ck-NN: A Clustered k-Nearest Neighbours Approach for Large-Scale Classification

k-Nearest Neighbor (k-NN) is a non-parametric algorithm widely used for the estimation and classification of data points especially when the dataset is distributed in several classes. It is considered to be a lazy machine learning algorithm as most of the computations are done during the testing phase instead of performing this task during the training of data. Hence it is practically inefficient, infeasible and inapplicable while processing huge datasets i.e. Big Data. On the other hand, clustering techniques (unsupervised learning) greatly affect results if you do normalization or standardization techniques, difficult to determine "k" Value. In this paper, some novel techniques are proposed to be used as pre-state mechanism of state-of-the-art k-NN Classification Algorithm. Our proposed mechanism uses unsupervised clustering algorithm on large dataset before applying k-NN algorithm on different clusters that might running on single machine, multiple machines or different nodes of a cluster in distributed environment. Initially dataset, possibly having multi dimensions, is pass through clustering technique (K-Means) at master node or controller to find the number of clusters equal to the number of nodes in distributed systems or number of cores in system, and then each cluster will be assigned to exactly one node or one core and then applies k-NN locally, each core or node in clusters sends their best result and the selector choose best and nearest possible class from all options. We will be using one of the gold standard distributed framework. We believe that our proposed mechanism could be applied on big data. We also believe that the architecture can also be implemented on multi GPUs or FPGA to take flavor of k-NN on large or huge datasets where traditional k-NN is very slow

Machine learning based data pre-processing for the purpose of medical data mining and decision support

Building an accurate and reliable model for prediction for different application domains, is one of the most significant challenges in knowledge discovery and data mining. Sometimes, improved data quality is itself the goal of the analysis, usually to improve processes in a production database and the designing of decision support. As medicine moves forward there is a need for sophisticated decision support systems that make use of data mining to support more orthodox knowledge engineering and Health Informatics practice. However, the real-life medical data rarely complies with the requirements of various data mining tools. It is often inconsistent, noisy, containing redundant attributes, in an unsuitable format, containing missing values and imbalanced with regards to the outcome class label.Many real-life data sets are incomplete, with missing values. In medical data mining the problem with missing values has become a challenging issue. In many clinical trials, the medical report pro-forma allow some attributes to be left blank, because they are inappropriate for some class of illness or the person providing the information feels that it is not appropriate to record the values for some attributes. The research reported in this thesis has explored the use of machine learning techniques as missing value imputation methods. The thesis also proposed a new way of imputing missing value by supervised learning. A classifier was used to learn the data patterns from a complete data sub-set and the model was later used to predict the missing values for the full dataset. The proposed machine learning based missing value imputation was applied on the thesis data and the results are compared with traditional Mean/Mode imputation. Experimental results show that all the machine learning methods which we explored outperformed the statistical method (Mean/Mode).The class imbalance problem has been found to hinder the performance of learning systems. In fact, most of the medical datasets are found to be highly imbalance in their class label. The solution to this problem is to reduce the gap between the minority class samples and the majority class samples. Over-sampling can be applied to increase the number of minority class sample to balance the data. The alternative to over-sampling is under-sampling where the size of majority class sample is reduced. The thesis proposed one cluster based under-sampling technique to reduce the gap between the majority and minority samples. Different under-sampling and over-sampling techniques were explored as ways to balance the data. The experimental results show that for the thesis data the new proposed modified cluster based under-sampling technique performed better than other class balancing techniques.In further research it is found that the class imbalance problem not only affects the classification performance but also has an adverse effect on feature selection. The thesis proposed a new framework for feature selection for class imbalanced datasets. The research found that, using the proposed framework the classifier needs less attributes to show high accuracy, and more attributes are needed if the data is highly imbalanced.The research described in the thesis contains the flowing four novel main contributions.a) Improved data mining methodology for mining medical datab) Machine learning based missing value imputation methodc) Cluster Based semi-supervised class balancing methodd) Feature selection framework for class imbalance datasetsThe performance analysis and comparative study show that the use of proposed method of missing value imputation, class balancing and feature selection framework can provide an effective approach to data preparation for building medical decision support

Predicting Alzheimer's disease by segmenting and classifying 3D-brain MRI images using clustering technique and SVM classifiers.

Alzheimer's disease (AD) is the most common form of dementia affecting seniors age 65 and over. When AD is suspected, the diagnosis is usually confirmed with behavioural assessments and cognitive tests, often followed by a brain scan. Advanced medical imaging and pattern recognition techniques are good tools to create a learning database in the first step and to predict the class label of incoming data in order to assess the development of the disease, i.e., the conversion from prodromal stages (mild cognitive impairment) to Alzheimer's disease. Advanced medical imaging such as the volumetric MRI can detect changes in the size of brain regions due to the loss of the brain tissues. Measuring regions that atrophy during the progress of Alzheimer's disease can help neurologists in detecting and staging the disease. In this thesis, we want to diagnose the Alzheimer’s disease from MRI images. We segment brain MRI images to extract the brain chambers. Then, features are extracted from the segmented area. Finally, a classifier is trained to differentiate between normal and AD brain tissues. We discuss an automatic scheme that reads volumetric MRI, extracts the middle slices of the brain region, performs 2-dimensional (volume slices) and volumetric segmentation methods in order to segment gray matter, white matter and cerebrospinal fluid (CSF), generates a feature vector that characterizes this region, creates a database that contains the generated data, and finally classifies the images based on the extracted features. For our results, we have used the MRI data sets from the Alzheimer’s disease Neuroimaging Initiative (ADNI) database1. We assessed the performance of the classifiers by using results from the clinical tests.Master of Science (M.Sc.) in Computational Science

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

[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

Machine learning for detection and prediction of crop diseases and pests: A comprehensive survey

Considering the population growth rate of recent years, a doubling of the current worldwide crop productivity is expected to be needed by 2050. Pests and diseases are a major obstacle to achieving this productivity outcome. Therefore, it is very important to develop efficient methods for the automatic detection, identification, and prediction of pests and diseases in agricultural crops. To perform such automation, Machine Learning (ML) techniques can be used to derive knowledge and relationships from the data that is being worked on. This paper presents a literature review on ML techniques used in the agricultural sector, focusing on the tasks of classification, detection, and prediction of diseases and pests, with an emphasis on tomato crops. This survey aims to contribute to the development of smart farming and precision agriculture by promoting the development of techniques that will allow farmers to decrease the use of pesticides and chemicals while preserving and improving their crop quality and production.info:eu-repo/semantics/publishedVersio

Deep Learning in Single-Cell Analysis

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.Comment: 77 pages, 11 figures, 15 tables, deep learning, single-cell analysi

Analysis and improvement proposal on self-supervised deep learning

Self-supervised learning is an emerging deep learning paradigm that aims at removing the label-dependency problems suffered by most supervised learning algorithms. Instance discrimination algorithms have proved to be very successful as they have reduced the gap between supervised and self-supervised ones to less than 5%. While most instance discrimination approaches focus on contrasting two augmentations of the same image, Neighbour Contrastive Learning approaches aim to increase the generalization of deep networks by pulling together representations from different images (neighbours) that belong to the same semantical class. However, they are limited mainly by their low accuracy regarding the neighbour selection. They also suffer from reduced efficiency while using multiple neighbours. Instance discrimination algorithms have their own particularities in solving the learning problem, and combining different approaches, bringing in the best of algorithms, is very interesting. In this thesis, we propose a neighbour contrast learning method called Musketeer. This method introduces Self-attention operations to create single representations, defined as centroids, from the extracted neighbours. Directly contrasting these centroids increases the neighbour retrieval accuracy while avoiding any efficiency loss. Moreover, Musketeer combines its neighbour contrast objective with a feature redundancy reduction objective, forming a symbiosis that proves to be beneficial in the overall performance of the framework. Our proposed symbiotic approach consistently outperforms SoTA instance discrimination frameworks on popular image classification benchmarking datasets, namely, CIFAR-10, CIFAR-100 and ImageNet-100. Additionally, we build an analysis pipeline that further explores the quantitative and qualitative results, providing numerous insights into the explainability of instance discrimination approaches

Towards Personalized and Human-in-the-Loop Document Summarization

The ubiquitous availability of computing devices and the widespread use of the internet have generated a large amount of data continuously. Therefore, the amount of available information on any given topic is far beyond humans' processing capacity to properly process, causing what is known as information overload. To efficiently cope with large amounts of information and generate content with significant value to users, we require identifying, merging and summarising information. Data summaries can help gather related information and collect it into a shorter format that enables answering complicated questions, gaining new insight and discovering conceptual boundaries. This thesis focuses on three main challenges to alleviate information overload using novel summarisation techniques. It further intends to facilitate the analysis of documents to support personalised information extraction. This thesis separates the research issues into four areas, covering (i) feature engineering in document summarisation, (ii) traditional static and inflexible summaries, (iii) traditional generic summarisation approaches, and (iv) the need for reference summaries. We propose novel approaches to tackle these challenges, by: i)enabling automatic intelligent feature engineering, ii) enabling flexible and interactive summarisation, iii) utilising intelligent and personalised summarisation approaches. The experimental results prove the efficiency of the proposed approaches compared to other state-of-the-art models. We further propose solutions to the information overload problem in different domains through summarisation, covering network traffic data, health data and business process data.Comment: PhD thesi