skip to main content
10.1145/3319619.3326864acmconferencesArticle/Chapter ViewAbstractPublication PagesgeccoConference Proceedingsconference-collections
research-article

Semantic learning machine improves the CNN-Based detection of prostate cancer in non-contrast-enhanced MRI

Published:13 July 2019Publication History

ABSTRACT

Considering that Prostate Cancer (PCa) is the most frequently diagnosed tumor in Western men, considerable attention has been devoted in computer-assisted PCa detection approaches. However, this task still represents an open research question. In the clinical practice, multiparametric Magnetic Resonance Imaging (MRI) is becoming the most used modality, aiming at defining biomarkers for PCa. In the latest years, deep learning techniques have boosted the performance in prostate MR image analysis and classification. This work explores the use of the Semantic Learning Machine (SLM) neuroevolution algorithm to replace the backpropagation algorithm commonly used in the last fully-connected layers of Convolutional Neural Networks (CNNs). We analyzed the non-contrast-enhanced multispectral MRI sequences included in the PROSTATEx dataset, namely: T2-weighted, Proton Density weighted, Diffusion Weighted Imaging. The experimental results show that the SLM significantly outperforms XmasNet, a state-of-the-art CNN. In particular, with respect to XmasNet, the SLM achieves higher classification accuracy (without neither pre-training the underlying CNN nor relying on backprogation) as well as a speed-up of one order of magnitude.

References

  1. Martín Abadi, Paul Barham, Jianmin Chen, Zhifeng Chen, Andy Davis, Jeffrey Dean, Matthieu Devin, Sanjay Ghemawat, Geoffrey Irving, Michael Isard, et al. 2015. TensorFlow: Large-Scale Machine Learning on Heterogeneous Systems. https://www.tensorflow.org/ Software available from tensorflow.org.Google ScholarGoogle Scholar
  2. Samuel G Armato, Henkjan Huisman, Karen Drukker, Lubomir Hadjiiski, Justin S Kirby, Nicholas Petrick, George Redmond, Maryellen L Giger, Kenny Cha, Artem Mamonov, et al. 2018. PROSTATEx Challenges for computerized classification of prostate lesions from multiparametric magnetic resonance images. J. Med. Imaging 5, 4 (2018), 044501.Google ScholarGoogle ScholarCross RefCross Ref
  3. Léon Bottou. 2010. Large-scale machine learning with stochastic gradient descent. In Proc. COMPSTAT'2010. Springer, 177--186.Google ScholarGoogle ScholarCross RefCross Ref
  4. Stefano Cagnoni, Andrew B Dobrzeniecki, Riccardo Poli, and Jacquelyn C Yanch. 1999. Genetic algorithm-based interactive segmentation of 3D medical images. Image Vis. Comput. 17, 12 (1999), 881--895.Google ScholarGoogle ScholarCross RefCross Ref
  5. Young Jun Choi, Jeong Kon Kim, Namkug Kim, Kyoung Won Kim, Eugene K. Choi, and Kyoung-Sik Cho. 2007. Functional MR Imaging of Prostate Cancer. RadioGraphics 27, 1 (jan 2007), 63--75.Google ScholarGoogle ScholarCross RefCross Ref
  6. François Chollet et al. 2015. Keras. https://keras.io.Google ScholarGoogle Scholar
  7. Kenneth Clark, Bruce Vendt, Kirk Smith, John Freymann, Justin Kirby, Paul Koppel, Stephen Moore, Stanley Phillips, David Maffitt, Michael Pringle, et al. 2013. The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository. J. Digit. Imaging 26, 6 (2013), 1045--1057.Google ScholarGoogle ScholarCross RefCross Ref
  8. Tyler Clark, Junjie Zhang, Sameer Baig, Alexander Wong, Masoom A Haider, and Farzad Khalvati. 2017. Fully automated segmentation of prostate whole gland and transition zone in diffusion-weighted MRI using convolutional neural networks. J. Med. Imaging 4, 4 (2017), 041307.Google ScholarGoogle ScholarCross RefCross Ref
  9. Anna Fabijańska. 2016. A novel approach for quantification of time-intensity curves in a DCE-MRI image series with an application to prostate cancer. Comput. Biol. Med. 73 (2016), 119--130. Google ScholarGoogle ScholarDigital LibraryDigital Library
  10. Eleftherios Garyfallidis, Matthew Brett, Bagrat Amirbekian, Ariel Rokem, Stefan Van Der Walt, Maxime Descoteaux, and Ian Nimmo-Smith. 2014. DIPy, a library for the analysis of diffusion MRI data. Front. Neuroinform. 8 (2014), 8.Google ScholarGoogle ScholarCross RefCross Ref
  11. Ivo Gonçalves, Sara Silva, and Carlos M Fonseca. 2015. On the generalization ability of geometric semantic genetic programming. In Genetic Programming. Springer, 41--52.Google ScholarGoogle Scholar
  12. Ivo Gonçalves, Sara Silva, and Carlos M. Fonseca. 2015. Semantic learning machine: a feedforward neural network construction algorithm inspired by geometric semantic genetic programming. In Progress in Artificial Intelligence. Lecture Notes in Computer Science, Vol. 9273. Springer, 280--285.Google ScholarGoogle Scholar
  13. Ivo Gonçalves, Sara Silva, Carlos M Fonseca, and Mauro Castelli. 2016. Arbitrarily close alignments in the error space: a geometric semantic genetic programming approach. In Proceedings of the 2016 on Genetic and Evolutionary Computation Conference Companion. ACM, 99--100. Google ScholarGoogle ScholarDigital LibraryDigital Library
  14. Ivo Gonçalves. 2017. An Exploration of Generalization and Overfitting in Genetic Programming: Standard and Geometric Semantic Approaches. Ph.D. Dissertation. Department of Informatics Engineering, University of Coimbra, Portugal.Google ScholarGoogle Scholar
  15. Ivo Gonçalves, Sara Silva, Carlos M. Fonseca, and Mauro Castelli. 2017. Unsure when to Stop? Ask Your Semantic Neighbors. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO). ACM, New York, NY, USA, 929--936. Google ScholarGoogle ScholarDigital LibraryDigital Library
  16. Vikas Gulani, Fernando Calamante, Frank G Shellock, Emanuel Kanal, Scott B Reeder, et al. 2017. Gadolinium deposition in the brain: summary of evidence and recommendations. Lancet Neurol. 16, 7 (2017), 564--570.Google ScholarGoogle ScholarCross RefCross Ref
  17. Yanrong Guo, Yaozong Gao, and Dinggang Shen. 2016. Deformable MR prostate segmentation via deep feature learning and sparse patch matching. IEEE Trans. Med. Imaging 35, 4 (2016), 1077--1089.Google ScholarGoogle ScholarCross RefCross Ref
  18. Masoom A Haider, Theodorus H Van Der Kwast, Jeff Tanguay, Andrew J Evans, Ali-Tahir Hashmi, Gina Lockwood, and John Trachtenberg. 2007. Combined T2-weighted and diffusion-weighted MRI for localization of prostate cancer. AJR Am. J. Roentgenol. 189, 2 (2007), 323--328.Google ScholarGoogle ScholarCross RefCross Ref
  19. Thomas Hambrock, Pieter C Vos, Christina A Hulsbergen-van de Kaa, Jelle O Barentsz, and Henkjan J Huisman. 2013. Prostate cancer: computer-aided diagnosis with multiparametric 3-T MR imaging-effect on observer performance. Radiology 266, 2 (2013), 521--530.Google ScholarGoogle ScholarCross RefCross Ref
  20. Jan-Benedikt Jagusch, Ivo Gonçalves, and Mauro Castelli. 2018. Neuroevolution under unimodal error landscapes: an exploration of the semantic learning machine algorithm.In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO) Companion. ACM, New York, NY, USA, 159--160. Google ScholarGoogle ScholarDigital LibraryDigital Library
  21. Haozhe Jia, Yong Xia, Yang Song, Weidong Cai, Michael Fulham, and David Dagan Feng. 2018. Atlas registration and ensemble deep convolutional neural network-based prostate segmentation using magnetic resonance imaging. Neurocomputing 275 (2018), 1358--1369. Google ScholarGoogle ScholarDigital LibraryDigital Library
  22. Daniel Junker, Fabian Steinkohl, Veronika Fritz, Jasmin Bektic, Theodoros Tokas, Friedrich Aigner, Thomas RW Herrmann, Michael Rieger, and Udo Nagele. 2018. Comparison of multiparametric and biparametric MRI of the prostate: are gadolinium-based contrast agents needed for routine examinations? World J. Urol. (2018), 1--9.Google ScholarGoogle Scholar
  23. Konstantinos Kamnitsas, Christian Ledig, V. F. J. Newcombe, Joanna P. Simpson, Andrew D. Kane, David K. Menon, et al. 2017. Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation. Med. Image Anal. 36 (2017), 61--78.Google ScholarGoogle ScholarCross RefCross Ref
  24. Diederik P Kingma and Jimmy Ba. 2014. Adam: a method for stochastic optimization.arXiv preprint arXiv:1412.6980 (2014).Google ScholarGoogle Scholar
  25. Deukwoo Kwon, Isildinha M Reis, Adrian L Breto, Yohann Tschudi, Nicole Gautney, Olmo Zavala-Romero, Christopher Lopez, John C Ford, Sanoj Pun-nen, Alan Pollack, et al. 2018. Classification of suspicious lesions on prostate multiparametric MRI using machine learning. J. Med. Imaging 5, 3 (2018), 034502.Google ScholarGoogle Scholar
  26. Guillaume Lemaître, Robert Martí, Jordi Freixenet, Joan C Vilanova, Paul M Walker, and Fabrice Meriaudeau. 2015. Computer-aided detection and diagnosis for prostate cancer based on mono and multi-parametric MRI: a review. Comput. Biol. Med. 60 (2015), 8--31. Google ScholarGoogle ScholarDigital LibraryDigital Library
  27. Roger Li, Gregory C Ravizzini, Michael A Gorin, Tobias Maurer, Matthias Eiber, Matthew R Cooperberg, Mehrdad Alemozzaffar, Matthew K Tollefson, Scott E Delacroix, and Brian F Chapin. 2018. The use of PET/CT in prostate cancer. Prostate Cancer Prostatic Dis. 21, 1 (2018), 4.Google ScholarGoogle ScholarCross RefCross Ref
  28. Geert Litjens, Oscar Debats, Jelle Barentsz, Nico Karssemeijer, and Henkjan Huisman. 2014. Computer-aided detection of prostate cancer in MRI IEEE Trans. Med. Imaging 33, 5 (2014), 1083--1092.Google ScholarGoogle ScholarCross RefCross Ref
  29. Geert Litjens, Oscar Debats, Jelle Barentsz, Nico Karssemeijer, and Henkjan Huisman. 2017. "PROSTATEx Challenge data", The Cancer Imaging Archive. https://wiki.cancerimagingarchive.net/display/Public/SPIE-AAPM-NCI+PROSTATEx+Challenges. Online; Accessed on January 25, 2019.Google ScholarGoogle Scholar
  30. Saifeng Liu, Huaixiu Zheng, Yesu Feng, and Wei Li. 2017. Prostate cancer diagnosis using deep learning with 3D multiparametric MRI. In Medical Imaging 2017: Computer-Aided Diagnosis (Proceedings SPIE), Vol. 10134. International Society for Optics and Photonics, 1013428.Google ScholarGoogle Scholar
  31. F. Maes, A. Collignon, D. Vandermeulen, G. Marchal, and P. Suetens. 1997. Multi-modality image registration by maximization of mutual information. IEEE Trans. Med. Imaging 16, 2 (apr 1997), 187--198.Google ScholarGoogle ScholarCross RefCross Ref
  32. Lukasz Matulewicz, Jacobus FA Jansen, Louisa Bokacheva, Hebert Alberto Vargas, Oguz Akin, Samson W Fine, Amita Shukla-Dave, James A Eastham, Hedvig Hricak, Jason A Koutcher, et al. 2014. Anatomic segmentation improves prostate cancer detection with artificial neural networks analysis of 1H magnetic resonance spectroscopic imaging. J. Magn. Reson. Imaging 40, 6 (2014), 1414--1421.Google ScholarGoogle ScholarCross RefCross Ref
  33. Fausto Milletari, Nassir Navab, and Seyed-Ahmad Ahmadi. 2016. V-Net: fully convolutional neural networks for volumetric medical image segmentation.In Proceedings of the International Conference on 3D Vision (3DV). IEEE, 565--571.Google ScholarGoogle Scholar
  34. Alberto Moraglio, Krzysztof Krawiec, and Colin G Johnson. 2012. Geometric semantic genetic, programming. In Parallel Problem Solving from Nature-PPSN XII. Springer, 21--31. Google ScholarGoogle ScholarDigital LibraryDigital Library
  35. Alberto Moraglio and Andrea Mambrini. 2013. Runtime analysis of mutation-based geometric semantic genetic programming for basis functions regression. In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation (GECCO). ACM, 989--996. Google ScholarGoogle ScholarDigital LibraryDigital Library
  36. Olaf Ronneberger, Philipp Fischer, and Thomas Brox. 2015. U-Net: convolutional Networks for Biomedical Image Segmentation. In Proceedings of the Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) (LNCS), Vol. 9351. Springer, 234--241.Google ScholarGoogle ScholarCross RefCross Ref
  37. Andrew B Rosenkrantz, Ruth P Lim, Mershad Haghighi, Molly B Somberg, James S Babb, and Samir S Taneja. 2013. Comparison of interreader reproducibility of the prostate imaging reporting and data system and Likert scales for evaluation of multiparametric prostate MRI. AJR Am. J. Roentgenol. 201, 4 (2013), W612-W618.Google ScholarGoogle ScholarCross RefCross Ref
  38. Leonardo Rundo, Carmelo Militello, Giorgio Russo, Antonio Garufi, Salvatore Vitabile, Maria Carla Gilardi, and Giancarlo Mauri. 2017. Automated prostate gland segmentation based on an unsupervised fuzzy c-means clustering technique using multispectral T1w and T2w MR imaging. Information 8, 2 (2017), 49.Google ScholarGoogle ScholarCross RefCross Ref
  39. L. Rundo, A. Stefano, C. Militello, G. Russo, M. G. Sabini, C. D'Arrigo, F. Marletta, M. Ippolito, G. Mauri, S. Vitabile, and M. C. Gilardi. 2017. A fully automatic approach for multimodal PET and MR image segmentation in Gamma Knife treatment planning. Comput. Methods Programs Biomed. 144 (2017), 77--96. Google ScholarGoogle ScholarDigital LibraryDigital Library
  40. Leonardo Rundo, Andrea Tangherloni, Paolo Cazzaniga, Marco S Nobile, Giorgio Russo, Maria Carla Gilardi, Salvatore Vitabile, Giancarlo Mauri, Daniela Besozzi, and Carmelo Militello. 2019. A novel framework for MR image segmentation and quantification by using MedGA. Comput. Methods Programs Biomed. (2019). In press.Google ScholarGoogle Scholar
  41. Leonardo Rundo, Andrea Tangherloni, Carmelo Militello, Maria Carla Gilardi, and Giancarlo Mauri. 2016. Multimodal medical image registration using particle swarm optimization: a review. In Proc. Symposium Series on Computational Intelligence (SSCI). IEEE, 1--8.Google ScholarGoogle ScholarCross RefCross Ref
  42. Leonardo Rundo, Aandrea Tangherloni, Marco S. Nobile, Carmelo Militello, Daniela Besozzi, Giancarlo Mauri, and Paolo Cazzaniga. 2019. MedGA: a novel evolutionary method for image enhancement in medical imaging systems. Expert Syst. Appl. 119 (2019), 387--399.Google ScholarGoogle ScholarCross RefCross Ref
  43. Angela Serra, Paola Galdi, and Roberto Tagliaferri. 2018. Machine learning for bioinformatics and neuroimaging. Wiley Interdisc. Rev. Data Min. Knowl. Discov. 8, 5 (2018), e1248.Google ScholarGoogle ScholarCross RefCross Ref
  44. Rebecca L Siegel, Kimberly D Miller, and Ahmedin Jemal. 2019. Cancer statistics, 2019. CA Cancer J. Clin. 69, 1 (2019), 7--34.Google ScholarGoogle ScholarCross RefCross Ref
  45. Karen Simonyan and Andrew Zisserman. 2015. Very deep convolutional networks for large-scale image recognition. In Proceedings of the International Conference on Learning Representations (ICLR). arXiv preprint arXiv:1409.1556.Google ScholarGoogle Scholar
  46. Jost Tobias Springenberg, Alexey Dosovitskiy, Thomas Brox, and Martin Ried-miller. 2014. Striving for simplicity: The all convolutional net. In Proceedings of the International Conference on Learning Representations (ICLR). 1--14. arXiv preprint arXiv:1412.6806.Google ScholarGoogle Scholar
  47. Radka Stoyanova, Mandeep Takhar, Yohann Tschudi, John C Ford, Gabriel Solórzano, Nicholas Erho, Yoganand Balagurunathan, Sanoj Punnen, Elai Davi-cioni, Robert J Gillies, et al. 2016. Prostate cancer radiomics and the promise of radiogenomics. Transl. Cancer Res. 5, 4 (2016), 432.Google ScholarGoogle ScholarCross RefCross Ref
  48. Yohan Sumathipala, Nathan Lay, Baris Turkbey, Clayton Smith, Peter L Choyke, and Ronald M Summers. 2018. Prostate cancer detection from multi-institution multiparametric MRIs using deep convolutional neural networks. J. Med. Imaging 5, 4 (2018), 044507.Google ScholarGoogle ScholarCross RefCross Ref
  49. Jinquan Sun, Yinghuan Shi, Yang Gao, and Dinggang Shen. 2017. A point says a lot: an interactive segmentation method for MR prostate via one-point labeling. In Proceendigs of the International Workshop on Machine Learning in Medical Imaging (MLMI). Springer, 220--228.Google ScholarGoogle ScholarCross RefCross Ref
  50. Baris Turkbey, Anna M Brown, Sandeep Sankineni, Bradford J Wood, Peter A Pinto, and Peter L Choyke. 2016. Multiparametric prostate magnetic resonance imaging in the evaluation of prostate cancer. CA: A Cancer Journal for Clinicians 66, 4 (2016), 326--336.Google ScholarGoogle ScholarCross RefCross Ref
  51. Zhiwei Wang, Chaoyue Liu, Danpeng Cheng, Liang Wang, Xin Yang, and Kwang-Ting Cheng. 2018. Automated detection of clinically significant prostate cancer in mp-MRI images based on an end-to-end deep neural network. IEEE Trans. Med. Imaging 37, 5 (2018), 1127--1139.Google ScholarGoogle ScholarCross RefCross Ref
  52. David H Wolpert and William G Macready. 1997. No free lunch theorems for optimization. IEEE Trans. Evol. Computat. 1, 1 (1997), 67--82. Google ScholarGoogle ScholarDigital LibraryDigital Library

Index Terms

  1. Semantic learning machine improves the CNN-Based detection of prostate cancer in non-contrast-enhanced MRI

          Recommendations

          Comments

          Login options

          Check if you have access through your login credentials or your institution to get full access on this article.

          Sign in
          • Published in

            cover image ACM Conferences
            GECCO '19: Proceedings of the Genetic and Evolutionary Computation Conference Companion
            July 2019
            2161 pages
            ISBN:9781450367486
            DOI:10.1145/3319619

            Copyright © 2019 ACM

            Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

            Publisher

            Association for Computing Machinery

            New York, NY, United States

            Publication History

            • Published: 13 July 2019

            Permissions

            Request permissions about this article.

            Request Permissions

            Check for updates

            Qualifiers

            • research-article

            Acceptance Rates

            Overall Acceptance Rate1,669of4,410submissions,38%

            Upcoming Conference

            GECCO '24
            Genetic and Evolutionary Computation Conference
            July 14 - 18, 2024
            Melbourne , VIC , Australia

          PDF Format

          View or Download as a PDF file.

          PDF

          eReader

          View online with eReader.

          eReader