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Automated Detection of Tuberculosis from Sputum Smear Microscopic Images Using Transfer Learning Techniques

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Intelligent Systems Design and Applications (ISDA 2019)

Abstract

Tuberculosis is a contagious disease and is one of the leading causes of death especially in low and middle income countries such as Uganda. While there are several ways to diagnose tuberculosis, sputum smear microscopy is the commonest method practised. However, this method can be error prone and also requires trained medical personnel who are not always readily available. In this research, we apply deep learning models based on two pre-trained Convolutional Neural Networks: VGGNet and GoogLeNet Inception v3 to diagnose tuberculosis from 148 Ziehl-Neelsen stained sputum smear microscopic images from two different datasets. These networks are used in three different scenarios, namely, fast feature extraction without data augmentation, fast feature extraction with data augmentation and fine-tuning. Our results show that using Inception v3 for fast feature extraction without data augmentation produces the best results with an accuracy score of 86.7%. This provides a much better approach to disease diagnosis based on the use of diverse datasets from different sources and the results of this work can be leveraged in medical imaging for faster tuberculosis diagnosis.

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Notes

  1. 1.

    http://air.ug/microscopy.

References

  1. Activation functions in Neural Networks. https://www.geeksforgeeks.org/activation-functions-neural-networks/

  2. Adgaonkar, A., Atreya, A., Mulgund, A.D., Nath, J.R.: Identification of Tuberculosis Bacilli using Image Processing. Int. J. Comput. Appl. (IJCA) ICONET-2014, 0975–8887 (2014)

    Google Scholar 

  3. A Beginners Guide to Convolutional Neural Networks (CNNs). https://skymind.ai/wiki/convolutional-network

  4. Bakatoor, M., Radosav, D.: Deep learning and medical diagnosis: a review of literature. Multimodal Technol. Interact. 2(3) (2018). https://doi.org/10.3390/mti2030047

  5. Bwambale, T.: Tuberculosis prevalence rises by 60% survey. http://www.newvision.co.ug/newvision/news/1460677/tuberculosis-prevalence-rises-survey

  6. Damien: How to split a dataset. https://www.beyondthelines.net/machine-learning/how-to-split-a-dataset

  7. Fogel, N.: Tuberculosis: a disease without boundaries. Tuberculosis 95(5), 527–531 (2015). https://doi.org/10.1016/j.tube.2015.05.017

    Article  Google Scholar 

  8. Gupta, D.S.: Transfer learning & The art of using Pre-trained Models in Deep Learning. https://www.analyticsvidhya.com/blog/2017/06/transfer-learning-the-art-of-fine-tuning-a-pre-trained-model

  9. Health Access Corps “Healthcare in Uganda. Lets do the numbers. http://healthaccesscorps.org/blog/2014/12/3/healthcare-in-uganda-lets-do-the-numbers

  10. Kant, S., Srivastava, M.M.: Towards automated tuberculosis detection using deep learning. In: 2018 IEEE Symposium Series on Computational Intelligence (SSCI), pp.1250-1253. IEEE, Bangalore, India (2018). https://doi.org/10.1109/SSCI.2018.8628800

  11. Karpathy, A., Toderici, G., Shetty, S., Leung , T., Sukthankar, R., Fei-Fei, L.: Large-scale video classification with convolutional neural networks. In: 2014 IEEE Conference on Computer Vision and Pattern Recognition. IEEE, Columbus, OH, USA (2014). https://doi.org/10.1109/CVPR.2014.223

  12. Lopes, U.K., Valiati, J.F.: Pre-trained convolutional neural networks as feature extractors for tuberculosis detection in biology and medicine 89, 135–143 (2017). https://doi.org/10.1016/j.compbiomed.2017.08.001

  13. Lopez, Y. P., Filho, C. F. F C., Aguilera, L. M. R., Costa, M. G. F.: Automatic classification of light field smear microscopy patches using Convolutional Neural Networks for identifying Mycobacterium Tuberculosis. In: CHILECON. IEEE, Pucon Chile (2017). https://doi.org/10.1109/CHILECON.2017.8229512

  14. Marcelino, P.: Transfer learning from pre-trained models. http://towardsdatascience.com/transfer-learning-from-pre-trained-models-f2393f124751

  15. Molicotti, P., Bua, A., Zanetti, S.: Cost-effectiveness in the diagnosis of tuberculosis: choices in developing countries. J. Infect. Dev. Countries 8(01), 024–038 (2014). https://doi.org/10.3855/jidc.3295

    Article  Google Scholar 

  16. Mwesigwa, A.: Uganda crippled by medical brain drain. http://www.theguardian.com/global-development/2015/feb/10/Uganda-crippled-medical-brain-drain-doctors

  17. Özgenel, Ç. F., Sorguç, A.G.: Performance comparison of pretrained convolutional neural networks on crack detection in buildings. In: 35th International Symposium on Automation and Robotics in Construction (ISARC) (2018). https://doi.org/10.22260/ISARC2018/0094

  18. Panicker, R.O., Kalmady, K.S., Rajan, J., Sabu, M.K.: Automatic detection of tuberculosis bacilli from microscopic sputum images using deep learning methods. Biocybern. Biomed. Eng. 38, 691–699 (2018). https://doi.org/10.1016/j.bbe.2018.05

    Article  Google Scholar 

  19. Quinn, J.A., Nakasi, R., Mugagga, P.K.B., Byanyima, P., Lubega, W., Andama, A.: Deep convolutional neural networks for microscopy-based point of care diagnostics. In: Machine Learning for Healthcare Conference, pp. 271-281. Los Angeles, California (2016)

    Google Scholar 

  20. Razavian, A., Azizpour, H., Sullivan, J., Carlsson, S.: CNN features off-the-shelf: an astounding baseline for recognition. In: CVPR 2014 Deep Vision Workshop, pp. 512–519. IEEE, Columbus, OH, USA (2014). https://doi.org/10.1109/CVPRW.2014.131

  21. Surgitha, G.E., Murugesan, G.: Detection of tuberculosis bacilli from microscopic sputum smear images. In: ICBSII. IEEE Press, Chennai, India (2017). https://doi.org/10.1109/ICBSII.2017.8082271

  22. Szegedy, C., Liu, W., Jia, Y., Sermanet, P., Reed, S., Anguelov, D., Erhan, D., Vanhoucke, V., Rabinovich A.: Going deeper with convolutions. In: IEEE Conference on Computer Vision and Pattern Recognition (CVPR). IEEE Press, Boston (2015). https://doi.org/10.1109/CVPR.2015.7298594

  23. Szegedy, C., Vanhoucke, V., Ioffe S., Shlens, J.,Wojna, Z.: Rethinking the inception architecture for computer vision. In: IEEE Conference on Computer Vision and Pattern Recognition (CVPR). IEEE Press, Las Vegas (2016). https://doi.org/10.1109/CVPR.2016.308

  24. Transfer Learning Using Pretrained ConvNets. http://www.tensorflow.org/tutorials/images/transferlearning

  25. Visual Geometry Group. http://www.robots.ox.ac.uk/vgg/research/verydeep/

  26. World Health Organization: World Health Organization Global Tuberculosis Report 2017. World Health Organization, Geneva, Switzerland. https://www.who.int/tb/publications/global_report/gtbr2017_main_text.pdf

  27. Zheng, L., Yang, Y., Tian, Q.: SIFT meets CNN: a decade survey of instance retrieval. IEEE Trans. Pattern Anal. Mach. Intell. 40(5), 1224–44 (2017)

    Article  Google Scholar 

  28. ZNSM iDB: Ziehl Neelsen Sputum Smear Microscopy Image Database. https://14.139.240.55/znsm/

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Acknowledgments

This work was supported by the SIDA project 381 under the Makerere-Swedish bilateral research programme 2015–2020.

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Correspondence to Joyce Nakatumba-Nabende .

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Muyama, L., Nakatumba-Nabende, J., Mudali, D. (2021). Automated Detection of Tuberculosis from Sputum Smear Microscopic Images Using Transfer Learning Techniques. In: Abraham, A., Siarry, P., Ma, K., Kaklauskas, A. (eds) Intelligent Systems Design and Applications. ISDA 2019. Advances in Intelligent Systems and Computing, vol 1181. Springer, Cham. https://doi.org/10.1007/978-3-030-49342-4_6

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