Detection and Classification of Colorectal Polyp Using Deep Learning.

Colorectal Cancer (CRC) is the third most dangerous cancer in the world and also increasing day by day. So, timely and accurate diagnosis is required to save the life of patients. Cancer grows from polyps which can be either cancerous or noncancerous. So, if the cancerous polyps are detected accurately and removed on time, then the dangerous consequences of cancer can be reduced to a large extent. The colonoscopy is used to detect the presence of colorectal polyps. However, manual examinations performed by experts are prone to various errors. Therefore, some researchers have utilized machine and deep learning-based models to automate the diagnosis process. However, existing models suffer from overfitting and gradient vanishing problems. To overcome these problems, a convolutional neural network- (CNN-) based deep learning model is proposed. Initially, guided image filter and dynamic histogram equalization approaches are used to filter and enhance the colonoscopy images. Thereafter, Single Shot MultiBox Detector (SSD) is used to efficiently detect and classify colorectal polyps from colonoscopy images. Finally, fully connected layers with dropouts are used to classify the polyp classes. Extensive experimental results on benchmark dataset show that the proposed model achieves significantly better results than the competitive models. The proposed model can detect and classify colorectal polyps from the colonoscopy images with 92% accuracy.

1. Introduction

Colorectal Cancer (CRC) is one of the most dangerous cancers in the world and is the third most cause of death in India and the fourth cause of cancer deaths in the world [1-3]. It has been found that 85% of colorectal cases grow from adenomas because of genetic or epigenetic reasons. It can be reduced by endoscopic resection of colorectal polyps [4, 5]. According to pathology, the polyps are categorized into four major categories, namely, adenoma, sessile serrated adenoma/polyp (SSAP), and hyperplastic which include inflammation and juvenile polyps. Each of these categories has a different risk of developing cancer [4, 6]. The adenoma and SSAP polyps have a very high possibility of converting into cancer. On the other hand, hyperplastic polyps are less likely to develop into cancer [6, 7]. According to the Preservation and Incorporation of Valuable Endoscopic Innovation (PIVI) strategy, the polyps having a size less than 5 mm after resection can be omitted [8, 9]. Also, the hyperplastic polyps in the colon and rectum do not require sampling or endoscopic resection as they are nonmalignant [9]. Hence, the accurate classification of polyps can save a lot of risks, resources, and efforts of the patients and medical authorities [10, 11].

Although colorectal cancer is very dangerous, it takes a very large time to convert into cancer. So, it should be detected and removed before the time it converts into cancer. The most common test used these days for the detection of cancer is colonoscopy. In 2012, an updated guideline regarding colorectal cancer was issued by the US Multisociety Task Force by colonoscopy screening which had key features like risk assessment and a follow-up that was based on recommendation according to the histopathology findings of polyps [12]. Hence, detection and classification of polyps is an important task in colorectal cancer screening by which the malignant polyps can be differentiated from low-risk polyps [13]. This categorization of polyps helps in reducing the risk of developing the polyp and timing of the follow-up to be taken. But the correct characterization of a polyp can be a difficult task as there exists a large variability in the techniques by which the pathologists classify the polyps [14-18]. The sessile serrated polyp can convert into colorectal polyp faster as compared to the other polyps as they find the serrated way in tumorigenesis. Hence, it is required to differentiate between sessile serrated polyps and other types of polyps for appropriate treatment.

According to recent research, deep learning has given very good results in the area of speech recognition, object detection, and computer vision [19]. It has overcome the human potential in playing games and recognition tasks [20]. In medical imaging, deep learning has also provided promising results. The tasks like detection, recognition, and classification in medical images have become easier [21]. Automated diagnosis systems of endoscopic images are interpreted by an AI system with higher accuracy than a trained expert or specialist [22]. Reports show that the longer the time devoted to endoscopy, the lesser is the rate of detection of adenoma polyp being fatigue. Therefore, automated detection systems need to develop that are more reliable and fast [23, 24].

A lot of research has been done in the diagnosis and classification of colorectal polyps. But most of those studies talk about computer-aided diagnosis systems that are helpful only in either detection or classification [25-29]. A system that can do both detection and classification will be very useful. It can also have a large number of applications in the real world. By motivating from this, we have proposed a deep learning-based technique for detection and classification of colorectal polyps in this paper. The main contributions of this paper are as follows:

To overcome overfitting and gradient vanishing problems, a convolutional neural network- (CNN-) based deep learning model is proposed

Guided image filter and dynamic histogram equalization approaches are used to filter and enhance the colonoscopy images

Single Shot MultiBox Detector (SSD) is used to efficiently detect and classify colorectal polyps from colonoscopy images

Finally, fully connected layers with dropouts are used to classify the polyp classes

The remaining paper is organized as follows: Section 2 presents the related work. Section 3 discusses the proposed methodology. Section 4 presents the results and discussion. The concluding remarks and future scope are outlined in Section 5.

2. Literature Survey

A technique discussed in [30] can detect and localize Crohn's disease affected areas in the abdomen automatically. In this, texture anisotropy, intensity statistics, and shape asymmetry of 3D region features were used to differentiate the damaged areas from healthy areas. In [31], a similar approach was presented by using feature texture and intensity. In [32], contrast enhancement was used to find colitis in tomography scans. In [33], Crohn's disease was detected using a neurofuzzy logic-based technique. The neurofuzzy model was combined with a neural network–fuzzy classifier to perform tests on different levels of fuzzy partition. They also used factor analysis for dimensionality reduction.

In [34], three machine learning models were utilized for classification. The first model worked on endoscopic image data and provided 71% classification accuracy. The second model used histological data and provided an accuracy of 76.9%. The third model used both types of data and gave a classification accuracy of around 81.6%. In [35], two different diseases namely Crohn's disease and ulcerative colitis were classified with the help of genes and calculating individualized pathways. In [36], deep transfer learning, deep convolutional neural network (CNN), and global features were used to differentiate among various diseases. They also created a group of data named “KVASIR”. In [37], a CNN and endoscopic domain knowledge were used to classify the seriousness of ulcerative colitis. [38] utilized deep CNN to classify the depth of ulcerative colitis. In [39], GoogLeNet architecture was used to find the depth of ulcerative colitis. In [40], a computer-aided diagnosis system was implemented for predicting the intensity of ulcerative colitis.

In [41], a filter bank-based technique was applied for the classification of CRC polyps. Filter-bank used filter masks for classifying different polyps [42]. In [43], a local binary pattern variant was used for the automatic classification of endoscopic images. The similarity among neighboring pixels was utilized to create a color vector field. A kNN classifier was used for classification. [44] used a wavelet transform for feature extraction and proposed three different approaches that can automatically classify colonic polyps. In [45], local features for detection and support vector machine (SVM) for classification were utilized. In [46], monogenic local binary pattern combined with Gabor filter was used to generate a new feature. The new feature was able to extract shape and edge details at multiresolution and prevented the color information. The use of linear discriminant analysis was made for reducing features. In [47], the features were extracted using segmentation techniques and further utilized for classification. CNN has reduced the use of handcrafted features for the extraction of features and classification [48].

In [49-51], different techniques were used like deep learning, feature analysis, and information retrieval for polyp classification, detection, and colonic polyp localization. In [52], texture classification and deep learning were used for the classification of gastrointestinal diseases. In [53], deep CNN was used to detect colonic polyp. It was capable of detecting all the polyps that were confirmed by radiologists. In [54], three CNN architectures and an SVM classifier were used to classify celiac disease from the colonic polyp. This approach was able to get better results than other CNN-based approaches by combining and concatenating the results obtained from different layers.

3. Methodology

3.1. Data Used for Training and Validation

The dataset used is available online for free at http://www.virtualpathology.leeds.ac.uk/. The dataset contains whole slide images (WSI). It is available online and does not provide any information about the patients. We had taken a total of 27508 images from the dataset. We divided those images into two sets as training and test datasets. Among the training, the dataset had 16418 images of the histologically proven polyp and 4013 images of the colorectal mucosa. The images that were observed under white light imaging (WLI) or narrow-band imaging (NBI) were utilized. To train the CNN, we took 15,418 images among which 3254 images were histologically proven polyps of 3001 patients and 4001 images of normal colorectal mucosa of 356 patients. In test data, we had a total of 7077 images of 174 patients having 1172 regions containing colorectal polyp. The malignancy present in the images was proven histologically. The images having feces and improper insufflations were also taken to track the performance of the trained model. The images were seen under normal white light. The description of the dataset is given in Table 1.

Table 1

Description of the dataset.

Training dataset
Type of polyp		Polyps	White light images	Narrow band images	Total images
Ad		3413	9310	2085	11395
Hp		1058	2002	519	2521
SS		22	116	23	139
Cn		68	1468	131	1599
O		91	657	107	764
Normal			4013	0	4013
Total		4752	17566	2865	20431
Validation set
Ad n = 217	≤5 mm	156	639	208	847
	6-9 mm	52
	>10 mm	10
Hp n = 63	≤5 mm	56	145	69	214
	6-9 mm	7
	>10 mm	0
SS n = 7	≤5 mm	0	33	8	41
	6-9 mm	4
	>10 mm	3
Cn (all ≥ 10 mm)		4	30	3	33
O (all ≤ 5 mm)		17	27	10	37
Normal			5874	31	5905
Total		309	6748	329	7077

3.2. Algorithm

A Single Shot MultiBox Detector (SSD) is used for implementing the detection and classification of colorectal polyps. No changes are made in the algorithm of SSD. It is a deep neural network that has 5 or more layers. One more CNN named Caffe deep learning framework is used for training and validating purposes. The size of the images is changed to 300 × 300 pixels and the bounding box is also resized according to the images. All the values are set by the hit and trial method to make the data SSD compatible. With the help of a specialist, the images are annotated. The colorectal polyp present in the image is put in a rectangular box and added to the training set.

Figure 1 shows the diagrammatic flow of the proposed Single Shot MultiBox Detector- (SSD-) based model. The trained CNN also puts a rectangular shape around the region of interest and names them as CNN boxes and the output class is numbered from 0 to 1 to classify the image. For preprocessing, guided image filter and dynamic histogram equalization techniques are utilized.

Figure 1

Diagrammatic flow of the proposed Single Shot MultiBox Detector- (SSD-)based model.

The mathematical description of the proposed methodology is as follows:

Here, L represents the number of layers, where i = 1, ⋯, 5. L represents the jth layer in the ith group F represents the filter corresponding to L

3.3. Experimental Outcomes

The images in the validation data were also annotated by making rectangular boxes around a colorectal polyp. The trained system was able to shape the region of interest with rectangular boundaries and gave the output in the form of 0 and 1, which showed the probability to which the region of interest belongs. Based on the probability, the confidence gained by CNN is calculated. If the probability score is higher, then more will be the confidence to include the region of interest to a class of colorectal polyp. To check the outcome, the following cases are considered.

If the overlapping between the CNN and the true region of the colorectal polyp was more than 80%, then the detection was considered correct

If two boxes were found on a single region of interest, then the one with a higher probability score is considered

Similarly, for evaluating the classification performance, all the images detected as colorectal polyp were also analyzed [55].

In Table 1, Ad, Hp, SS, Cn, and O denote adenoma, hyperplastic, SSAP, cancer, and others, respectively.

4. Experimental Results

4.1. Relation between Probability Score and Sensitivity

The relation between the cut-off value and sensitivity is shown in Figure 2. Finally, 0.3 was taken as the optimal value for the probability score. The convolutional neural network considered only those regions of interest a colorectal polyp that had a probability score greater than or equal to 0.3.

Figure 2

The relation between the probability score cut-off values and Positive predictive value (PPV).

4.2. Outputs of the CNN

The trained network was able to perform diagnosis in colonoscopy images at the rate of 47.1 images/second which is equivalent to 21 ms for each frame. The neural network was able to correctly identify the colorectal polyps as depicted in Figures 3(a) and 3(b). In some cases, it gave false-positive results in which it identified the polyp but actually there was no polyp (see Figures 3(c) and 3(d)). Figures 3(e) and 3(f) show the false negative cases in which wrong classification made by the network, although it correctly identified the polyp but missed the correct type. To check the detection performance, we checked for the correct detection instead of correct classifications. The network was able to correctly detect a total of 1073 polyps among 1172 polyps with a sensitivity of 91% and PPV of 85%. In the data, there was more than one image of each polyp and the network was able to detect 304 out of 309 polyps among the test set in at least one image. By considering only WLI images, the trained network showed 89% sensitivity and 82% PPV for the detection task. For narrow band images, it showed sensitivity and PPV as 96%, but less images were considered in this category.

Figure 3

Polyp classification analyses: (a and b) Correctly classified, (c and d) False positive results, and (e and f) False negatives.

4.3. Evaluation of False Results

To enhance the performance of the network, it is important to check the missed polyps. Therefore, all the false positives and false negatives are categorized into several categories. The false negatives are divided into three categories (as shown in Figure 4).

Figure 4

Misclassified analyses: Green boxes represent actual polyp and white boxes represent the area obtained from the proposed model. Complete green indicates nothing is detected. White area represents nothing was there but the proposed model classified to adenoma polyp.

Those whose pattern is difficult to identify due to their small size or nonvisibility of light

The images that are not captured properly or are lateral or partial

The very large images

In total, there were 173 false positives, around 69 (i.e., 40%) were normal that can be easily identified by the endoscopists, most of them were the ileocecal valves. 32% regions were colorectal folds that were around 56 false-positive regions and most of them did not have sufficient insufflations. 20% images became abnormal because of haze, feces, blur lens, halation, etc. So, these can be easily distinguished from the colorectal polyps. The remaining 8% looked like colorectal polyps but their confirmation was not available.

Table 2 shows the confusion matrix analyses for white light and narrow band images. It shows that the trained network classifies 82% colorectal polyps correctly. It also classifies the adenomas with 96% accuracy along with 85% PPV and 84% NPV when observed in white light images. For hyperplastic classification, the network achieves only 46% correct results along with 63% PPV and 89% NPV. The network classified sessile serrated adenomas/polyps as an adenoma with 27% accuracy.

Table 2

CNN classification % for white light images and narrow band images.

		Ad	Hp	SS	Cn	O
White light images
True histology	Ad	562	14	0	4	2
	Hp	64	59	0	0	2
	SS	6	12	5	0	0
	Cn	6	0	0	23	0
	O	14	7	0	0	3
Narrow band images
True histology	Ad	197	5	0	1	0
	Hp	31	37	0	0	0
	SS	2	4	0	0	0
	Cn	3	0	0	0	0
	O	3	7	0	0	0

Around 80% of colorectal polyps in narrow band images are classified correctly with 96% sensitivity along with 82% PPV and 90% NPV, the NBI images available were less in number. The performance is also measured for colorectal polyps which are less than 5 mm in size. The network is able to correctly classify 348 out of 356 adenoma images with 80% PPV rate and 88% NPV rate in WLI. For hyperplastic, the classification performance is moderate having 50% sensitivity, 85% PPV, and 89% NPV, as the number of images was limited. In NBI, the network is able to correctly classify 138 among 142 adenoma images with an accuracy of 97%, PPV of 84%, and NPV of 88% (see Table 3).

Table 3

CNN classification % for diminutive polyps.

		Ad	Hp	O
White light images	Ad	348	8	0
	Hp	49	50	1
	O	14	7	3
Narrow band images	Ad	138	4	0
	Hp	24	22	0
	O	3	7	0

Ad: adenoma; Hp: hyperplastic; SS: SSAP; Cn: cancer; O: others.

In this study, the detection and classification of colorectal polyps have been demonstrated. We have trained a CNN on our dataset and it has provided a considerable accuracy and good speed even with small polyps which might get overlooked in colonoscopy. The trained CNN also showed a good performance in detecting colorectal polyps which can help both patients and physicians from unnecessary treatments. For feature extraction, we have used SSD for detecting and classifying colorectal polyps [24, 56]. It can encapsulate the processes into a single network and hence save the time. The trained networks classify adenomas with a sensitivity of 96% and accuracy of 86% in white light images, which is better than the existing models.

5. Conclusion and Future Scope

From extensive review, it was found that the existing models suffer from overfitting and gradient vanishing problems. To overcome these problems, a convolutional neural network- (CNN-) based deep learning model was proposed to efficiently detect and classify colorectal polyps from colonoscopy images. Initially, guided image filter and dynamic histogram equalization approaches were used to filter and enhance the colonoscopy images. Thereafter, Single Shot MultiBox Detector (SSD) was used to efficiently detect and classify colorectal polyps from colonoscopy images. Finally, fully connected layers with dropouts were used to classify the polyp classes. We have trained the proposed model on benchmark dataset and it has achieved better results with good computational speed even with small polyps which might get overlooked in colonoscopy. The trained proposed model achieved a good performance in detecting colorectal polyps which can help both patients and physicians from unnecessary treatments. For feature extraction, SSD was used for detecting and classifying colorectal polyps. Extensive experimental results revealed that the proposed model achieves significantly better results than the competitive models. The proposed model detected and classified colorectal polyps from the colonoscopy images with 92% accuracy.