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Ensemble of Handcrafted and Deep Learned Features for Cervical Cell Classification

Part of the Intelligent Systems Reference Library book series (ISRL,volume 186)

Abstract

The aim of this work is to propose an ensemble of descriptors for Cervical Cell Classification. The system proposed here achieves strong discriminative power that generalizes well thanks to the combination of multiple descriptors based on different approaches, both learned and handcrafted. For each descriptor, a separate classifier is trained, then the set of classifiers is combined by sum rule. The system we propose here also presents a simple and effective method for boosting the performance of trained CNNs by combining the scores (using sum rule) of multiple CNNs into an ensemble. Different types of ensembles and different CNN topologies with different learning parameter sets are evaluated. Moreover, features extracted from tuned CNNs are used for training a set of Support Vector Machines (SVM). First, we validate our method on two cervical cell-related datasets; then, for more in-depth validation, we test the same system on other bioimage classification problems. Results show that the proposed system obtains state-of-the-art performance in all datasets, despite not being tuned on a specific dataset, i.e. the same descriptors with the same parameters are used in all the datasets. The MATLAB code of the descriptors will be available at https://github.com/LorisNanni.

Keywords

  • Deep learning
  • Ensemble of classifiers
  • Bioimage classification
  • Cancer data analysis

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References

  1. Zhou, J., Lamichhane, S., Sterne, G., Ye, B., Peng, H.: BIOCAT: a pattern recognition platform for customizable biological image classification and annotation. BMC Bioinform. 14, 291 (2013)

    CrossRef  Google Scholar 

  2. Misselwitz, B., et al.: Enhanced CellClassifier: a multi-class classification tool for microscopy images. BMC Bioinform. 11(30) (2010)

    Google Scholar 

  3. Pau, G., Fuchs, F., Sklyar, O., Boutros, M., Huber, W.: EBImage—an R package for image processing with applications to cellular phenotypes. Bioinformatics 26(7), 979–981 (2010)

    CrossRef  Google Scholar 

  4. Uhlmann, V., Singh, S., Carpenter, A.E.: CP-CHARM: segmentation-free image classification made accessible. BMC Bioinform. 17, 51 (2016)

    CrossRef  Google Scholar 

  5. Vailaya, A., Figueiredo, M.A.T., Jain, A.K., Zhang, H.J.: Image classification for content-based indexing. IEEE Trans. Image Process. 10(1), 117–130 (2001)

    CrossRef  MATH  Google Scholar 

  6. Gonzalez, R.C., Woods, R.E.: Digital Image Processing, 2nd edn. Addison-Wesley Longman Publishing Co., Inc, Boston (2001)

    Google Scholar 

  7. Xu, Y., Huang, S., Ji, H., Fermüller, C.: Scale-space texture description on SIFT-like textons. Comput. Vis. Image Underst. 116(9), 999–1013 (2012)

    CrossRef  Google Scholar 

  8. Ojala, T., Pietikainen, M., Maeenpaa, T.: Multiresolution gray-scale and rotation invariant texture classification with local binary patterns. IEEE Trans. Pattern Anal. Mach. Intell. 24(7), 971–987 (2002)

    CrossRef  Google Scholar 

  9. Nanni, L., Lumini, A., Brahnam, S.: Survey on LBP based texture descriptors for image classification. Expert Syst. Appl. 39(3), 3634–3641 (2012)

    CrossRef  Google Scholar 

  10. Vu, T.H., Mousavi, H.S., Monga, V., Rao, G., Rao, A.: Histopathological image classification using discriminative feature-oriented dictionary learning. IEEE Trans. Med. Imaging 35(3), 738–751 (2016)

    CrossRef  Google Scholar 

  11. Otalora, S., et al.: Combining unsupervised feature learning and riesz wavelets for histopathology image representation: application to identifying anaplastic medulloblastoma. Presented at the international conference on medical image computing and computer assisted intervention, Munich (2015)

    Google Scholar 

  12. Schmidhuber, J.: Deep learning in neural networks: an overview. Neural Netw. 61, 85–117 (2015)

    CrossRef  Google Scholar 

  13. Greenspan, H., van Ginneken, B., Summers, R.M.: Deep learning in medical imaging: overview and future promise of an exciting new technique. IEEE Trans. Med. Imaging 35, 1153–1159 (2016)

    CrossRef  Google Scholar 

  14. Janowczyk, A., Madabhushi, A.: Deep learning for digital pathology image analysis: a comprehensive tutorial with selected use cases. J. Pathol. Inform. 7(29) (2016)

    Google Scholar 

  15. Gua, J., et al.: Recent advances in convolutional neural networks. Pattern Recogn. 77, 354–377 (2018)

    CrossRef  Google Scholar 

  16. Russakovsky, O., Deng, J., Su, H.: ImageNet large scale visual recognition challenge. Int. J. Comput. Vis. (IJCV) 115(3), 211–252 (2015)

    CrossRef  MathSciNet  Google Scholar 

  17. LeCun, Y., Bottou, L., Bengio, Y., Haffner, P.: Gradient-based learning applied to document recognition. Proc. IEEE 86(11), 2278–2323 (1998)

    CrossRef  Google Scholar 

  18. Krizhevsky, A., Sutskever, I., Hinton, G.E.: ImageNet classification with deep convolutional neural networks. In: Pereira, F., Burges, C.J.C., Bottou, L., Weinberger, K.Q. (eds.) Advances in Neural Information Processing Systems, pp. 1097–1105. Curran Associates Inc, Red Hook, NY (2012)

    Google Scholar 

  19. Zeiler, M.D., Fergus, R.: Visualizing and understanding convolutional networks. In: Fleet, D., Pajdla, T., Schiele, B., Tuytelaars, T. (eds.) Computer Vision—ECCV 2014. ECCV 2014, Lecture Notes in Computer Science, vol. 8689. Springer, Berlin, Cham (2014)

    Google Scholar 

  20. Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. Cornell University (2014). arXiv:1409.1556v6

  21. Szegedy, C., et al.: Going deeper with convolutions. Presented at the IEEE computer society conference on computer vision and pattern recognition (2015)

    Google Scholar 

  22. He, K., Zhang, X., Ren, S., Sun, J.: Deep residual learning for image recognition. Presented at the 2016 IEEE conference on computer vision and pattern recognition (CVPR), Las Vegas, NV (2016)

    Google Scholar 

  23. Yosinski, J., Clune, J., Bengio, Y., Lipson, H.: How transferable are features in deep neural networks? Cornell University. arXiv:1411.17922014

  24. Shin, H.-C., et al.: Deep convolutional neural networks for computer-aided detection: Cnn architectures, dataset characteristics and transfer learning. IEEE Trans. Med. Imaging 35(5), 1285–1298 (2016)

    CrossRef  Google Scholar 

  25. Pan, Y., et al.: Brain tumor grading based on neural networks and convolutional neural networks. Presented at the 37th IEEE engineering in medicine and biology society (EMBC) (2015)

    Google Scholar 

  26. Nanni, L., Brahnam, S., Ghidoni, S., Lumini, A.: Bioimage classification with handcrafted and learned features. IEEE/ACM Trans. Comput. Biol. Bioinf. 16(3), 874–885 (2018)

    CrossRef  Google Scholar 

  27. van Ginneken, B., Setio, A.A.A., Jacobs, C., Ciompi, F.: Off-the-shelf convolutional neural network features for pulmonary nodule detection in computed tomography scans. Presented at the IEEE 12th international symposium on biomedical imaging (ISBI) (2015)

    Google Scholar 

  28. Li, R., et al.: Deep learning based imaging data completion for improved brain disease diagnosis. Med. Image Comput. Comput.-Assist. Interv. 17(Pt 3), 305–312 (2014)

    Google Scholar 

  29. Kumar, A., Kim, J., Lyndon, D., Fulham, M., Feng, D.: An ensemble of fine-tuned convolutional neural networks for medical image classification. IEEE J. Biomed. Health Inform. 21(1), 31–40 (2017)

    CrossRef  Google Scholar 

  30. Nanni, L., Ghidoni, S., Brahnam, S.: Ensemble of convolutional neural networks for bioimage classification. In: Applied Computing and Informatics. In press

    Google Scholar 

  31. Tan, X., Triggs, B.: Enhanced local texture feature sets for face recognition under difficult lighting conditions. In: Analysis and Modelling of Faces and Gestures, LNCS, vol. 4778, pp. 168–182 (2007)

    Google Scholar 

  32. Nanni, L., Brahnam, S., Lumini, A.: A very high performing system to discriminate tissues in mammograms as benign and malignant. Expert Syst. Appl. 39(2), 1968–1971 (2012)

    CrossRef  Google Scholar 

  33. Guo, Z., Zhang, L., Zhang, D.: A completed modeling of local binary pattern operator for texture classification. IEEE Trans. Image Process. 19(6), 1657–1663 (2010)

    CrossRef  MathSciNet  MATH  Google Scholar 

  34. Nosaka, R., Fukui, K.: HEp-2 cell classification using rotation invariant co-occurrence among local binary patterns. Pattern Recognit. Bioinform. 47(7), 2428–2436 (2014)

    CrossRef  Google Scholar 

  35. Serra, G., Grana, C., Manfredi, M., Cucchiara, R.: Gold: Gaussians of local descriptors for image representation. Comput. Vis. Image Underst. 134(May), 22–32 (2015)

    CrossRef  Google Scholar 

  36. Dalal, N., Triggs, B.: Histograms of oriented gradients for human detection. Presented at the 9th European conference on computer vision, San Diego, CA (2005)

    Google Scholar 

  37. Zhu, Z., et al.: An adaptive hybrid pattern for noise-robust texture analysis. Pattern Recogn. 48, 2592–2608 (2015)

    CrossRef  Google Scholar 

  38. Nanni, L., Paci, M., Santos, F.L.C.D., Brahnam, S., Hyttinen, J.: Review on texture descriptors for image classification. In: Alexander, S. (ed.) Computer Vision and Simulation: Methods, Applications and Technology. Nova Publications, Hauppauge, NY (2016)

    Google Scholar 

  39. Bianconi, F., Fernández, A., González, E., Saetta, S.A.: Performance analysis of colour descriptors for parquet sorting. Expert. Syst. Appl. 40(5), 1636–1644 (2013)

    CrossRef  Google Scholar 

  40. Strandmark, P., Ulén, J., Kahl, F.: HEp-2 staining pattern classification. Presented at the international conference on pattern recognition (ICPR2012) (2012). https://lup.lub.lu.se/search/ws/files/5709945/3437301.pdf

  41. Wang, Q., Li, P., Zhang, L., Zuoc, W.: Towards effective codebookless model for image classification. Pattern Recogn. 59, 63–71 (2016)

    CrossRef  Google Scholar 

  42. Song, T., Meng, F.: Letrist: locally encoded transform feature histogram for rotation-invariant texture classification. IEEE Trans. Circuits Syst. Video Technol. PP(99) (2017)

    Google Scholar 

  43. Nanni, L., Brahnam, S., Lumini, A., Barrier, T.: Ensemble of local phase quantization variants with ternary encoding. In: Brahnam, S., Jain, L.C., Lumini, A., Nanni, L. (eds.) Local Binary Patterns: New Variants and Applications, pp. 177–188. Springer, Berlin (2014)

    CrossRef  MATH  Google Scholar 

  44. Kannala, J., Rahtu, E.: Bsif: binarized statistical image features. Presented at the 21st international conference on pattern recognition (ICPR 2012), Tsukuba, Japan (2012)

    Google Scholar 

  45. Nowak, E., Jurie, F., Triggs, B.: Sampling strategies for bag-of-features image classification. Presented at the European conference on computer vision (ECCV) (2006)

    Google Scholar 

  46. Goodfellow, A., Ian, B., Yoshua, C.: Deep Learning. MIT Press (2016)

    Google Scholar 

  47. Szegedy, C., Ioffe, S., Vanhoucke, V., Alemi, A.: Inception-v4, inception-ResNet and the impact of residual connections on learning. “arxiv.org,” Cornell University. https://arxiv.org/pdf/1602.07261.pdf2016

  48. Huang, G., Liu, Z., Van Der Maaten, L., Weinberger, K.Q.: Densely connected convolutional networks. CVPR 1(2), 3 (2017)

    Google Scholar 

  49. Jantzen, J., Norup, J., Dounias, G., Bjerregaard, B.: Pap-smear benchmark data for pattern classification. Presented at the nature inspired smart information systems (NiSIS), Albufeira, Portugal (2005)

    Google Scholar 

  50. Shamir, L., Orlov, N.V., Eckley, D.M., Goldberg, I.: IICBU 2008: a proposed benchmark suite for biological image analysis. Med. Biol. Eng. Compu. 46(9), 943–947 (2008)

    CrossRef  Google Scholar 

  51. Junior, G.B., Cardoso de Paiva, A., Silva, A.C., Muniz de Oliveira, A.C.: Classification of breast tissues using Moran’s index and Geary’s coefficient as texture signatures and SVM. Comput. Biol. Med. 39(12), 1063–1072 (2009)

    CrossRef  Google Scholar 

  52. Cruz-Roa, A., Caicedo, J.C., González, F.A.: Visual pattern mining in histology image collections using bag of features. Artif. Intell. Med. 52, 91–106 (2011)

    CrossRef  Google Scholar 

  53. Nanni, L., Ghidoni, S., Brahnam, S.: Handcrafted vs non-handcrafted features for computer vision classification. Pattern Recogn. 71, 158–172 (2017)

    CrossRef  Google Scholar 

  54. Xhang, L., Lu, L., Nogues, I.: Deeppap: deep convolutional networks for cervical cell classification. IEEE J. Biomed. Health Inform. 21(6) (2017)

    Google Scholar 

  55. Dimitropoulos, K., Barmpoutis, P., Zioga, C., Kamas, A., Patsiaoura, K., Grammalidis, N.: Grading of invasive breast carcinoma through Grassmannian VLAD encoding. PLoS ONE 12, 1–18 (2017)

    CrossRef  Google Scholar 

  56. Moccia, S., et al.: Confident texture-based laryngeal tissue classification for early stage diagnosis support. J. Med. Imaging (Bellingham) 4(3), 34502 (2017)

    Google Scholar 

  57. Kather, J.N., et al.: Multi-class texture analysis in colorectal cancer histology. Sci. Rep. 6, 27988 (2016)

    CrossRef  Google Scholar 

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Acknowledgements

We gratefully acknowledge the support of: NVIDIA Corporation “NVIDIA Hardware Donation Grant” with the donation of the Titan X used for this research; National Natural Science Foundation of China (81501545).

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Correspondence to Loris Nanni .

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Nanni, L., Ghidoni, S., Brahnam, S., Liu, S., Zhang, L. (2020). Ensemble of Handcrafted and Deep Learned Features for Cervical Cell Classification. In: Nanni, L., Brahnam, S., Brattin, R., Ghidoni, S., Jain, L. (eds) Deep Learners and Deep Learner Descriptors for Medical Applications. Intelligent Systems Reference Library, vol 186. Springer, Cham. https://doi.org/10.1007/978-3-030-42750-4_4

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