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Transfer Learning for the Recognition of Immunogold Particles in TEM Imaging

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Advances in Computational Intelligence (IWANN 2015)

Abstract

We present a (TL) framework based on (SDA) for the recognition of immunogold particles. These particles are part of a high-resolution method for the selective localization of biological molecules at the subcellular level only visible through (TEM). Four new datasets were acquired encompassing several thousands of immunogold particles. Due to the particles size (for a particular dataset a particle has a radius of 4 pixels in an image of size 4008\(\times \)2670) the annotation of these datasets is extremely time taking. Thereby, we apply a (TL) approach by reusing the learning model that can be used on other datasets containing particles of different (or similar) sizes. In our experimental study we verified that our (TL) framework outperformed the baseline (not involving TL) approach by more than 20% of accuracy on the recognition of immunogold particles.

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References

  1. Amaral, T., Silva, L.M., Alexandre, L.A., Kandaswamy, C., Santos, J.M., de Sá, J.M.: Using different cost functions to train stacked auto-encoders. In: 2013 12th Mexican International Conference on Artificial Intelligence (MICAI), pp. 114–120. IEEE (2013)

    Google Scholar 

  2. Amaral, T., Silva, L.M., Alexandre, L.M., Kandaswamy, C., de Sá, J.M., Santos, J.: Improving Performance on Problems with Few Labelled Data by Reusing Stacked Auto-Encoders. In: ICMLA (2014)

    Google Scholar 

  3. Bastien, F., Lamblin, P., Pascanu, R., Bergstra, J., Goodfellow, I.J., Bergeron, A., Bouchard, N., Bengio, Y.: Theano: new features and speed improvements. Deep Learning and Unsupervised Feature Learning NIPS 2012 Workshop (2012)

    Google Scholar 

  4. Becker, C., Christoudias, C., Fua, P.: Domain adaptation for microscopy imaging. IEEE Transactions on Medical Imaging, PP(99), 1–1 (2014)

    Google Scholar 

  5. Ben-David, S., Blitzer, J., Crammer, K., Kulesza, A., Pereira, F., Vaughan, J.W.: A theory of learning from different domains. Machine Learning 79(1–2), 151–175 (2009)

    MathSciNet  Google Scholar 

  6. Bengio, Y.: Deep learning of representations for unsupervised and transfer learning. Journal of Machine Learning Research-Proceedings Track 27, 17–36 (2012)

    Google Scholar 

  7. de Chaumont, F., Dallongeville, S., Chenouard, N., Hervé, N., Pop, S., Provoost, T., Meas-Yedid, V., Pankajakshan, P., Lecomte, T., Le Montagner, Y., et al.: Icy: an open bioimage informatics platform for extended reproducible research. Nature methods 9(7), 690–696 (2012)

    Article  Google Scholar 

  8. Fisker, R., Carstensen, J.M., Hansen, M.F.: Bødker, F., Mørup, S.: Estimation of nanoparticle size distributions by image analysis. Journal of Nanoparticle Research 2(3), 267–277 (2000)

    Article  Google Scholar 

  9. Huang, J., Gretton, A., Borgwardt, K.M., Schölkopf, B., Smola, A.J.: Correcting sample selection bias by unlabeled data. In: Advances in Neural Information Processing Systems, pp. 601–608 (2006)

    Google Scholar 

  10. Kandaswamy, C., Silva, L.M., Alexandre, L.M., Sousa, R., Santos, J., de Sá, J.M.: Improving transfer learning accuracy by reusing stacked denoising autoencoders. In: Proceedings of the IEEE SMC Conference (2014)

    Google Scholar 

  11. Kandaswamy, Chetak, Silva, Luís M., Alexandre, Luís A., Santos, Jorge M., de Sá, Joaquim Marques: Improving Deep Neural Network Performance by Reusing Features Trained with Transductive Transference. In: Wermter, Stefan, Weber, Cornelius, Duch, Włodzisław, Honkela, Timo, Koprinkova-Hristova, Petia, Magg, Sven, Palm, Günther, Villa, Alessandro E.P. (eds.) ICANN 2014. LNCS, vol. 8681, pp. 265–272. Springer, Heidelberg (2014)

    Chapter  Google Scholar 

  12. Kandaswamy, C., Silva, L.M., Alexandre, L.A., Sousa, R., Santos, J.M., de Sá, J.M.: Improving transfer learning accuracy by reusing stacked denoising autoencoders. In: 2014 IEEE International Conference on Systems, Man and Cybernetics (SMC), pp. 1380–1387. IEEE (2014)

    Google Scholar 

  13. Mallick, S.P., Zhu, Y., Kriegman, D.: Detecting particles in cryo-em micrographs using learned features. Journal of Structural Biology 145(1), 52–62 (2004)

    Article  Google Scholar 

  14. Mitchell, T.M.: The need for biases in learning generalizations. Laboratory for Computer Science Research, Rutgers Univ, Department of Computer Science (1980)

    Google Scholar 

  15. Monjardino, P., Rocha, S., Tavares, A.C., Fernandes, R., Sampaio, P., Salema, R., da, Câmara Machado, A.: Development of flange and reticulate wall ingrowths in maize (Zea mays L.) endosperm transfer cells. Protoplasma 250(2), 495–503 (2013)

    Google Scholar 

  16. Nguyen, Nhat H., Norris, Eric, Clemens, Mark G., Shin, Min C.: Rapidly Adaptive Cell Detection Using Transfer Learning with a Global Parameter. In: Suzuki, Kenji, Wang, Fei, Shen, Dinggang, Yan, Pingkun (eds.) MLMI 2011. LNCS, vol. 7009, pp. 209–216. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  17. Olivo-Marin, J.C.: Extraction of spots in biological images using multiscale products. Pattern Recognition 35(9), 1989–1996 (2002)

    Article  MATH  Google Scholar 

  18. Patricia, N., Caputo, B.: Learning to learn, from transfer learning to domain adaptation: a unifying perspective. In: 2014 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 1442–1449. IEEE (2014)

    Google Scholar 

  19. Ribeiro, E., Shah, M.: Computer vision for nanoscale imaging. Machine Vision and Applications 17(3), 147–162 (2006)

    Article  Google Scholar 

  20. Rifai, S., Vincent, P., Muller, X., Glorot, X., Bengio, Y.: Contractive auto-encoders: Explicit invariance during feature extraction. In: Proceedings of the 28th International Conference on Machine Learning (ICML 2011). pp. 833–840 (2011)

    Google Scholar 

  21. Tommasi, T., Orabona, F., Caputo, B.: Learning categories from few examples with multi model knowledge transfer. IEEE Transactions on Pattern Analysis and Machine Intelligence 36(5), 928–941 (2014)

    Article  Google Scholar 

  22. Vincent, P., Larochelle, H., Lajoie, I., Bengio, Y., Manzagol, P.A.: Stacked denoising autoencoders: Learning useful representations in a deep network with a local denoising criterion. The Journal of Machine Learning Research 11, 3371–3408 (2010)

    MATH  MathSciNet  Google Scholar 

  23. Voss, N., Yoshioka, C., Radermacher, M., Potter, C., Carragher, B.: Dog picker and tiltpicker: software tools to facilitate particle selection in single particle electron microscopy. Journal of Structural Biology 166(2), 205–213 (2009)

    Article  Google Scholar 

  24. Woolford, D., Hankamer, B., Ericksson, G.: The laplacian of gaussian and arbitrary \(z\)-crossings approach applied to automated single particle reconstruction. Journal of Structural Biology 159(1), 122–134 (2007)

    Article  Google Scholar 

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Correspondence to Luís A. Alexandre .

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Sousa, R.G. et al. (2015). Transfer Learning for the Recognition of Immunogold Particles in TEM Imaging. In: Rojas, I., Joya, G., Catala, A. (eds) Advances in Computational Intelligence. IWANN 2015. Lecture Notes in Computer Science(), vol 9094. Springer, Cham. https://doi.org/10.1007/978-3-319-19258-1_32

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  • DOI: https://doi.org/10.1007/978-3-319-19258-1_32

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