Deep Learning for Smart Healthcare—A Survey on Brain Tumor Detection from Medical Imaging
<p>The structure of this survey.</p> "> Figure 2
<p>Deep learning in healthcare.</p> "> Figure 3
<p>Flow diagram of the CAD system.</p> "> Figure 4
<p>CNN layers, consist of 7 layers, input: [[CONV to RELU] × 2 to pool] × 3 to FC.</p> "> Figure 5
<p>A representation of GAN network.</p> ">
Abstract
:1. Introduction
2. Background
2.1. MRI Images—Segmentation and Classification
2.2. AI techniques
2.2.1. Deep Learning
2.2.2. Neural Network
2.2.3. Machine Learning and Image Processing
2.3. Deep Learning Applications
2.3.1. Anomaly Detection
2.3.2. Object Detection
2.3.3. Pattern Recognition
2.3.4. Natural Language Processing
3. Literature Review
3.1. Tumor Detection—Classic Approach
3.2. Deep Learning and AI for Medical Imaging
3.3. CNN for Medical Imaging
3.4. Modeling in CNN
3.4.1. Ensembles of Multiple Models and Architectures (EMMA)
3.4.2. CNN-Based Segmentation of Medical Imaging Data
3.4.3. Auto Encoder Regularization Based
3.5. Hybrid Techniques in Classification
4. Learning Methods and Related Concepts
4.1. Method of Learning
4.1.1. Supervised Learning
4.1.2. Unsupervised Learning
4.1.3. Semi-Supervised Learning
4.2. Review of CAD System
Example of Studied Based on CAD System
4.3. Segmentation and Classification
4.4. Semantic Segmentation
5. Convolutional Neural Networks
5.1. Importance of CNN
5.2. U-Net and Fully Convolutional Network
5.3. Comparison of Different CNN Architectures
5.4. Usages of CNN Methods in Medicine
Usages of CNN in E-Health
6. Neural Networks and Beyond
6.1. Representation Learning
6.2. Pre-Trained Unsupervised Networks
6.2.1. Autoencoders
6.2.2. Generative Adversarial Networks
6.2.3. Deep Belief Networks
6.3. Recurrent Neural Networks
7. Discussion
7.1. Challenges and Solutions
7.1.1. First Time Consuming
7.1.2. Accuracy of Diagnosis
7.1.3. Need Second Opinion
7.1.4. Complexity of Computational
7.1.5. User Rights
7.2. Future Directions
7.2.1. Data Perspective
7.2.2. Modeling Perspective
8. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Ref. | Year | Focus of the Survey | Description | Distinguishing Features to Our Study |
---|---|---|---|---|
[1] | 2014 | Brain tumor segmentation | General overview for MRI-based brain tumor segmentation methods. | Only focus on MRI-based brain tumor segmentation |
[4] | 2017 | Brain tumor segmentation | A deep convolutional neural network for an automatic brain tumor segmentation. | Presented a fully automatic brain tumor segmentation method based on DCNN by considering different architectures and their impacts. |
[5] | 2018 | Subcortical brain structure segmentation | A 3D-CNN for segmentation of the subcortical brain in MRI images. | Presented a method based on fully-convolutional networks, they show their performance on the ISBR dataset. |
[6] | 2016 | Brain extraction of MR images | For extraction brain MRI images using 3D convolutional deep learning. | It is about the 3D convolutional deep learning architecture which handles an optional number of modalities for large-scale studies. |
[7] | 2017 | Brain lesion segmentation | Brain lesion segmentation based on 3D-CNN architecture, DeepMedic. | For brain lesion segmentation presented a dual pathway 3D-CNN. |
[8] | 2019 | Classifying glioma brain tumor | A combined method from CNN and genetic algorithm for classifying glioma brain tumor from MRI images. | They focused on a combination of genetic algorithm and CNN |
[3] | 2020 | Brain tumor detection for MR images | Review of numbers of segmentation and classification techniques which are used in detection of brain diseases. | Mostly they discussed different types of MRI images and focused on the medical sides of brain tumor classification. |
[9] | 2021 | Brain tumor diagnosis | Diagnosis the hardest tumor situation in radiology with Deep CNN | Using MATLAB software for processing and their database collected on 1258 MRI images from 2015 to 2020 |
Dataset | Description | Ref. | Features |
---|---|---|---|
BRATS | Brain Tumor Segmentation Challenge (BRATS) always focus on the evaluation of current and novel methods for brain tumors segmentation in multimodal MR images and has the dataset available from 2012 to 2020. | [17,18,19] | Fully Convolutional Neural Network (FCNN) and Conditional Random Fields (CRF) used in Brain tumor segmentation and this is based in conjunction with the MICCAI 2012 and 2013 conferences. |
OASIS | Open Access Series of Imaging Studies is contained over 2000 MR sessions are collected among several ongoing projects through the WUSTL Knight ADRC | [20,21] | Diagnosis of Alzheimer’s Disease. |
TCIA | The Cancer Imaging Archive (TCIA) is a big archive of cancer images and available for public download. | [22,23,24] | Prediction of head and neck cancer and Prediction of pancreatic cancer. Segmentation of brain tumors. |
IBSR | The Internet Brain Segmentation Repository. Its goal is to encourage the evaluation and expansion of segmentation methods. | [6,25,26] | Segmentation of MRI images and skull stripping. |
BrainWeb | It is a Simulated Brain Database. | [27,28,29] | Reconstruction of 3D MR images based on CNN and reduction of noise from MRI images and segmentation of cerebrospinal fluid and brain volume-based CNN |
NBIA | National Biomedical Imaging Archive that is for in vivo images, these images are related to biomedical research community, industry, and academia with access to image archives. | [30] | Quantitative Imaging Network. |
The Whole Brain Atlas | This site has dozens of real images of the brain and the Harvard Whole Brain Atlas provides you with access to PET and MRI scans of normal and diseased brains. | [31,32] | Features Extracted from brain images by CNN and Serotonin Neurons. |
ISLES | Ischemic Stroke Lesion Segmentation a medical image segmentation challenge at the MICCAI 2018 and a new dataset is consist of 103 stroke patients and matches profesional segmentations. | [7,33] | Brain lesion segmentation and stroke lesion segmentation. |
Technique | Ref. | Target | Result |
---|---|---|---|
Wavelet transform (WT), Genetic algorithm (GA) and supervised learning methods (SVM). | [76,77] | Classification of brain tissues in MRI images | This technique is accurate, Easy to operate, Non-invasive and inexpensive. |
K-means, Sobel edge detection and morphological operations. | [78] | Segmentation of Brain Lesions in MRI and CT Scan Images | Achieves a high accuracy 94% in compared with manual delineation performed. |
Support vector machine (SVM) and Fuzzy c-means (FCM). | [79,80] | Detection of Brain Tumor in MRI Images | Provide accurate and more effective result for classification of brain MRI images in minimal execution time. |
K-Means, Nonsubsampled contourlet transform (NSCT) and SVM. | [81] | MRI Brain Tumor Images Classification | Higher classification accuracy. |
K-Means, Gray Level Co-occurrence Matrix (GLCM), Berkeley Wavelet Transform (BWT), Principal Component Analysis (PCA) and Kernel Support Vector Machine (KSVM). | [82] | Detection and classification of MRI images | proposed method can be used for clinical purpose for screening and then diagnosed by the radiologists with high performance and accuracy. |
Fuzzy Clustering, Gabor feature extraction and ANN. | [83] | Detection and Classification for Brain tumor | The classifier’s output helps the radiologist to make the decisions without any hesitation and achieved classification accuracy of 92.5%. |
Scheme | Dataset | Ref. | Ways of Training and Testing | Achievement |
---|---|---|---|---|
Rely on CNN | BRATS 2015 and ISLES 2015 | [7] | Dual pathway | An efficient solution processing for multi-scale processing for large image context using parallel convolutional pathways. |
BRATS 2017 and BRATS 2015 | [68] | Dual-force | For learning high-quality multi-level features used a dual-force training strategy | |
BRATS 2013 and BRATS 2015 | [65] | Patch-based | Used 3 × 3 kernels to permit deeper architectures for CNN-based segmentation method for brain MRI images. | |
Rely on DCNN | ImageNet LSVRC-2010 | [96] | Patch-based | Gained top-1 and top-5 error rates of 37.5% and 17.0% |
ISBI 2012& 2015 | [95] | End-to-end | Enabled precise localization. | |
BRATS 2013 | [71] | T1, T1c, T2 and FLAIR images | 3D segmentation problem is converted into triplanar 2D CNNs. | |
BRATS 2013 | [4] | T1, T1c, T2 and FLAIR images | Novel CNN architecture which improved accuracy and speed as presented in MICCAI 2013. | |
Rely on FCN | BRATS 2013 & 2016 | [17] | T1, T1c, T2 and FLAIR images | Integration of FCN and Conditional Random Fields for brain tumor segmentation. |
BRATS 2013 | [97] | End-to-end | Improve brain tumor segmentation performance by a symmetry-driven FCN | |
ISBR and ABIDE (17 different sites) | [5] | End-to-end | Used 3D convolutional filters and FCN for an automatic segmentation of subcortical brain regions. |
Ref. | Architectures | Layers | Advantages | Disadvantages |
---|---|---|---|---|
[102] | LeNet-5 | 7 layers | Ability to process higher resolution images need larger firmer layers. | Overfitting in some cases and no built-in mechanism to avoid this |
[103] | AlexNet | 8 layers 60 M parameters | A very rapid downsampling of the intermediate representations through convolutions and max-pooling layers. | The use of large convolution filters (5 × 5) is not encouraged shortly after that, Is not deep enough rather than another techniques. |
[104] | ZFNet | 8 layers | Improved image classification rate error in compared with Alexnet, winner of ILSVRC2012 | Feature maps are not divided across two different GPU, Thus connections between layers are dense. |
[103] | GoogleNet | 22 layers 4–5 M parameters | Winner of ILSVRC2014, Decreased the number of parameters from 60 million (AlexNet) to 4 million so network can have a large width and depth. | Consists of a hierarchy of complex inception modules/blocks that consist of operations over different scales in each of the modules. |
[105] | VGGNet | Between 11 to 19 layers the best one is 16 layers 138 M parameters | At present it is the most prefer election for extracting features from images. | Consists of 138 million parameters, which can be a bit challenging to handle. |
[105] | ResNet | 152 layers | Network learns difference to an identity mapping (residual), Faster convergence if identity is closer to the optimum. | Lower complexity than VGGNet, Overfitting would increase test but decrease training error. |
Architectures | Examples | Target | Accuracy |
---|---|---|---|
LeNet-5 | [106] | Detection of brain cancer by tensorflow | 99% |
[38] | classify Alzheimer’s brain | 96.85% | |
Alex Net | [107] | Lung nodules in chest X-ray | 64.86% |
[108] | Diagnosis of Thyroid Ultrasound Image | 90.8% | |
[109] | Classification of skin lesion | 96.86% | |
VGGNet-16 | [110] | Brain tumor classification | 84% |
[111] | Diagnosis of Prostate Cancer | 95% | |
Google Net | [112] | Thyroid Nodule Classification in Ultrasound Images | 98.29% |
[107] | Lung nodules in chest X-ray | 68.92% | |
ResNet | [113] | Brain tumor classification | 89.93% |
[114] | Pancreatic tumor classification | 91% | |
ZefNet | [115] | The trends and challenges for future edge reconfigurable platforms of deep learning. |
Ref. | Features | Methods | Testing Sample | Achievement | Accuracy |
---|---|---|---|---|---|
[112] | Type, size, shape, tumor features | DCNN and googleNet | Thyroid nodules | Improving the performance of fine-tuning and augmenting the image samples. | 98.29% |
[91] | Size, tumor features, doughnut-shaped lesion | FCN, VGG-16, U-Net | Colorectal tumors | Can remodel the current, time-consuming and non-reproducible manual segmentation method. | - |
[114] | Type, size | ResNet18, ResNet34, ResNet52 and Inception-ResNet | Pancreatic Tumors | ResNet18 with the proposed weighted loss function method achieves the best results to classify tumors. | 91% |
[117] | Type, size, shape | CAD system using a multi-view convolutional network | Pulmonary Nodule | Boosts the detection sensitivity from 85.7% to 93.3%. | - |
[38] | Shape, scale | CNN and LeNet-5 | Alzheimer’s disease classification | Possible to generalize this method to predict different stages of Alzheimer’s disease for different age groups. | 96.85% |
[109] | Type, color image lesions | transfer learning and Alex-net | skin lesions classification | Higher performance than existing methods. | 96.86% |
[111] | Image lesion, type | VGGNet and patch-based DCNN | Prostate cancer | Enhanced prediction | 95% |
[119] | Textures | AlexNet | Breast cancer | Showed that accuracy obtained by CNN on BreaKHis dataset was improved. | - |
Existing Challenges | Example | Ideas as Potential Solution |
---|---|---|
Often classification or segmentation in medical imaging is introduced as a binary task, normal versus abnormal, object versus background. | In some rare situations, normal tissues and categories can find benign categories. | By presenting accurate annotations of all possible subclasses, we can convert the deep learning system into a multi-class system [39]. |
Depending on the task performed in medical imaging, images for the unusual class might be challenging to find. | Most cancerous lesions do not cause death; in mammograms, a suspicious lesion is usually not cancerous. | Conducted a thorough evaluation of data augmentation strategies for lesion segmentation [65]. |
In a deep learning network, balancing between the number of imaging features with the number of clinical features is a challenge. | Physicians, for an accurate diagnosis, usually need to use descriptive information. | Connect the whole image to the deep network and use different types of evaluation to guide learning [39]. |
In CAD, the biggest challenges are the diversity in shape and intensity of tumors or lesions as well as the existence of differences in the imaging protocol in the same imaging modality. | Use of simpler machine learning appeals in Rician noise, non-isotropic resolution, and bias field effects. Automatic handling is not usable in MRI. | For classification of hand-designed features in a through, separate step, conventional machine learning approaches are trained [138]. |
Deep learning does not leave a search trail to clarify its decisions, so it is considered a black box. | To specify an exact feature, such as an edge, circle, or class activation maps (CAMs), that localizes the important regions in an input used for the prediction. | Feature visualization is a feature which is identified in the feature maps. Attribution is a part of the input responsible for the corresponding prediction [84]. |
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Arabahmadi, M.; Farahbakhsh, R.; Rezazadeh, J. Deep Learning for Smart Healthcare—A Survey on Brain Tumor Detection from Medical Imaging. Sensors 2022, 22, 1960. https://doi.org/10.3390/s22051960
Arabahmadi M, Farahbakhsh R, Rezazadeh J. Deep Learning for Smart Healthcare—A Survey on Brain Tumor Detection from Medical Imaging. Sensors. 2022; 22(5):1960. https://doi.org/10.3390/s22051960
Chicago/Turabian StyleArabahmadi, Mahsa, Reza Farahbakhsh, and Javad Rezazadeh. 2022. "Deep Learning for Smart Healthcare—A Survey on Brain Tumor Detection from Medical Imaging" Sensors 22, no. 5: 1960. https://doi.org/10.3390/s22051960
APA StyleArabahmadi, M., Farahbakhsh, R., & Rezazadeh, J. (2022). Deep Learning for Smart Healthcare—A Survey on Brain Tumor Detection from Medical Imaging. Sensors, 22(5), 1960. https://doi.org/10.3390/s22051960