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Published in: International Journal of Computer Assisted Radiology and Surgery 10/2018

01-10-2018 | Original Article

Evolutionary image simplification for lung nodule classification with convolutional neural networks

Authors: Daniel Lückehe, Gabriele von Voigt

Published in: International Journal of Computer Assisted Radiology and Surgery | Issue 10/2018

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Abstract

Purpose

Understanding decisions of deep learning techniques is important. Especially in the medical field, the reasons for a decision in a classification task are as crucial as the pure classification results. In this article, we propose a new approach to compute relevant parts of a medical image. Knowing the relevant parts makes it easier to understand decisions.

Methods

In our approach, a convolutional neural network is employed to learn structures of images of lung nodules. Then, an evolutionary algorithm is applied to compute a simplified version of an unknown image based on the learned structures by the convolutional neural network. In the simplified version, irrelevant parts are removed from the original image.

Results

In the results, we show simplified images which allow the observer to focus on the relevant parts. In these images, more than 50% of the pixels are simplified. The simplified pixels do not change the meaning of the images based on the learned structures by the convolutional neural network. An experimental analysis shows the potential of the approach. Besides the examples of simplified images, we analyze the run time development.

Conclusions

Simplified images make it easier to focus on relevant parts and to find reasons for a decision. The combination of an evolutionary algorithm employing a learned convolutional neural network is well suited for the simplification task. From a research perspective, it is interesting which areas of the images are simplified and which parts are taken as relevant.
Appendix
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Literature
1.
go back to reference Abdou IE, Pratt WK (1979) Quantitative design and evaluation of enhancement/thresholding edge detectors. Proc IEEE 67(5):753–763CrossRef Abdou IE, Pratt WK (1979) Quantitative design and evaluation of enhancement/thresholding edge detectors. Proc IEEE 67(5):753–763CrossRef
3.
go back to reference Armato SG III, McLennan G, Bidaut L, McNitt-Gray M, Meyer C, Reeves A, Zhao B, Aberle D, Henschke C, Hoffman E, Kazerooni E, MacMahon H, van Beek E, Yankelevitz D (2011) The lung image database consortium (LIDC) and image database resource initiative (IDRI): a completed reference database of lung nodules on ct scans. Med Phys 38:915–931CrossRefPubMedPubMedCentral Armato SG III, McLennan G, Bidaut L, McNitt-Gray M, Meyer C, Reeves A, Zhao B, Aberle D, Henschke C, Hoffman E, Kazerooni E, MacMahon H, van Beek E, Yankelevitz D (2011) The lung image database consortium (LIDC) and image database resource initiative (IDRI): a completed reference database of lung nodules on ct scans. Med Phys 38:915–931CrossRefPubMedPubMedCentral
5.
go back to reference Bäck T (1998) An overview of parameter control methods by self-adaption in evolutionary algorithms. Fundam Inf 35(1–4):51–66 Bäck T (1998) An overview of parameter control methods by self-adaption in evolutionary algorithms. Fundam Inf 35(1–4):51–66
6.
go back to reference Benitez JM, Castro JL, Requena I (1997) Are artificial neural networks black boxes? IEEE Trans Neural Netw 8(5):1156–1164CrossRefPubMed Benitez JM, Castro JL, Requena I (1997) Are artificial neural networks black boxes? IEEE Trans Neural Netw 8(5):1156–1164CrossRefPubMed
7.
go back to reference Chapelle O, Haffner P, Vapnik VN (1999) Support vector machines for histogram-based image classification. IEEE Trans Neural Netw 10(5):1055–1064CrossRefPubMed Chapelle O, Haffner P, Vapnik VN (1999) Support vector machines for histogram-based image classification. IEEE Trans Neural Netw 10(5):1055–1064CrossRefPubMed
8.
go back to reference Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F (2013) The cancer imaging archive (TCIA): maintaining and operating a public information repository. J Digit Imaging 26(6):1045–1057CrossRefPubMedPubMedCentral Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F (2013) The cancer imaging archive (TCIA): maintaining and operating a public information repository. J Digit Imaging 26(6):1045–1057CrossRefPubMedPubMedCentral
9.
go back to reference Eiben AE, Smith JE (2003) Introduction to evolutionary computing. Springer, BerlinCrossRef Eiben AE, Smith JE (2003) Introduction to evolutionary computing. Springer, BerlinCrossRef
10.
go back to reference Fukushima K (1986) A neural network model for selective attention in visual pattern recognition. Biol Cybern 55(1):5–15CrossRefPubMed Fukushima K (1986) A neural network model for selective attention in visual pattern recognition. Biol Cybern 55(1):5–15CrossRefPubMed
11.
go back to reference Goodfellow I, Bengio Y, Courville A (2016) Deep learning. Adaptive computation and machine learning. MIT Press, Cambridge Goodfellow I, Bengio Y, Courville A (2016) Deep learning. Adaptive computation and machine learning. MIT Press, Cambridge
12.
go back to reference Hastie T, Tibshirani R, Friedman J (2009) The elements of statistical learning. Springer, BerlinCrossRef Hastie T, Tibshirani R, Friedman J (2009) The elements of statistical learning. Springer, BerlinCrossRef
13.
go back to reference Holyoak K, Morrison R (2005) The Cambridge handbook of thinking and reasoning. Cambridge handbooks in psychology. Cambridge University Press, Cambridge Holyoak K, Morrison R (2005) The Cambridge handbook of thinking and reasoning. Cambridge handbooks in psychology. Cambridge University Press, Cambridge
14.
go back to reference Huang M, Huang B, Li X, Huang AHL, Goldberg MD, Mehta A (2015) Massive parallelization of the WRF GCE model toward a gpu-based end-to-end satellite data simulator unit. IEEE J Sel Top Appl Earth Obs Remote Sens 8(5):2260–2272CrossRef Huang M, Huang B, Li X, Huang AHL, Goldberg MD, Mehta A (2015) Massive parallelization of the WRF GCE model toward a gpu-based end-to-end satellite data simulator unit. IEEE J Sel Top Appl Earth Obs Remote Sens 8(5):2260–2272CrossRef
15.
go back to reference Iandola FN, Moskewicz MW, Ashraf K, Han S, Dally WJ, Keutzer K (2016) SqueezeNet: AlexNet-level accuracy with 50x fewer parameters and \(< 1\) MB model size. CoRR. arXiv:1602.07360 Iandola FN, Moskewicz MW, Ashraf K, Han S, Dally WJ, Keutzer K (2016) SqueezeNet: AlexNet-level accuracy with 50x fewer parameters and \(< 1\) MB model size. CoRR. arXiv:​1602.​07360
16.
go back to reference Jacobs C, van Rikxoort EM, Twellmann T, Scholten ET, de Jong PA, Kuhnigk JM, Oudkerk M, de Koning HJ, Prokop M, Schaefer-Prokop C, van Ginneken B (2014) Automatic detection of subsolid pulmonary nodules in thoracic computed tomography images. Med Image Anal 18:374–384CrossRefPubMed Jacobs C, van Rikxoort EM, Twellmann T, Scholten ET, de Jong PA, Kuhnigk JM, Oudkerk M, de Koning HJ, Prokop M, Schaefer-Prokop C, van Ginneken B (2014) Automatic detection of subsolid pulmonary nodules in thoracic computed tomography images. Med Image Anal 18:374–384CrossRefPubMed
17.
go back to reference Jolliffe I (1986) Principal component analysis. Springer series in statistics. Springer, New YorkCrossRef Jolliffe I (1986) Principal component analysis. Springer series in statistics. Springer, New YorkCrossRef
19.
go back to reference Kramer O (2014) A brief introduction to continuous evolutionary optimization. Springer briefs in applied sciences and technology. Springer, BerlinCrossRef Kramer O (2014) A brief introduction to continuous evolutionary optimization. Springer briefs in applied sciences and technology. Springer, BerlinCrossRef
20.
go back to reference Kramer O (2018) Evolution of convolutional highway networks. In: Applications of evolutionary computation—21st international conference, EvoApplications 2018, Parma, Italy, April 4–6, 2018, Proceedings, pp 395–404 Kramer O (2018) Evolution of convolutional highway networks. In: Applications of evolutionary computation—21st international conference, EvoApplications 2018, Parma, Italy, April 4–6, 2018, Proceedings, pp 395–404
21.
go back to reference Krizhevsky A, Sutskever I, Hinton GE (2012) Imagenet classification with deep convolutional neural networks. In: Pereira F, Burges CJC, Bottou L, Weinberger KQ (eds) Advances in neural information processing systems, vol 25. Curran Associates, Inc., Red Hook, pp 1097–1105 Krizhevsky A, Sutskever I, Hinton GE (2012) Imagenet classification with deep convolutional neural networks. In: Pereira F, Burges CJC, Bottou L, Weinberger KQ (eds) Advances in neural information processing systems, vol 25. Curran Associates, Inc., Red Hook, pp 1097–1105
22.
go back to reference Krupinski EA (2010) Current perspectives in medical image perception. Atten Percept Psychophys 72(5):1943–3921CrossRef Krupinski EA (2010) Current perspectives in medical image perception. Atten Percept Psychophys 72(5):1943–3921CrossRef
23.
go back to reference Langer SG (2011) Challenges for data storage in medical imaging research. J Digit Imaging 24(2):203–207CrossRefPubMed Langer SG (2011) Challenges for data storage in medical imaging research. J Digit Imaging 24(2):203–207CrossRefPubMed
25.
go back to reference LeCun Y, Haffner P, Bottou L, Bengio Y (1999) Object recognition with gradient-based learning. Springer, Berlin, pp 319–345 LeCun Y, Haffner P, Bottou L, Bengio Y (1999) Object recognition with gradient-based learning. Springer, Berlin, pp 319–345
26.
go back to reference Leutbecher M, Palmer TN (2008) Ensemble forecasting. J Comput Phys 227(7):3515–3539CrossRef Leutbecher M, Palmer TN (2008) Ensemble forecasting. J Comput Phys 227(7):3515–3539CrossRef
27.
go back to reference Lu L, Zheng Y, Carneiro G, Yang L (2017) Deep learning and convolutional neural networks for medical image computing: precision medicine, high performance and large-scale datasets. advances in computer vision and pattern recognition. Springer, BerlinCrossRef Lu L, Zheng Y, Carneiro G, Yang L (2017) Deep learning and convolutional neural networks for medical image computing: precision medicine, high performance and large-scale datasets. advances in computer vision and pattern recognition. Springer, BerlinCrossRef
28.
go back to reference Lückehe D, Kramer O (2015) Alternating optimization of unsupervised regression with evolutionary embeddings. Springer, Berlin, pp 471–480 Lückehe D, Kramer O (2015) Alternating optimization of unsupervised regression with evolutionary embeddings. Springer, Berlin, pp 471–480
29.
go back to reference Lückehe D, Oehmcke S, Kramer O (2017) Manifold learning with iterative dimensionality photo-projection. In: 2017 international joint conference on neural networks, IJCNN, pp 2555–2561 Lückehe D, Oehmcke S, Kramer O (2017) Manifold learning with iterative dimensionality photo-projection. In: 2017 international joint conference on neural networks, IJCNN, pp 2555–2561
30.
go back to reference Lückehe D, Wagner M, Kramer O (2016) Constrained evolutionary wind turbine placement with penalty functions. In: IEEE congress on evolutionary computation, CEC, pp 4903–4910 Lückehe D, Wagner M, Kramer O (2016) Constrained evolutionary wind turbine placement with penalty functions. In: IEEE congress on evolutionary computation, CEC, pp 4903–4910
31.
go back to reference MacQueen JB (1967) Some methods for classification and analysis of multivariate observations. In: Cam LML, Neyman J (eds) Proceedings of the fifth Berkeley symposium on mathematical statistics and probability, vol 1. University of California Press, Oakland, pp 281–297 MacQueen JB (1967) Some methods for classification and analysis of multivariate observations. In: Cam LML, Neyman J (eds) Proceedings of the fifth Berkeley symposium on mathematical statistics and probability, vol 1. University of California Press, Oakland, pp 281–297
32.
go back to reference Mader K, Cyriac J, Stieltjes B, Erdal BS, Prevedello LM (2017) Introduction to machine learning and texture analysis for lesion characterization (hands-on). RSNA training session Mader K, Cyriac J, Stieltjes B, Erdal BS, Prevedello LM (2017) Introduction to machine learning and texture analysis for lesion characterization (hands-on). RSNA training session
33.
go back to reference Mader K, Stampanoni M (2016) Moving image analysis to the cloud: a case study with a genome-scale tomographic study. AIP Conf Proc 1696(1):020,045CrossRef Mader K, Stampanoni M (2016) Moving image analysis to the cloud: a case study with a genome-scale tomographic study. AIP Conf Proc 1696(1):020,045CrossRef
34.
go back to reference Meier A, Kramer O (2017) An experimental study of dimensionality reduction methods. Springer, Berlin, pp 178–192 Meier A, Kramer O (2017) An experimental study of dimensionality reduction methods. Springer, Berlin, pp 178–192
35.
go back to reference Murphy K, van Ginneken B, Schilham AMR, de Hoop BJ, Gietema HA, Prokop M (2009) A large scale evaluation of automatic pulmonary nodule detection in chest CT using local image features and k-nearest-neighbour classification. Med Image Anal 13:757–770CrossRefPubMed Murphy K, van Ginneken B, Schilham AMR, de Hoop BJ, Gietema HA, Prokop M (2009) A large scale evaluation of automatic pulmonary nodule detection in chest CT using local image features and k-nearest-neighbour classification. Med Image Anal 13:757–770CrossRefPubMed
36.
go back to reference Oehmcke S, Heinermann J, Kramer O (2015) Analysis of diversity methods for evolutionary multi-objective ensemble classifiers. Springer, Berlin, pp 567–578 Oehmcke S, Heinermann J, Kramer O (2015) Analysis of diversity methods for evolutionary multi-objective ensemble classifiers. Springer, Berlin, pp 567–578
37.
go back to reference Olden JD, Jackson DA (2002) Illuminating the black box: a randomization approach for understanding variable contributions in artificial neural networks. Ecol Model 154(1):135–150CrossRef Olden JD, Jackson DA (2002) Illuminating the black box: a randomization approach for understanding variable contributions in artificial neural networks. Ecol Model 154(1):135–150CrossRef
38.
go back to reference Rawat W, Wang Z (2017) Deep convolutional neural networks for image classification: a comprehensive review. Neural Comput 29(9):2352–2449CrossRefPubMed Rawat W, Wang Z (2017) Deep convolutional neural networks for image classification: a comprehensive review. Neural Comput 29(9):2352–2449CrossRefPubMed
39.
go back to reference Rudolph G (1996) Convergence of evolutionary algorithms in general search spaces. In: Proceedings of IEEE international conference on evolutionary computation, pp 50–54 Rudolph G (1996) Convergence of evolutionary algorithms in general search spaces. In: Proceedings of IEEE international conference on evolutionary computation, pp 50–54
40.
go back to reference Schmidhuber J (2015) Deep learning in neural networks: an overview. Neural Netw 61(Supplement C):85–117CrossRefPubMed Schmidhuber J (2015) Deep learning in neural networks: an overview. Neural Netw 61(Supplement C):85–117CrossRefPubMed
41.
go back to reference Setio AAA, Jacobs C, Gelderblom J, van Ginneken B (2015) Automatic detection of large pulmonary solid nodules in thoracic ct images. Med Phys 42(10):5642–5653CrossRefPubMed Setio AAA, Jacobs C, Gelderblom J, van Ginneken B (2015) Automatic detection of large pulmonary solid nodules in thoracic ct images. Med Phys 42(10):5642–5653CrossRefPubMed
42.
go back to reference Setio AAA, Traverso A, de Bel T, Berens MS, van den Bogaard C, Cerello P, Chen H, Dou Q, Fantacci ME, Geurts B, van der Gugten R, Heng PA, Jansen B, de Kaste MM, Kotov V, Lin JYH, Manders JT, Sora-Mengana A, Garca-Naranjo JC, Papavasileiou E, Prokop M, Saletta M, Schaefer-Prokop CM, Scholten ET, Scholten L, Snoeren MM, Torres EL, Vandemeulebroucke J, Walasek N, Zuidhof GC, van Ginneken B, Jacobs C (2017) Validation, comparison, and combination of algorithms for automatic detection of pulmonary nodules in computed tomography images: the LUNA16 challenge. Med Image Anal 42(Supplement C):1–13. https://doi.org/10.1016/j.media.2017.06.015 CrossRefPubMed Setio AAA, Traverso A, de Bel T, Berens MS, van den Bogaard C, Cerello P, Chen H, Dou Q, Fantacci ME, Geurts B, van der Gugten R, Heng PA, Jansen B, de Kaste MM, Kotov V, Lin JYH, Manders JT, Sora-Mengana A, Garca-Naranjo JC, Papavasileiou E, Prokop M, Saletta M, Schaefer-Prokop CM, Scholten ET, Scholten L, Snoeren MM, Torres EL, Vandemeulebroucke J, Walasek N, Zuidhof GC, van Ginneken B, Jacobs C (2017) Validation, comparison, and combination of algorithms for automatic detection of pulmonary nodules in computed tomography images: the LUNA16 challenge. Med Image Anal 42(Supplement C):1–13. https://​doi.​org/​10.​1016/​j.​media.​2017.​06.​015 CrossRefPubMed
43.
go back to reference Smith-Bindman R, Miglioretti DL, Larson EB (2008) Rising use of diagnostic medical imaging in a large integrated health system. Health Aff (Millwood) 27(6):1491–1502CrossRef Smith-Bindman R, Miglioretti DL, Larson EB (2008) Rising use of diagnostic medical imaging in a large integrated health system. Health Aff (Millwood) 27(6):1491–1502CrossRef
44.
go back to reference Song Q, Zhao L, Luo X, Dou X (2017) Using deep learning for classification of lung nodules on computed tomography images. J Healthc Eng 2017:2040–2295CrossRef Song Q, Zhao L, Luo X, Dou X (2017) Using deep learning for classification of lung nodules on computed tomography images. J Healthc Eng 2017:2040–2295CrossRef
45.
go back to reference Tzeng FY, Ma KL (2005) Opening the black box—data driven visualization of neural networks. In: VIS 05. IEEE visualization, pp 383–390 Tzeng FY, Ma KL (2005) Opening the black box—data driven visualization of neural networks. In: VIS 05. IEEE visualization, pp 383–390
46.
go back to reference van Rikxoort EM, de Hoop B, Viergever MA, Prokop M, van Ginneken B (2009) Automatic lung segmentation from thoracic computed tomography scans using a hybrid approach with error detection. Med Phys 4236(10):2934–2947CrossRef van Rikxoort EM, de Hoop B, Viergever MA, Prokop M, van Ginneken B (2009) Automatic lung segmentation from thoracic computed tomography scans using a hybrid approach with error detection. Med Phys 4236(10):2934–2947CrossRef
47.
go back to reference Xiao T, Xu Y, Yang K, Zhang J, Peng Y, Zhang Z (2015) The application of two-level attention models in deep convolutional neural network for fine-grained image classification. In: The IEEE conference on computer vision and pattern recognition (CVPR) Xiao T, Xu Y, Yang K, Zhang J, Peng Y, Zhang Z (2015) The application of two-level attention models in deep convolutional neural network for fine-grained image classification. In: The IEEE conference on computer vision and pattern recognition (CVPR)
48.
go back to reference Zeiler MD, Fergus R (2014) Visualizing and understanding convolutional networks. Springer, Cham, pp 818–833 Zeiler MD, Fergus R (2014) Visualizing and understanding convolutional networks. Springer, Cham, pp 818–833
Metadata
Title
Evolutionary image simplification for lung nodule classification with convolutional neural networks
Authors
Daniel Lückehe
Gabriele von Voigt
Publication date
01-10-2018
Publisher
Springer International Publishing
Published in
International Journal of Computer Assisted Radiology and Surgery / Issue 10/2018
Print ISSN: 1861-6410
Electronic ISSN: 1861-6429
DOI
https://doi.org/10.1007/s11548-018-1794-7

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