., & Goes, C. E. (2006). Contrast Enhancement in Dense Breast Images to Aid Clustered Microcalcifications Detection. Journal of Digital Imaging, 20(1), 53-66. doi:10.1007/s10278-005-6976-5Dinnes, J., Moss, S., Melia, J., Blanks, R., Song, F., & Kleijnen, J. (2001). Effectiveness and cost-effectiveness of double reading of mammograms in breast cancer screening: findings of a systematic review. The Breast, 10(6), 455-463. doi:10.1054/brst.2001.0350Robinson, P. J. (1997). Radiology’s Achilles’ heel: error and variation in the interpretation of the Röntgen image. The British Journal of Radiology, 70(839), 1085-1098. doi:10.1259/bjr.70.839.9536897Rangayyan, R. M., Ayres, F. J., & Leo Desautels, J. E. (2007). A review of computer-aided diagnosis of breast cancer: Toward the detection of subtle signs. Journal of the Franklin Institute, 344(3-4), 312-348. doi:10.1016/j.jfranklin.2006.09.003Vyborny, C. J., Giger, M. L., & Nishikawa, R. M. (2000). COMPUTER-AIDED DETECTION AND DIAGNOSIS OF BREAST CANCER. Radiologic Clinics of North America, 38(4), 725-740. doi:10.1016/s0033-8389(05)70197-4Giger, M. L. (2018). Machine Learning in Medical Imaging. Journal of the American College of Radiology, 15(3), 512-520. doi:10.1016/j.jacr.2017.12.028Xu, Y., Wang, Y., Yuan, J., Cheng, Q., Wang, X., & Carson, P. L. (2019). Medical breast ultrasound image segmentation by machine learning. Ultrasonics, 91, 1-9. doi:10.1016/j.ultras.2018.07.006Shan, J., Alam, S. K., Garra, B., Zhang, Y., & Ahmed, T. (2016). Computer-Aided Diagnosis for Breast Ultrasound Using Computerized BI-RADS Features and Machine Learning Methods. Ultrasound in Medicine & Biology, 42(4), 980-988. doi:10.1016/j.ultrasmedbio.2015.11.016Zhang, Q., Xiao, Y., Dai, W., Suo, J., Wang, C., Shi, J., & Zheng, H. (2016). Deep learning based classification of breast tumors with shear-wave elastography. Ultrasonics, 72, 150-157. doi:10.1016/j.ultras.2016.08.004Cheng, J.-Z., Ni, D., Chou, Y.-H., Qin, J., Tiu, C.-M., Chang, Y.-C., … Chen, C.-M. (2016). Computer-Aided Diagnosis with Deep Learning Architecture: Applications to Breast Lesions in US Images and Pulmonary Nodules in CT Scans. Scientific Reports, 6(1). doi:10.1038/srep24454Shin, S. Y., Lee, S., Yun, I. D., Kim, S. M., & Lee, K. M. (2019). Joint Weakly and Semi-Supervised Deep Learning for Localization and Classification of Masses in Breast Ultrasound Images. IEEE Transactions on Medical Imaging, 38(3), 762-774. doi:10.1109/tmi.2018.2872031Wang, J., Ding, H., Bidgoli, F. A., Zhou, B., Iribarren, C., Molloi, S., & Baldi, P. (2017). Detecting Cardiovascular Disease from Mammograms With Deep Learning. IEEE Transactions on Medical Imaging, 36(5), 1172-1181. doi:10.1109/tmi.2017.2655486Kooi, T., Litjens, G., van Ginneken, B., Gubern-Mérida, A., Sánchez, C. I., Mann, R., … Karssemeijer, N. (2017). Large scale deep learning for computer aided detection of mammographic lesions. Medical Image Analysis, 35, 303-312. doi:10.1016/j.media.2016.07.007Debelee, T. G., Schwenker, F., Ibenthal, A., & Yohannes, D. (2019). Survey of deep learning in breast cancer image analysis. Evolving Systems, 11(1), 143-163. doi:10.1007/s12530-019-09297-2Keen, J. D., Keen, J. M., & Keen, J. E. (2018). Utilization of Computer-Aided Detection for Digital Screening Mammography in the United States, 2008 to 2016. Journal of the American College of Radiology, 15(1), 44-48. doi:10.1016/j.jacr.2017.08.033Henriksen, E. L., Carlsen, J. F., Vejborg, I. M., Nielsen, M. B., & Lauridsen, C. A. (2018). The efficacy of using computer-aided detection (CAD) for detection of breast cancer in mammography screening: a systematic review. Acta Radiologica, 60(1), 13-18. doi:10.1177/0284185118770917Gao, Y., Geras, K. J., Lewin, A. A., & Moy, L. (2019). New Frontiers: An Update on Computer-Aided Diagnosis for Breast Imaging in the Age of Artificial Intelligence. American Journal of Roentgenology, 212(2), 300-307. doi:10.2214/ajr.18.20392Pacilè, S., Lopez, J., Chone, P., Bertinotti, T., Grouin, J. M., & Fillard, P. (2020). Improving Breast Cancer Detection Accuracy of Mammography with the Concurrent Use of an Artificial Intelligence Tool. Radiology: Artificial Intelligence, 2(6), e190208. doi:10.1148/ryai.2020190208Huynh, B. Q., Li, H., & Giger, M. L. (2016). Digital mammographic tumor classification using transfer learning from deep convolutional neural networks. Journal of Medical Imaging, 3(3), 034501. doi:10.1117/1.jmi.3.3.034501Yap, M. H., Pons, G., Marti, J., Ganau, S., Sentis, M., Zwiggelaar, R., … Marti, R. (2018). Automated Breast Ultrasound Lesions Detection Using Convolutional Neural Networks. IEEE Journal of Biomedical and Health Informatics, 22(4), 1218-1226. doi:10.1109/jbhi.2017.2731873Moon, W. K., Lee, Y.-W., Ke, H.-H., Lee, S. H., Huang, C.-S., & Chang, R.-F. (2020). Computer‐aided diagnosis of breast ultrasound images using ensemble learning from convolutional neural networks. Computer Methods and Programs in Biomedicine, 190, 105361. doi:10.1016/j.cmpb.2020.105361LeCun, Y., Bengio, Y., & Hinton, G. (2015). Deep learning. Nature, 521(7553), 436-444. doi:10.1038/nature14539Miotto, R., Wang, F., Wang, S., Jiang, X., & Dudley, J. T. (2017). Deep learning for healthcare: review, opportunities and challenges. Briefings in Bioinformatics, 19(6), 1236-1246. doi:10.1093/bib/bbx044Shin, H.-C., Roth, H. R., Gao, M., Lu, L., Xu, Z., Nogues, I., … Summers, R. M. (2016). Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning. IEEE Transactions on Medical Imaging, 35(5), 1285-1298. doi:10.1109/tmi.2016.2528162Lee, J.-G., Jun, S., Cho, Y.-W., Lee, H., Kim, G. B., Seo, J. B., & Kim, N. (2017). Deep Learning in Medical Imaging: General Overview. Korean Journal of Radiology, 18(4), 570. doi:10.3348/kjr.2017.18.4.570Suzuki, K. (2017). Overview of deep learning in medical imaging. Radiological Physics and Technology, 10(3), 257-273. doi:10.1007/s12194-017-0406-5Moher, D., Liberati, A., Tetzlaff, J., & Altman, D. G. (2010). Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement. International Journal of Surgery, 8(5), 336-341. doi:10.1016/j.ijsu.2010.02.007Khan, K. S., Kunz, R., Kleijnen, J., & Antes, G. (2003). Five Steps to Conducting a Systematic Review. Journal of the Royal Society of Medicine, 96(3), 118-121. doi:10.1177/014107680309600304Han, S., Kang, H.-K., Jeong, J.-Y., Park, M.-H., Kim, W., Bang, W.-C., & Seong, Y.-K. (2017). A deep learning framework for supporting the classification of breast lesions in ultrasound images. Physics in Medicine & Biology, 62(19), 7714-7728. doi:10.1088/1361-6560/aa82ecMoreira, I. C., Amaral, I., Domingues, I., Cardoso, A., Cardoso, M. J., & Cardoso, J. S. (2012). INbreast. Academic Radiology, 19(2), 236-248. doi:10.1016/j.acra.2011.09.014Abdelhafiz, D., Yang, C., Ammar, R., & Nabavi, S. (2019). Deep convolutional neural networks for mammography: advances, challenges and applications. BMC Bioinformatics, 20(S11). doi:10.1186/s12859-019-2823-4Byra, M., Jarosik, P., Szubert, A., Galperin, M., Ojeda-Fournier, H., Olson, L., … Andre, M. (2020). Breast mass segmentation in ultrasound with selective kernel U-Net convolutional neural network. Biomedical Signal Processing and Control, 61, 102027. doi:10.1016/j.bspc.2020.102027Jiao, Z., Gao, X., Wang, Y., & Li, J. (2016). A deep feature based framework for breast masses classification. Neurocomputing, 197, 221-231. doi:10.1016/j.neucom.2016.02.060Arevalo, J., González, F. A., Ramos-Pollán, R., Oliveira, J. L., & Guevara Lopez, M. A. (2016). Representation learning for mammography mass lesion classification with convolutional neural networks. Computer Methods and Programs in Biomedicine, 127, 248-257. doi:10.1016/j.cmpb.2015.12.014Peng, W., Mayorga, R. V., & Hussein, E. M. A. (2016). An automated confirmatory system for analysis of mammograms. Computer Methods and Programs in Biomedicine, 125, 134-144. doi:10.1016/j.cmpb.2015.09.019Al-Dhabyani, W., Gomaa, M., Khaled, H., & Fahmy, A. (2020). Dataset of breast ultrasound images. Data in Brief, 28, 104863. doi:10.1016/j.dib.2019.104863Piotrzkowska-Wróblewska, H., Dobruch-Sobczak, K., Byra, M., & Nowicki, A. (2017). Open access database of raw ultrasonic signals acquired from malignant and benign breast lesions. Medical Physics, 44(11), 6105-6109. doi:10.1002/mp.12538Fujita, H. (2020). AI-based computer-aided diagnosis (AI-CAD): the latest review to read first. Radiological Physics and Technology, 13(1), 6-19. doi:10.1007/s12194-019-00552-4Sengupta, S., Singh, A., Leopold, H. A., Gulati, T., & Lakshminarayanan, V. (2020). Ophthalmic diagnosis using deep learning with fundus images – A critical review. Artificial Intelligence in Medicine, 102, 101758. doi:10.1016/j.artmed.2019.101758Ganesan, K., Acharya, U. R., Chua, K. C., Min, L. C., & Abraham, K. T. (2013). Pectoral muscle segmentation: A review. Computer Methods and Programs in Biomedicine, 110(1), 48-57. doi:10.1016/j.cmpb.2012.10.020Huang, Q., Luo, Y., & Zhang, Q. (2017). Breast ultrasound image segmentation: a survey. International Journal of Computer Assisted Radiology and Surgery, 12(3), 493-507. doi:10.1007/s11548-016-1513-1Noble, J. A., & Boukerroui, D. (2006). Ultrasound image segmentation: a survey. IEEE Transactions on Medical Imaging, 25(8), 987-1010. doi:10.1109/tmi.2006.877092Kallergi, M., Woods, K., Clarke, L. P., Qian, W., & Clark, R. A. (1992). Image segmentation in digital mammography: Comparison of local thresholding and region growing algorithms. Computerized Medical Imaging and Graphics, 16(5), 323-331. doi:10.1016/0895-6111(92)90145-yTsantis, S., Dimitropoulos, N., Cavouras, D., & Nikiforidis, G. (2006). A hybrid multi-scale model for thyroid nodule boundary detection on ultrasound images. Computer Methods and Programs in Biomedicine, 84(2-3), 86-98. doi:10.1016/j.cmpb.2006.09.006Ilesanmi, A. E., Idowu, O. P., & Makhanov, S. S. (2020). Multiscale superpixel method for segmentation of breast ultrasound. Computers in Biology and Medicine, 125, 103879. doi:10.1016/j.compbiomed.2020.103879Chen, D.-R., Chang, R.-F., Kuo, W.-J., Chen, M.-C., & Huang, Y. .-L. (2002). Diagnosis of breast tumors with sonographic texture analysis using wavelet transform and neural networks. Ultrasound in Medicine & Biology, 28(10), 1301-1310. doi:10.1016/s0301-5629(02)00620-8Cheng, H. D., Shan, J., Ju, W., Guo, Y., & Zhang, L. (2010). Automated breast cancer detection and classification using ultrasound images: A survey. Pattern Recognition, 43(1), 299-317. doi:10.1016/j.patcog.2009.05.012Chan, H.-P., Wei, D., Helvie, M. A., Sahiner, B., Adler, D. D., Goodsitt, M. M., & Petrick, N. (1995). Computer-aided classification of mammographic masses and normal tissue: linear discriminant analysis in texture feature space. Physics in Medicine and Biology, 40(5), 857-876. doi:10.1088/0031-9155/40/5/010Tanaka, T., Torii, S., Kabuta, I., Shimizu, K., & Tanaka, M. (2007). Pattern Classification of Nevus with Texture Analysis. IEEJ Transactions on Electrical and Electronic Engineering, 3(1), 143-150. doi:10.1002/tee.20246Singh, B., Jain, V. K., & Singh, S. (2014). Mammogram Mass Classification Using Support Vector Machine with Texture, Shape Features and Hierarchical Centroid Method. Journal of Medical Imaging and Health Informatics, 4(5), 687-696. doi:10.1166/jmihi.2014.1312Pal, N. R., Bhowmick, B., Patel, S. K., Pal, S., & Das, J. (2008). A multi-stage neural network aided system for detection of microcalcifications in digitized mammograms. Neurocomputing, 71(13-15), 2625-2634. doi:10.1016/j.neucom.2007.06.015Ayer, T., Chen, Q., & Burnside, E. S. (2013). Artificial Neural Networks in Mammography Interpretation and Diagnostic Decision Making. Computational and Mathematical Methods in Medicine, 2013, 1-10. doi:10.1155/2013/832509Sumbaly, R., Vishnusri, N., & Jeyalatha, S. (2014). Diagnosis of Breast Cancer using Decision Tree Data Mining Technique. International Journal of Computer Applications, 98(10), 16-24. doi:10.5120/17219-7456Landwehr, N., Hall, M., & Frank, E. (2005). Logistic Model Trees. Machine Learning, 59(1-2), 161-205. doi:10.1007/s10994-005-0466-3Abdel-Zaher, A. M., & Eldeib, A. M. (2016). Breast cancer classification using deep belief networks. Expert Systems with Applications, 46, 139-144. doi:10.1016/j.eswa.2015.10.015Nishikawa, R. M., Giger, M. L., Doi, K., Metz, C. E., Yin, F.-F., Vyborny, C. J., & Schmidt, R. A. (1994). Effect of case selection on the performance of computer-aided detection schemes. Medical Physics, 21(2), 265-269. doi:10.1118/1.597287Guo, R., Lu, G., Qin, B., & Fei, B. (2018). Ultrasound Imaging Technologies for Breast Cancer Detection and Management: A Review. Ultrasound in Medicine & Biology, 44(1), 37-70. doi:10.1016/j.ultrasmedbio.2017.09.012Kang, C.-C., Wang, W.-J., & Kang, C.-H. (2012). Image segmentation with complicated background by using seeded region growing. AEU - International Journal of Electronics and Communications, 66(9), 767-771. doi:10.1016/j.aeue.2012.01.011Prabusankarlal, K. M., Thirumoorthy, P., & Manavalan, R. (2014). Computer Aided Breast Cancer Diagnosis Techniques in Ultrasound: A Survey. Journal of Medical Imaging and Health Informatics, 4(3), 331-349. doi:10.1166/jmihi.2014.1269Abdallah, Y. M., Elgak, S., Zain, H., Rafiq, M., A. Ebaid, E., & A. Elnaema, A. (2018). Breast cancer detection using image enhancement and segmentation algorithms. Biomedical Research, 29(20). doi:10.4066/biomedicalresearch.29-18-1106K.U, S., & S, G. R. (2016). Objective Quality Assessment of Image Enhancement Methods in Digital Mammography - A Comparative Study. Signal & Image Processing : An International Journal, 7(4), 01-13. doi:10.5121/sipij.2016.7401Pizer, S. M., Amburn, E. P., Austin, J. D., Cromartie, R., Geselowitz, A., Greer, T., … Zuiderveld, K. (1987). Adaptive histogram equalization and its variations. Computer Vision, Graphics, and Image Processing, 39(3), 355-368. doi:10.1016/s0734-189x(87)80186-xPisano, E. D., Zong, S., Hemminger, B. M., DeLuca, M., Johnston, R. E., Muller, K., … Pizer, S. M. (1998). Contrast Limited Adaptive Histogram Equalization image processing to improve the detection of simulated spiculations in dense mammograms. Journal of Digital Imaging, 11(4), 193-200. doi:10.1007/bf03178082Wan, J., Yin, H., Chong, A.-X., & Liu, Z.-H. (2020). Progressive residual networks for image super-resolution. Applied Intelligence, 50(5), 1620-1632. doi:10.1007/s10489-019-01548-8Umehara, K., Ota, J., & Ishida, T. (2017). Super-Resolution Imaging of Mammograms Based on the Super-Resolution Convolutional Neural Network. Open Journal of Medical Imaging, 07(04), 180-195. doi:10.4236/ojmi.2017.74018Dong, C., Loy, C. C., He, K., & Tang, X. (2016). Image Super-Resolution Using Deep Convolutional Networks. IEEE Transactions on Pattern Analysis and Machine Intelligence, 38(2), 295-307. doi:10.1109/tpami.2015.2439281Jiang, Y., & Li, J. (2020). Generative Adversarial Network for Image Super-Resolution Combining Texture Loss. Applied Sciences, 10(5), 1729. doi:10.3390/app10051729Schultz, R. R., & Stevenson, R. L. (1994). A Bayesian approach to image expansion for improved definition. IEEE Transactions on Image Processing, 3(3), 233-242. doi:10.1109/83.287017Lei Zhang, & Xiaolin Wu. (2006). An edge-guided image interpolation algorithm via directional filtering and data fusion. IEEE Transactions on Image Processing, 15(8), 2226-2238. doi:10.1109/tip.2006.877407Shorten, C., & Khoshgoftaar, T. M. (2019). A survey on Image Data Augmentation for Deep Learning. Journal of Big Data, 6(1). doi:10.1186/s40537-019-0197-0Weiss, K., Khoshgoftaar, T. M., & Wang, D. (2016). A survey of transfer learning. Journal of Big Data, 3(1). doi:10.1186/s40537-016-0043-6Ling Shao, Fan Zhu, & Xuelong Li. (2015). Transfer Learning for Visual Categorization: A Survey. IEEE Transactions on Neural Networks and Learning Syste

    Representation learning for breast cancer lesion detection

    Get PDF
    Breast Cancer (BC) is the second type of cancer with a higher incidence in women, it is responsible for the death of hundreds of thousands of women every year. However, when detected in the early stages of the disease, treatment methods have proven to be very effective in increasing life expectancy and, in many cases, patients fully recover. Several medical image modalities, such as MG – Mammography (X-Rays), US - Ultrasound, CT - Computer Tomography, MRI - Magnetic Resonance Imaging, and Tomosynthesis have been explored to support radiologists/physicians in clinical decision-making work- flows for the detection and diagnosis of BC. MG is the imaging modality more used at the worldwide level, however, recent research results have demonstrated that breast MRI is more sensitive than mam- mography to find pathological lesions, and it is not limited/affected by breast density issues. Therefore, it is currently a trend to introduce MRI-based breast assessment into clinical workflows (screening and diagnosis), but when compared to MG the workload of radiologists/physicians increases, MRI assess- ment is a more time-consuming task, and its effectiveness is affected not only by the variety of morpho- logical characteristics of each specific tumor phenotype and its origin but also by human fatigue. Com- puter-Aided Detection (CADe) methods have been widely explored primarily in mammography screen- ing tasks, but it remains an unsolved problem in breast MRI settings. This work aims to explore and validate BC detection models using Machine (Deep) Learning algorithms. As the main contribution, we have developed and validated an innovative method that improves the “breast MRI preprocessing phase” to select the patient’s image slices and bounding boxes representing pathological lesions. With this, it is possible to build a more robust training dataset to feed the deep learning models, reducing the computation time and the dimension of the dataset, and more importantly, to identify with high accuracy the specific regions (bounding boxes) for each of the patient images, in which a possible pathological lesion (tumor) has been identified. In experimental settings using a fully annotated (released for public domain) dataset comprising a total of 922 MRI-based BC patient cases, we have achieved, as the most accurate trained model, an accuracy rate of 97.83%, and subsequently, applying a ten-fold cross-validation method, a mean accuracy on the trained models of 94.46% and an associated standard deviation of 2.43%.O cancro da mama (CdM) é o segundo tipo de cancro com maior incidência nas mulheres. É respon- sável pela morte de centenas de milhares de mulheres todos os anos. Contudo, quando detetado nas fases iniciais da doença, os métodos de tratamento provaram ser muito eficazes aumentando a espe- rança de vida e, em muitos casos, os pacientes recuperam totalmente. Têm sido exploradas várias modalidades de imagem médica, tais como MG - Mamografia (Raios-X), US - Ultra-som, CT - Tomo- grafia Computadorizada, MRI - Ressonância Magnética e Tomossíntese, para apoiar radiologistas nos fluxos de trabalho clínico para a deteção e diagnóstico do CdM. A MG é a modalidade de imagem mais utilizada a nível mundial, contudo, resultados de pesquisas recentes demonstraram que o MRI é mais sensível do que a mamografia para encontrar lesões patológicas e, também, não é limitada ou afetada por questões de densidade mamária. Consequentemente, atualmente é uma tendência introduzir a avaliação mamográfica baseada em MRI nos fluxos de trabalho clínico - rastreio e diagnóstico -, mas quando comparada com a MG, a carga de trabalho dos radiologistas aumenta. A avaliação por MRI é uma tarefa mais demorada, e a sua eficácia é afetada não só pela variedade de características morfo- lógicas e origem de cada fenótipo tumoral específico, mas, também pela fadiga humana. Os métodos de deteção assistida por computador (CADe) têm sido amplamente explorados principalmente em ta- refas de rastreio mamográfico, mas continua a ser um problema por resolver em ambientes de resso- nância magnética mamária. Este trabalho visa explorar e validar modelos de deteção de CdM usando algoritmos de Machine (Deep) Learning. Como contributo principal, desenvolvemos e validámos um método inovador que me- lhora a "fase de pré-processamento das imagens de ressonância magnética mamária" para selecionar as fatias de imagem do paciente e as respetivas caixas de contorno que representam as lesões pato- lógicas. Com isto, é possível construir um conjunto de dados de treino mais robusto para alimentar os modelos de deep learning, reduzir o tempo de computação, reduzir a dimensão do conjunto de dados e, mais importante, para identificar com alta precisão as regiões específicas para cada uma das ima- gens do paciente nas quais foi identificada uma possível lesão patológica (tumor). Os resultados expe- rimentais, num conjunto de imagens de ressonância magnética de domínio público totalmente anotado com 922 casos de doentes com CdM, mostram no melhor modelo uma taxa de exatidão de 97.83%. Foi aplicado um método de validação cruzada de 10 folds do qual resultou uma exatidão média de 94,46% com um desvio padrão de 2,43% nos modelos treinados

    NOVEL APPLICATIONS OF MACHINE LEARNING IN BIOINFORMATICS

    Get PDF
    Technological advances in next-generation sequencing and biomedical imaging have led to a rapid increase in biomedical data dimension and acquisition rate, which is challenging the conventional data analysis strategies. Modern machine learning techniques promise to leverage large data sets for finding hidden patterns within them, and for making accurate predictions. This dissertation aims to design novel machine learning-based models to transform biomedical big data into valuable biological insights. The research presented in this dissertation focuses on three bioinformatics domains: splice junction classification, gene regulatory network reconstruction, and lesion detection in mammograms. A critical step in defining gene structures and mRNA transcript variants is to accurately identify splice junctions. In the first work, we built the first deep learning-based splice junction classifier, DeepSplice. It outperforms the state-of-the-art classification tools in terms of both classification accuracy and computational efficiency. To uncover transcription factors governing metabolic reprogramming in non-small-cell lung cancer patients, we developed TFmeta, a machine learning approach to reconstruct relationships between transcription factors and their target genes in the second work. Our approach achieves the best performance on benchmark data sets. In the third work, we designed deep learning-based architectures to perform lesion detection in both 2D and 3D whole mammogram images

    Enhanced Digital Breast Tomosynthesis diagnosis using 3D visualization and automatic classification of lesions

    Get PDF
    Breast cancer represents the main cause of cancer-related deaths in women. Nonetheless, the mortality rate of this disease has been decreasing over the last three decades, largely due to the screening programs for early detection. For many years, both screening and clinical diagnosis were mostly done through Digital Mammography (DM). Approved in 2011, Digital Breast Tomosynthesis (DBT) is similar to DM but it allows a 3D reconstruction of the breast tissue, which helps the diagnosis by reducing the tissue overlap. Currently, DBT is firmly established and is approved as a stand-alone modality to replace DM. The main objective of this thesis is to develop computational tools to improve the visualization and interpretation of DBT data. Several methods for an enhanced visualization of DBT data through volume rendering were studied and developed. Firstly, important rendering parameters were considered. A new approach for automatic generation of transfer functions was implemented and two other parameters that highly affect the quality of volume rendered images were explored: voxel size in Z direction and sampling distance. Next, new image processing methods that improve the rendering quality by considering the noise regularization and the reduction of out-of-plane artifacts were developed. The interpretation of DBT data with automatic detection of lesions was approached through artificial intelligence methods. Several deep learning Convolutional Neural Networks (CNNs) were implemented and trained to classify a complete DBT image for the presence or absence of microcalcification clusters (MCs). Then, a faster R-CNN (region-based CNN) was trained to detect and accurately locate the MCs in the DBT images. The detected MCs were rendered with the developed 3D rendering software, which provided an enhanced visualization of the volume of interest. The combination of volume visualization with lesion detection may, in the future, improve both diagnostic accuracy and also reduce analysis time. This thesis promotes the development of new computational imaging methods to increase the diagnostic value of DBT, with the aim of assisting radiologists in their task of analyzing DBT volumes and diagnosing breast cancer
    corecore