3D Spatial Pyramid Dilated Network for Pulmonary Nodule Classification
Abstract
:1. Introduction
- We propose a novel 3D spatial pyramid dilated network for the pulmonary nodule malignancy classification task. Compared with the 2D deep learning models, our model can capture more spatial and distinguishable information from the input data.
- Unlike the previous work by using the pooling layer, we exploit the dilated convolution to alleviate the loss of tiny information and feature maps resolution.
- A spatial pyramid dilated structure with multiple dilated rate is designed to learn the discriminative scale features from the nodule CT images. Extensive experiments show that our model has achieved a better result compared with other state-of-the-art methods.
2. Related Work
3. Methodology
3.1. 3D Spatial Convolution Layer
3.2. Pyramid Dilated Structure
3.3. Multiple Receptive Field Feature Fusion
3.4. Fully Connected Layer
3.5. Softmax Layer
3.6. Training Details
3.7. Evaluation Metrics
- The classification accuracy rate is the ratio of the number of samples correctly sorted by the classifier to the total number of samples when the probabilistic output of the classifier is threshold at t.
- Sensitivity or the true positive rate (TPR) is an empirical value used to measure the percentage of actual positives which are correctly identified. Sensitivity or TPR is defined as the function of threshold t, with the expressions below
- The false positive rate (FPR) which is defined as
- Finally, we draw the receiver operating characteristic (ROC) curve which shows the fit degree of ground-truth label and classifier-predicted label. The AUC score is the area under the ROC curve. It is an empirical value representing the probabilistic output of the classifier which is greater for a positive example than for a negative example.
4. Experiment
4.1. Data Description
4.2. The Influence of Different Sample Sizes
4.3. Compared with State-of-the-Art Method
4.4. The Effectiveness of Dilated Convolution Setting
4.5. Comparison with Different Feature Cropping and Fusion Modes
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Siegel, R.L.; Miller, K.D.; Jemal, A. Cancer statistics. CA Cancer J. Clin. 2016, 66, 7–30. [Google Scholar] [CrossRef] [PubMed]
- Stewart, B.; Wild, C.P. World Cancer Report 2014; International Agency for Research on Cancer: Lyon, France, 2014. [Google Scholar]
- Henschke, C.I.; McCauley, D.I.; Yankelevitz, D.F.; Naidich, D.P.; McGuinness, G.; Miettinen, O.S.; Libby, D.M.; Pasmantier, M.W.; Koizumi, J.; Altorki, N.K.; et al. Early Lung Cancer Action Project: Overall design and findings from baseline screening. Lancet 1999, 354, 99–105. [Google Scholar] [CrossRef]
- Farag, A.; Ali, A.; Graham, J.; Farag, A.; Elshazly, S.; Falket, R. Evaluation of geometric feature descriptors for detection and classification of lung nodules in low dose CT scans of the chest. In Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Chicago, IL, USA, 30 March–2 April 2011; pp. 169–172. [Google Scholar]
- Song, Y.; Cai, W.; Zhou, Y.; Feng, D.D. Feature-based image patch approximation for lung tissue classification. IEEE Trans. Med. Imaging 2013, 32, 797–808. [Google Scholar] [CrossRef] [PubMed]
- Sorensen, L.; Shaker, S.B.; De Bruijne, M. Quantitative analysis of pulmonary emphysema using local binary patterns. IEEE Trans. Med. Imaging 2010, 29, 559–569. [Google Scholar] [CrossRef] [PubMed]
- Bengio, Y.; Courville, A.; Vincent, P. Representation learning: A review and new perspectives. IEEE Trans. Pattern Anal. Mach. Intell. 2013, 35, 1798–1828. [Google Scholar] [CrossRef] [PubMed]
- Chen, L.C.; Papandreou, G.; Kokkinos, I.; Murphy, K.; Yuille, A.L. Deeplab: Semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected crfs. IEEE Trans. Pattern Anal. Mach. Intell. 2018, 40, 834–848. [Google Scholar] [CrossRef] [PubMed]
- Yu, F.; Koltun, V.; Funkhouser, T. Dilated residual networks. In Proceedings of the 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2017), Honolulu, HI, USA, 21–26 July 2017. [Google Scholar] [CrossRef]
- Dou, Q.; Chen, H.; Yu, L.; Qin, J.; Heng, P.A. Multilevel contextual 3-D CNNs for false positive reduction in pulmonary nodule detection. IEEE Trans. Biomed. Eng. 2017, 64, 1558–1567. [Google Scholar] [CrossRef] [PubMed]
- Krewer, H.; Geiger, B.; Hall, L.O.; Goldgof, D.B.; Gu, Y.; Tockman, M.; Gillies, R.J. Effect of texture features in computer aided diagnosis of pulmonary nodules in low-dose computed tomography. In Proceedings of the 2013 IEEE International Conference on Systems, Man and Cyberneticsms, Manchester, UK, 13–16 October 2013; pp. 3887–3891. [Google Scholar]
- Uchiyama, Y.; Katsuragawa, S.; Abe, H.; Shiraishi, J.; Li, F.; Li, Q.; Zhang, C.T.; Suzuki, K.; Doi, K. Quantitative computerized analysis of diffuse lung disease in high-resolution computed tomography. Med. Phys. 2003, 30, 2440–2454. [Google Scholar] [CrossRef] [PubMed]
- Messay, T.; Hardie, R.C.; Rogers, S.K. A new computationally efficient CAD system for pulmonary nodule detection in CT imagery. Med. Image Anal. 2010, 14, 390–406. [Google Scholar] [CrossRef] [PubMed]
- Orozco, H.M.; Villegas, O.O.V.; Sánchez, V.G.C.; Dominguez, H.D.J.O.; Alfaro, M.D.J.N. Automated system for lung nodules classification based on wavelet feature descriptor and support vector machine. Biomed. Eng. Online 2015, 14, 9. [Google Scholar] [CrossRef] [PubMed]
- Erdal, U.A. Shape and texture based novel features for automated juxtapleural nodule detection in lung cts. J. Med. Syst. 2015, 39, 46. [Google Scholar]
- Han, F.; Wang, H.; Zhang, G.; Han, H.; Song, B.; Li, L.; Moore, W.; Lu, H.; Zhao, H.; Liang, Z. Texture feature analysis for computer-aided diagnosis on pulmonary nodules. J. Digi. Imaging 2015, 28, 99–115. [Google Scholar] [CrossRef] [PubMed]
- Shi, J.; Zheng, X.; Li, Y.; Zhang, Q.; Ying, S. Multimodal neuroimaging feature learning with multimodal stacked deep polynomial networks for diagnosis of Alzheimer’s disease. IEEE J. Biomed. Health Inform. 2018, 22, 173–183. [Google Scholar] [CrossRef] [PubMed]
- Maninis, K.K.; Pont-Tuset, J.; Arbeláez, P.; Gool, L.V. Deep retinal image understanding. In Proceedings of the International Conference on Medical Image Computing and Computer-Assisted Intervention, Athens, Greece, 17–21 October 2016; pp. 140–148. [Google Scholar]
- Song, Y.; Zhang, L.; Chen, S.; Ni, D.; Lei, B.; Wang, T. Accurate segmentation of cervical cytoplasm and nuclei based on multiscale convolutional network and graph partitioning. IEEE Trans. Biomed. Eng. 2015, 62, 2421–2433. [Google Scholar] [CrossRef] [PubMed]
- Kashif, M.N.; Raza, S.E.A.; Sirinukunwattana, K.; Arif, M.; Rajpoot, N. Handcrafted features with convolutional neural networks for detection of tumor cells in histology images. In Proceedings of the 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), Prague, Czech Republic, 13–16 April 2016; pp. 1029–1032. [Google Scholar]
- Suk, H.I.; Lee, S.W.; Shen, D.; Alzheimers Disease Neuroimaging Initiative. Hierarchical feature representation and multimodal fusion with deep learning for AD/MCI diagnosis. NeuroImage 2014, 101, 569–582. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhu, Y.; Wang, L.; Liu, M.; Qian, C.; Yousuf, A.; Oto, A.; Shen, D. MRI-based prostate cancer detection with high-level representation and hierarchical classification. Med. Phys. 2017, 44, 1028–1039. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kumar, D.; Wong, A.; Clausi, D.A. Lung nodule classification using deep features in CT images. In Proceedings of the 12th Conference on Computer and Robot Vision, Halifax, NS, Canada, 3–5 June 2015; pp. 133–138. [Google Scholar]
- Li, W.; Cao, P.; Zhao, D.; Wang, J. Pulmonary nodule classification with deep convolutional neural networks on computed tomography images. Comput. Math. Methods Med. 2016. [Google Scholar] [CrossRef] [PubMed]
- Chen, S.; Qin, J.; Ji, X.; Lei, B.; Wang, T.F.; Ni, D.; Cheng, J.Z. Automatic scoring of multiple semantic attributes with multi-task feature leverage: A study on pulmonary nodules in CT images. IEEE Trans. Med. Imaging 2017, 36, 802–814. [Google Scholar] [CrossRef] [PubMed]
- Shen, W.; Zhou, M.; Yang, F.; Yu, D.; Ding, D.; Yang, C.; Zhang, Y.; Tian, J. Multi-crop convolutional neural networks for lung nodule malignancy suspiciousness classification. Pattern Recognit. 2017, 61, 663–673. [Google Scholar] [CrossRef]
- Setio, A.A.A.; Ciompi, F.; Litjens, G.; Gerke, P.; Jacobs, C.; Riel, S.J.V.; Wille, M.M.W.; Naqibullah, M.; Sánchez, C.I.; Ginneken, B.V. Pulmonary nodule detection in CT images: False positive reduction using multi-view convolutional networks. IEEE Trans. Med. Imaging 2016, 35, 1160–1169. [Google Scholar] [CrossRef] [PubMed]
- Yan, X.; Pang, J.; Qi, H.; Zhu, Y.; Bai, C.; Geng, X.; Liu, M.; Terzopoulos, D.; Ding, X. Classification of lung nodule malignancy risk on computed tomography images using convolutional neural network: A comparison between 2D and 3D strategies. In Computer Vision—ACCV 2016 Workshops; Springer: Switzerland, Sweden, 2017. [Google Scholar]
- Jiang, H.; Ma, H.; Qian, W.; Gao, M.; Li, Y. An automatic detection system of lung nodule based on multi-group patch-based deep learning network. IEEE J. Biomed. Health Inform. 2017, 22, 1227–1237. [Google Scholar] [CrossRef] [PubMed]
- Ji, S.; Xu, W.; Yang, M.; Yu, K. 3D convolutional neural networks for human action recognition. IEEE Trans. Pattern Anal. Mach. Intell. 2013, 35, 221–231. [Google Scholar] [CrossRef] [PubMed]
- Yu, F.; Koltun, V. Multi-scale context aggregation by dilated convolutions. In Proceedings of the International Conference on Learning Representations 2016, San Juan, PR, USA, 2–4 May 2016. [Google Scholar]
- Armato, S.G., III; McLennan, G.; Bidaut, L.; McNitt-Gray, M.F.; Meyer, C.R.; Reeves, A.P.; Zhao, B.; Henschke, C.I.; Hoffman, E.A.; Kazerooni, E.A.; et al. The lung image database consortium (LIDC) and image database resource initiative (IDRI): A completed reference database of lung nodules on CT scans. Med. Phys. 2011, 38, 915–931. [Google Scholar] [CrossRef] [PubMed]
- Dai, J.; Qi, H.; Xiong, Y.; Li, Y.; Zhang, G.; Hu, H.; Wei, Y. Deformable convolutional networks. In Proceedings of the 2017 IEEE International Conference on Computer Vision (ICCV), Venice, Italy, 22–29 October 2017; pp. 764–773. [Google Scholar]
- Tajbakhsh, N.; Suzuki, K. Comparing two classes of end-to-end machine-learning models in lung nodule detection and classification: MTANNs vs. CNNs. Pattern Recognit. 2017, 63, 476–486. [Google Scholar] [CrossRef]
- He, K.; Zhang, X.; Ren, S.; Sun, J. Deep residual learning for image recognition. In Proceedings of the 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Las Vegas, NV, USA, 27–30 June 2016; pp. 770–778. [Google Scholar]
- Shen, W.; Zhou, M.; Yang, F.; Yang, C.; Tian, J. Multi-scale convolutional neural networks for lung nodule classification. In Proceedings of the 24th International Conference on Information Processing in Medical Imaging (IPMI 2015), Isle of Skye, UK, 28 June–3 July 2015; pp. 588–599. [Google Scholar]
- Messay, T.; Hardie, R.C.; Tuinstra, T.R. Segmentation of pulmonary nodules in computed tomography using a regression neural network approach and its application to the lung image database consortium and image database resource initiative dataset. Med. Image Anal. 2015, 22, 48–62. [Google Scholar] [CrossRef] [PubMed]
Approach | Author | Year | Method |
---|---|---|---|
Hand-crafted feature | Uchiyama et al. [12] | 2003 | grey-scale histogram features |
Messay et al. [13] | 2010 | combined intensity thresholding with morphological processing to detect nodules | |
Krewer et al. [11] | 2013 | texture features | |
Orozco et al. [14] | 2015 | wavelet features and support vector machine | |
Han et al. [16] | 2015 | three-dimensional texture features | |
Deep convolution feature | Li W et al. [24] | 2016 | 2D CNN for solid, semisolid and ground glass opacity nodules classification |
Setio et al. [27] | 2016 | multi-view feature extraction for nodule classification | |
Chen et al. [8] | 2017 | multiple semantic features for nodules classification by 2D CNN | |
Shen et al. [26] | 2017 | multi-crop 3D CNN for nodule malignancy suspicious classification | |
Yan et al. [28] | 2017 | compared the classification performance of 2D CNN with 3D CNN |
Datasize | 177 | 353 | 706 |
---|---|---|---|
Accuracy (%) | 81.2 | 85.5 | 88.6 |
Sensitivity (%) | 82.2 | 84.2 | 86.3 |
Specificity (%) | 75.1 | 80.2 | 90.3 |
AUC | 0.721 | 0.832 | 0.883 |
Method | Accuracy (%) | Sensitivity (%) | Specificity (%) | AUC |
---|---|---|---|---|
Han et al. [16] | - | 89.4 | 86.0 | 0.941 |
Kumar et al. [23] | 75.0 | 83.3 | - | - |
Chen et al. [25] | 86.8 | 60.3 | 95.4 | - |
Shen et al. [26] | 87.1 | 77.0 | 93.0 | 0.930 |
Messay et al. [37] | 75.0 | 83.3 | - | - |
Proposed Model | 88.6 | 86.3 | 90.3 | 0.883 |
Method | Accuracy (%) |
---|---|
Crop Features + Dilated Fusion (Average) | 87.0 |
Crop Features + Dilated Fusion (Maximum) | 88.2 |
Crop Features + Dilated Fusion (Concatenate) | 88.6 |
No Crop Features + Dilated Fusion (Average) | 83.2 |
No Crop Features + Dilated Fusion (Maximum) | 84.1 |
No Crop Features + Dilated Fusion (Concatenate) | 84.5 |
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Zhang, G.; Liu, X.; Zhu, D.; He, P.; Liang, L.; Luo, Y.; Lu, J. 3D Spatial Pyramid Dilated Network for Pulmonary Nodule Classification. Symmetry 2018, 10, 376. https://doi.org/10.3390/sym10090376
Zhang G, Liu X, Zhu D, He P, Liang L, Luo Y, Lu J. 3D Spatial Pyramid Dilated Network for Pulmonary Nodule Classification. Symmetry. 2018; 10(9):376. https://doi.org/10.3390/sym10090376
Chicago/Turabian StyleZhang, Guokai, Xiao Liu, Dandan Zhu, Pengcheng He, Lipeng Liang, Ye Luo, and Jianwei Lu. 2018. "3D Spatial Pyramid Dilated Network for Pulmonary Nodule Classification" Symmetry 10, no. 9: 376. https://doi.org/10.3390/sym10090376