EnsemDeepCADx: Empowering Colorectal Cancer Diagnosis with Mixed-Dataset Features and Ensemble Fusion CNNs on Evidence-Based CKHK-22 Dataset
Abstract
:1. Introduction
- The initial stage is to generate a dataset for feature fusion by combining the CKHK-22 mixed image datasets with others, such as the Grey and LBP datasets.
- Developing and training three ensemble fusion CNNs using the feature fusion CNN and the other featured datasets is the next step.
- In the subsequent stage, all CNNs are trained with SVM and transfer learning.
- In the final stage, temporal and spatial information is extracted using transfer learning ensemble fusion CNNs with BILSTM and SVM multi-class classification.
- At each stage, the EnsemDeepCADx model is inspected for inconsistencies and other performance metrics, and the resulting data is compared to determine the optimal approach.
1.1. Organisation of Study
1.2. Literature Survey
2. Materials and Methods
2.1. Colonoscopy Medical Motion Images
Datasets
2.2. Image Pre-Processing
2.2.1. Google Cloud
- Sign up for Google Cloud and create your first project to start;
- To begin storing the data, create a new container using the Cloud Storage interface;
- Using the Cloud Storage user interface or the command line utility, the CKHK-22 dataset may be added to the container;
- Ensure that the bucket is accessible to the public before uploading the data;
- Launch Google Authenticator and log in to your Co-lab account;
- Using gcsfuse, it can mount the container to Co-lab and access its contents as you would any other local disc;
- After mounting the container, the CKHK-22 dataset in Co-lab becomes as accessible as if it had been saved locally.
2.2.2. Image Augmentation
- Resize: creates images that are 224 by 224 pixels in dimension;
- Noise reduction enhances image clarity by removing distracting ambient noise;
- Image colour correction is the process of standardising the image’s colour distribution to reduce variations;
- Using the zoom function, it can double or halve the image size;
- Images can be rotated by a maximum of 15 degrees;
- The horizontal flip function mirrors the image by horizontally rotating it.
2.3. Train Test Split
2.3.1. Extracting Grey Scale Features from Original Image Dataset
- Use a library for processing images, such as OpenCV, to read the source colour images;
- Apply the following formula to transform every image from the RGB colour space into the greyscale colour space;
- Create a new folder to store the greyscale images in so they may be used in the image classification model’s testing and training stages.
2.3.2. Extracting Local Binary Pattern Features from Greyscale Dataset
- Create greyscale images that are typically 3 × 3 or 5 × 5 pixels in size;
- Determine the LBP of each pixel in the region by comparing its intensity to that of its neighbouring pixels;
- Replace the pixel’s original intensity value with a binary code representing the pattern of intensity differences between the central pixel and its companions;
- The LBP values of each pixel in the sub-region are added together to generate a singular LBP code;
- To generate a full set of LBP codes, the procedure must be repeated for each image’s subregion;
- To generate a feature vector that adequately characterises the image, the LBP codes are aggregated across the entire image using a histogram-based technique.
2.3.3. Feature Fusion as New Dataset
2.4. Image Classification Using Ensemble Fusion CNNs
2.4.1. Bidirectional LSTM
2.4.2. Support Vector Machines
2.5. The Classification Step
- The input CKHK-22 mixed dataset contains 10 classes and 14,287 images;
- Before extracting local binary pattern (LBP) features, images from the CKHK-22 mixed dataset are converted to greyscale as part of the pre-processing step. The feature fusion dataset is created by combining these features with the RGB features from the original dataset;
- The CADx system’s ensemble fusion CNNs consist of four pre-trained CNN models: AlexNet, DarkNet-19, DenseNet-201, and ResNet-50. aDaDR-22, aDaR-22, and DaRD-22 are combined in three ways to create a more robust and accurate CNN model. The original RGB images and LBP features extracted from greyscale images are used to train ensemble CNNs on the CKHK-22 mixed dataset;
- The BILSTM recurrent neural network is capable of processing data sequences in both forward and reverse directions. In the EnsemDeepCADx system, the BILSTM is used as a transfer learning technique to enhance the efficacy of the ensemble CNNs. The resultant sequence of image features is then processed by the BILSTM layer, which receives input from the CNN ensemble. This method may improve the accuracy of a classification model by capturing temporal dependencies and correlations between visual features;
- SVMs are a family of machine learning algorithms used for classification and regression testing. SVMs are utilised as a post-processing stage in the EnsemDeepCADx system following the acquisition of classification results from an ensemble of CNNs and a BILSTM. An SVM classifier receives the results from the BILSTM layer and transforms the features into a higher dimension using a kernel function. The SVM classifier searches for the hyperplane that divides the input features into distinct categories in order to classify them. This technique helps improve the classification model’s accuracy by reducing false positives and enhancing class separation. This discovers how to partition data into the ten classes provided as input;
- Before performing transfer learning using ensemble CNNs, the final fully connected layer and SoftMax activation layer were eliminated from each CNN model. The feature maps produced by the final convolutional layer of each CNN were then provided to the BiLSTM layer. A total of 64 hidden units within the BiLSTM layer employed the tanh activation function. The output of the BiLSTM layer was input into a fully connected layer consisting of 32 hidden units and the ReLU activation function after final classification using a multi-Class SVM;
- Training the models: in this EnsemDeepCADx system, it can train the models using the pre-processed datasets and the hyperparameters specified for each model. The EnsemDeepCADx system can use techniques such as early stopping and learning rate scheduling to optimise the training process;
- Evaluating the models:Ie EnsemDeepCADx system can evaluate the models on the test set using metrics such as accuracy, precision, recall, and F1 score. In this system, the efficacy of a model is evaluated by producing ROC curves and calculating the area under the curve (AUC). To evaluate the efficacy of the trained models in real-world scenarios, an independent set of images from the CKHK-22 mixed dataset is used.
- Future images of colorectal cancer can be identified accurately using the completed EnsemDeepCADx system.
- Stage 1:
- The CKHK-22 mixed image dataset is pre-processed to extract features from the original RGB images, as well as grey and LBP images, resulting in the creation of three new feature datasets. These three datasets are then merged to form a new feature fusion dataset.
- Stage 2:
- Three ensemble fusion CNN models—ADaDR-22, ADaR-22, and DaRD-22—are trained and tested with each of the four feature datasets (original, grey, LBP, and feature fusion).
- Stage 3:
- The three trained ensemble fusion CNN models are combined with BiLSTM models through transfer learning. The resulting models are then trained and tested with each of the four feature datasets.
- Stage 4:
- The three trained ensemble fusion CNN models are combined with BiLSTM and multi-class SVM models through transfer learning. The resulting models are then trained and tested with each of the four feature datasets.
3. Experimental Setup
4. Results
4.1. Stage 1 Experimentation
4.2. Stage 2 Experimentation: Ensemble Fusion CNNs
4.3. Stage 3 Experimentation: Ensemble Fusion CNNs + Multi-Class SVM
4.4. Stage 4 Experimentation: Ensemble Fusion CNNs + BiLSTM + Multi-Class SVM
5. Discussion
- On the CVC Clinic DB dataset, Liew et al. (2021) [11] used an ensemble classifier approach with ResNet50 + Adaboost, AlexNet, GoogLeNet, and VGG-19 models to achieve an accuracy of 97.91%. Their method’s execution time was 2.5 h;
- Omneya Attallah et al. (2021) [17] obtained an accuracy of 97.3% and 99.7% on the Kvasir2 and Hyper Kvasir datasets, respectively, using the GastroCADx method with AlexNet, DarkNet19, ResNet50, DenseNet-201, DWT, DCT, and SVM. The duration of execution for both datasets was three hours;
- Maryem Souaidi et al. (2022) [21] applied the MP-FSSD technique with VGG16 and feature Fusion Module to the CVC Clinic DB and WCE datasets. They obtained an accuracy of 91.56 percent in 2.5 h of execution;
- Pallabi Sharma et al. (2022) [49] utilised an ensemble classifier technique with ResNet101, GoogleNet, and XceptionNet models on the CVC Clinic DB and Aichi Medical Dataset. They obtained a 98.3% accuracy rate in 2.45 h of execution;
- Nisha J.S. et al. (2022) [50] applied the DP-CNN technique with the Dual Path CNN model to the CVC Clinic DB and ETIS-Larib datasets, achieving a 99.6% accuracy. Their method’s execution time was two hours;
- ColoRectalCADx was developed by Akella S. Narasimha Raju et al. [51] using ResNet-50V2, DenseNet-201, VGG16, LSTM, and SVM models on Hyper Kvasir Balanced and Mixed Dataset Balanced. They attained 98.91% and 96.13% accuracy with execution times of 2.15 and 2.10 h, respectively;
- EnsemDeepCADx, the proposed model (2023), employed Ensemble CNN DaRD-22, BLSTM, and SVM with feature fusion on the CKHK-22 mixed dataset. The accuracy was 97.89% and the execution time was 2 h.
6. Conclusions and Future Work
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Classes | CKHK-22 Mixed Dataset | Images |
---|---|---|
0 | bbps-0-1 | 653 |
1 | bbps-2-3 | 1148 |
2 | cecum | 2009 |
3 | dyed-lifted-polyps | 2003 |
4 | dyed-resection-margins | 1990 |
5 | non-polyps | 818 |
6 | polyps | 818 |
7 | pylorus | 2150 |
8 | retroflex-stomach | 765 |
9 | z-line | 1933 |
Total images in dataset | 14,287 |
CNN Architecture Models | Introduced Year | Total Params | Trainable Params | Non-Trainable Params | Layers |
---|---|---|---|---|---|
ADaDR-22 | 2022 | 89,491,098 | 47,570,314 | 41,920,784 | 293 |
ADaR-22 | 2022 | 70,062,380 | 46,463,580 | 23,598,800 | 92 |
DaRD-22 | 2022 | 61,401,236 | 19,501,588 | 41,899,648 | 270 |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
---|---|---|---|---|---|---|
Original CKHK-22 | ADaDR-22 | 90.35 | 88.11 | 87.72 | 95.72 | 88.11 |
Datasets | ADaR-22 | 89.34 | 86.33 | 85.66 | 94.22 | 86.33 |
DaRD-22 | 90.78 | 89 | 88.52 | 96.2 | 89 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
Greyscale | ADaDR-22 | 85.33 | 82.97 | 82.22 | 92.82 | 82.97 |
CKHK-22 Datasets | ADaR-22 | 85.47 | 81.31 | 82.07 | 91.33 | 81.31 |
DaRD-22 | 81.95 | 80.66 | 79.57 | 89.66 | 81.66 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
LBP CKHK-22 | ADaDR-22 | 68.74 | 66.03 | 64.4 | 69.5 | 66.03 |
Datasets | ADaR-22 | 67.82 | 65.31 | 64.98 | 67.8 | 65.31 |
DaRD-22 | 69.92 | 68.96 | 67.56 | 71.83 | 68.96 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
Feature Fusion | ADaDR-22 | 92.62 | 90.2 | 89.57 | 92.06 | 90.2 |
CKHK-22 Datasets | ADaR-22 | 91.56 | 89.69 | 88.43 | 91.88 | 89.69 |
DaRD-22 | 93.87 | 92.31 | 91.3 | 95.46 | 92.31 |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
---|---|---|---|---|---|---|
Original CKHK-22 Datasets | ADaDR-22 | 85.56 | 86.44 | 82.61 | 87.72 | 86.44 |
ADaR-22 | 86.62 | 83.04 | 82.91 | 84.91 | 84.04 | |
DaRD-22 | 86.79 | 85.55 | 84.53 | 88.67 | 85.55 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
Greyscale CKHK-22 Datasets | ADaDR-22 | 81.32 | 79.91 | 78.83 | 87.84 | 79.91 |
ADaR-22 | 80.29 | 77.79 | 76.1 | 82.32 | 77.19 | |
DaRD-22 | 82.32 | 80.62 | 79.57 | 89.69 | 80.62 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
LBP CKHK-22 Datasets | ADaDR-22 | 65.94 | 64.81 | 63.32 | 68.31 | 64.82 |
ADaR-22 | 66.14 | 64.53 | 62.21 | 67.57 | 65.53 | |
DaRD-22 | 69.46 | 68.1 | 67.51 | 70.11 | 68.1 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
Feature Fusion CKHK-22 Datasets | ADaDR-22 | 91.88 | 89.16 | 88.95 | 91.43 | 89.16 |
ADaR-22 | 90.26 | 88.52 | 87.14 | 91.11 | 88.52 | |
DaRD-22 | 92.63 | 91.59 | 90.48 | 90.89 | 91.59 |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
---|---|---|---|---|---|---|
Original CKHK-22 Datasets | ADaDR-22 | 89.92 | 93.47 | 86.76 | 97.74 | 93.47 |
ADaR-22 | 92.12 | 91.58 | 85.61 | 96.95 | 91.58 | |
DaRD-22 | 95.31 | 94.96 | 93.47 | 98.64 | 95.96 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
Greyscale CKHK-22 Datasets | ADaDR-22 | 89.23 | 87.89 | 86.42 | 92.11 | 87.89 |
ADaR-22 | 84.92 | 83.09 | 82.57 | 85.54 | 83.09 | |
DaRD-22 | 90.46 | 88.79 | 87.62 | 95.56 | 88.79 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
LBP CKHK-22 Datasets | ADaDR-22 | 70.67 | 69.92 | 67.41 | 72.56 | 69.92 |
ADaR-22 | 71.11 | 68.85 | 67.96 | 71.87 | 68.85 | |
DaRD-22 | 75.11 | 73.54 | 72.67 | 75.89 | 73.54 | |
Datasets | Ensemble Fusion CNNs | Precision (%) | Recall (%) | F1 Score (%) | Training Accuracy (%) | Testing Accuracy (%) |
Feature Fusion CKHK-22 Datasets | ADaDR-22 | 95.69 | 94.96 | 93.37 | 95.67 | 94.96 |
ADaR-22 | 94.98 | 93.77 | 92.59 | 95.08 | 93.77 | |
DaRD-22 | 96.98 | 97.12 | 95.98 | 98.72 | 97.89 |
Classes | Precision | Recall | F1 Score | Support |
---|---|---|---|---|
bbps-0-1 | 0.99 | 0.98 | 0.99 | 594 |
bbps-2-3 | 0.99 | 0.99 | 0.99 | 1035 |
cecum | 0.88 | 0.99 | 0.93 | 1809 |
dyed-lifted-polyps | 0.58 | 0.92 | 0.71 | 1803 |
dyed-resection-margins | 0.86 | 0.43 | 0.57 | 1791 |
Non-Polyps | 0.98 | 0.96 | 0.97 | 771 |
polyps | 0.96 | 0.82 | 0.88 | 2604 |
pylorus | 0.97 | 1 | 0.98 | 1800 |
retroflex-stomach | 0.99 | 0.99 | 0.99 | 690 |
z-line | 1 | 0.99 | 0.99 | 1740 |
Author | Method | Model Approach | Dataset | Time Elapsed | Accuracy (%) |
---|---|---|---|---|---|
Omneya Attallah et al. (2021) [17] | GastroCADx | AlexNet, DarkNet19, ResNet50 and DenseNet-201, DWT and DCT functions, SVM | Kvasir2, | 3 h | 97.3 |
Hyper Kvasir | 3 h | 99.7 | |||
Liew et al. (2021) [11] | Ensemble classifier | ResNet50 + Adaboost, AlexNet, GoogLeNet, and VGG-19 | CVC Clinic DB | 2.5 h | 97.91 |
Pallabi Sharma et al. (2022) [49] | Ensemble classifier | ResNet101, GoogleNet and XceptionNet | CVC Clinic DB, Aichi Medical Dataset | 2.45 h | 98.3 |
Kvasir2, | 2.25 h | 97 | |||
Nisha J.S et al. (2022) [50] | DP-CNN | Dual Path CNN | CVC Clinic DB, ETIS-Larib | 2 h | 99.6 |
Maryem Souaidi et al. (2022) [21] | MP-FSSD | VGG16 with feature Fusion Module | CVC Clinic DB, WCE dataset | 2.5 h | 91.56 |
Akella S Narasimha Raju et al. (2022) [51] | ColoRectalCADx | ResNet-50V2, DenseNet-201, VGG16, LSTM and SVM | Hyper Kvasir Balanced | 2.15 h | 98.91 |
Mixed Dataset Balanced | 2.10 h | 96.13 | |||
Proposed Model (2023) | EnsemDeepCADx | Ensemble CNN DaRD-22, BLSTM, SVM with feature fusion | CKHK-22 Mixed Dataset | 2 h | 97.89 |
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Raju, A.S.N.; Venkatesh, K. EnsemDeepCADx: Empowering Colorectal Cancer Diagnosis with Mixed-Dataset Features and Ensemble Fusion CNNs on Evidence-Based CKHK-22 Dataset. Bioengineering 2023, 10, 738. https://doi.org/10.3390/bioengineering10060738
Raju ASN, Venkatesh K. EnsemDeepCADx: Empowering Colorectal Cancer Diagnosis with Mixed-Dataset Features and Ensemble Fusion CNNs on Evidence-Based CKHK-22 Dataset. Bioengineering. 2023; 10(6):738. https://doi.org/10.3390/bioengineering10060738
Chicago/Turabian StyleRaju, Akella Subrahmanya Narasimha, and Kaliyamurthy Venkatesh. 2023. "EnsemDeepCADx: Empowering Colorectal Cancer Diagnosis with Mixed-Dataset Features and Ensemble Fusion CNNs on Evidence-Based CKHK-22 Dataset" Bioengineering 10, no. 6: 738. https://doi.org/10.3390/bioengineering10060738
APA StyleRaju, A. S. N., & Venkatesh, K. (2023). EnsemDeepCADx: Empowering Colorectal Cancer Diagnosis with Mixed-Dataset Features and Ensemble Fusion CNNs on Evidence-Based CKHK-22 Dataset. Bioengineering, 10(6), 738. https://doi.org/10.3390/bioengineering10060738