We proposed and implemented a disease detection and semantic segmentation pipeline using a modified mask-RCNN infrastructure model on the EDD2020 dataset1. On the images provided for the phase-I test dataset, for ’BE’, we achieved an average precision of 51.14%, for ’HGD’ and ’polyp’ it is 50%. However, the detection score for ’suspicious’ and ’cancer’ were low. For phase-I, we achieved a dice coefficient of 0.4562 and an F2 score of 0.4508. We noticed the missed and mis-classification was due to the imbalance between classes. Hence, we applied a selective and balanced augmentation stage in our architecture to provide more accurate detection and segmentation. We observed an increase in detection score to 0.29 on phase-II images after balancing the dataset from our phase-I detection score of 0.24. We achieved an improved semantic segmentation score of 0.62 from our phase-I score of 0.52

Gao, X.

Pang, W.

Rezvy, S.

Taylor, S.

Zebin, T.

English

Middlesex University Research Repository

TRANSFER LEARNING FOR ENDOSCOPY DISEASE DETECTION AND SEGMENTATIONWITH MASK-RCNN BENCHMARK ARCHITECTUREShahadate Rezvy1,4, Tahmina Zebin2, Barbara Braden3, Wei Pang4, Stephen Taylor5, Xiaohong W Gao11School of Science and Technology, Middlesex University London, UK2School of Computing Sciences, University of East Anglia, UK3Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, UK4School of Mathematical & Computer Sciences, Heriot-Watt University, UK5MRC Weatherall Institute of Molecular Medicine, University of Oxford, UKABSTRACTWe proposed and implemented a disease detection and se-mantic segmentation pipeline using a modified mask-RCNNinfrastructure model on the EDD2020 dataset1. On the im-ages provided for the phase-I test dataset, for ’BE’, weachieved an average precision of 51.14%, for ’HGD’ and’polyp’ it is 50%. However, the detection score for ’suspi-cious’ and ’cancer’ were low. For phase-I, we achieved a dicecoefficient of 0.4562 and an F2 score of 0.4508. We noticedthe missed and mis-classification was due to the imbalancebetween classes. Hence, we applied a selective and balancedaugmentation stage in our architecture to provide more accu-rate detection and segmentation. We observed an increase indetection score to 0.29 on phase -II images after balancing thedataset from our phase-I detection score of 0.24. We achievedan improved semantic segmentation score of 0.62 from ourphase-I score of 0.52.1. INTRODUCTIONEndoscopy is an extensively used clinical procedure for theearly detection of cancers in various organs such as esopha-gus, stomach, colon, and bladder [1]. In recent years, deeplearning methods were used in various endoscopic imag-ing tasks including esophago-gastro-duodenoscopy (EGD),colonoscopy, and capsule endoscopy (CE) [2]. Most of thesewere inspired by artificial neural network-based solutionsfor accurate and consistent localization and segmentation ofdiseased region-of-interests enable precise quantification andmapping of lesions from clinical endoscopy videos. This en-ables critical and useful detection techniques for monitoringand surgical planning.For oesophageal cancer detection, Mendel et al. [3] pro-posed an automatic approach for early detection of adenocar-1https://edd2020.grand-challenge.orgCopyright c©2020 for this paper by its authors. Use permitted underCreative Commons License Attribution 4.0 International (CC BY 4.0).cinoma in the esophagus by using high-definition endoscopicimages (50 cancer, 50 Barrett). They adapted and fed the dataset to a deep Convolutional Neural Network (CNN) using atransfer learning approach. The model was evaluated to leaveone patient out cross-validation. With sensitivity and speci-ficity of 0.94 and 0.88, respectively. Horie et al. [4] reportedAI diagnoses of esophageal cancer including squamous cellcarcinoma (ESCC) and adenocarcinoma (EAC) using CNNs.The CNN correctly detected esophageal cancer cases with asensitivity of 98%. CNN could detect all small cancer lesionsless than 10 mm in size. It has reportedly distinguished super-ficial esophageal cancer from advanced cancer with an accu-racy of 98%. Very recently, Gao et al. [5] investigated the fea-sibility of mask-RCNN (Region-based convolutional neuralnetwork) and YOLOv3 architectures to detect various stagesof squamous cell carcinoma (SCC) cancer in real-time to de-tect subtle appearance changes. For the detection of SCC, thereported average accuracy for classification and detection was85% and 74% respectively.For colonoscopy, deep neural networks based solutionswere implemented to detect and classify colorectal polypsin research presented by the authors in reference [6, 7, 8].For gastric cancer, Wu et al. [9] identified EGC from non-malignancy with an accuracy of 92.5%, a sensitivity of94.0%, a specificity of 91.0%, a positive predictive valueof 91.3%, and a negative predictive value of 93.8%, outper-forming all levels of endoscopists. In real-time unprocessedEGD videos, the DCNN achieved automated performance fordetecting EGC and monitoring blind spots. Mori et al. [10]and Min et al. [2] provided a comprehensive review of somerecent literature in this field.For Endoscopy Disease Detection and SegmentationGrand Challenge, we proposed and implemented a diseasedetection and semantic segmentation pipeline using a mod-ified mask-RCNN architecture. The rest of the paper isorganized as follows. Section 2 introduces the dataset forthe task. Section 3 presents our proposed architecture withvarious settings and procedural stages, with results presentedTable 1. Class-wise object distribution [1]Disease Category (Class name) ObjectsNon-dysplastic Barrett’s oesophagus (BE) 160Subtle pre-cancerous lesion (Suspicious) 88Suspected Dysplasia (HGD) 74Adenocarcinoma (Cancer) 53Polyp 127and discussed in Section 4. Finally, conclusions are drawn inSection 5.2. DATASET DESCRIPTION AND IMAGEAUGMENTATIONThe annotated dataset provided for the competition contained388 frames from 5 different international centers and 3 organs(colon, esophagus, and stomach) targeting multiple popula-tions and varied endoscopy video modalities associated withpre-malignant and diseased regions. The dataset is labeled bymedical experts and experienced post-doctoral researchers. Itcame with object-wise binary masks and bounding box an-notation. The class-wise object distribution in the dataset isshown in Table 1. A detailed description of the dataset can befound at [1].We separated a small subset from the original training setwith various class labels as our external validation set. Thissubset had 25 images, and was programmatically chosen tohave similar size and resolution as the images in phase-I testdataset of 24 images. This set with ground truth labels servedas a checkpoint for us to the trained model’s performance.We applied image augmentation techniques [11] on therest of the images with their associated masks. Our obser-vation of the dataset revealed a co-location of ’BE’ regionswith ’suspicious, cancer and HGD’ area. We also noticed animbalance between classes and images coming from variousorgans. Hence, we opted for an instance cropping stage in ourpipeline that produced multiple images from these co-locatedimages, each with one target object and other objects are re-moved by a selective cropping mechanism (example shownon Figure 1). We kept 10% padding around the ground truthbounding box provided for the instance. This isolated the in-stances of ’cancer’, ’suspicious’ and ’HGD’ regions from co-localized ’BE’ regions. We applied transformations such asrotation, flip and crop on the individual classes and instancesto increase our training data. We then used the ’WeightedRan-domSampler’ from the PyTorch data loader to form the fi-nal balanced training set of almost equal class representation.This set included 1670 instances in total. Figure 1 illustratessome of the augmentation methods we applied in our pipeline.3. METHODSWe implemented the Endoscopic disease detection and se-mantic segmentation pipeline for the EDD2020 challenge us-ing a modified mask-RCNN [12] architecture trained in thefeature-representation transfer learning mode. Mask-RCNNwas proposed as an extension of Faster R-CNN and the ar-chitecture has reportedly outperformed all the previous state-of-the-art models used for the instance segmentation task onvarious image datasets. We used PyTorch, torchvision, im-gaug, pycoco-creator, maskrcnn-benchmark [13], apex, andOpenCV libraries in python for generating various functionsof the pipeline.3.1. Pre-trained model backbone and network head re-movalWe removed the network head or the final layers of the pre-trained model with a Resnet-101 backbone [12] that was ini-tially trained on the COCO dataset. This stage is crucial asthe pre-trained model was trained for a different classificationtask. The removal of network head removed weights and biasassociated to class score, bounding box predictor and maskpredictor layers. It is then replaced with new untrained layerswith desired number of classes for the new data. We adjusteda six-class network head for the EDD2020 dataset (five as-signed classes+ Background). We fed the augmented datasetand and the associated masks into the mask-RCNN model ar-chitecture as illustrated in figure 2.3.2. Transfer learning stagesAt the initial stage, we froze the weights of the earlier layersof the pre-trained ResNet-101 backbone to help us extract thegeneric low-level descriptors or patterns from the endoscopyimage data. Later layers of the CNN become progressivelymore specific to the details of the output classes of the newdata-set. Then a newly added network head is trained foradapting the weights according to the patterns and distribu-tion of the new dataset. The network head is updated and finetuned during model training. The training of the model hasbeen done offline on an Ubuntu machine with Intel(R) Corei9-9900X CPU @ 3.50GHz, 62GB memory and a GeForceRTX 2060 GPU. The final model was fine- tuned with anAdam optimizer with a learning rate of 0.0001 and a categor-ical cross-entropy for 50000 epochs. To be noted, the datasetafter augmentation is still quite small, so we employed a five-fold cross-validation during training to avoid the over-fittingof the model.4. RESULTS AND EVALUATION SCOREEquations (1) to (3) in this section summarises the detectionand segmentation matrices we are using to evaluate the per-formance of a model trained on this dataset [1]. The metric,Fig. 1. Augmentation methods applied on the images including transformation such as rotation, flip and instance cropping.Fig. 2. Illustration of the mask-RCNN architecture adaptedfor transfer learning on the EDD datasetmean average precision (mAP) measures the ability of an ob-ject detector to accurately retrieve all instances of the groundtruth bounding boxes. The higher the mAP the better the per-formance. In Equation (1), N = 5 and APi indicates Averageprecision of individual disease class i for this dataset.mAP =1N∑iAPi (1)scored = 0.6×mAPd + 0.4× IoUd (2)scores = 0.25 ∗∑iprecision+ recall + F1 + F2 (3)For the detection task, the competition uses a a final meanscore (scored), which is a weighted score of mAP and IoUand formula is presented in Equation (2). Here, IoU - inter-section over union measures the overlap between the groundtruth and predicted bounding boxes. For scoring of the se-mantic segmentation task, an average measure (scores) is cal-culated as per Equation (3), which is the average score of F1-score (Dice Coefficient), F2-score, precision and recall. Adetail description of these matrices can be found in [1].Table 2. Validation set bounding-box detection and segmen-tation score before and after fine-tuningFine-tuningTask mAP AP (50), AP (75) AP (m), AP (l)No bbox 0.291 0.361; 0.319 0.450; 0.328No segment 0.254 0.347; 0.252 0.250; 0.292Yes bbox 0.479 0.689; 0.600 0.675; 0.493Yes segment 0.513 0.683; 0.549 0.563; 0.566Table 3. Out-of-sample detection and segmentation scoreTraining Dataset (Test data) scored scoresOriginal+ Flip, rotate,crop(Phase-I) 0.2460 0.5243Original+Instance-crop+class-balance(Phase-II) 0.2906 0.62644.1. Results on validation datasetTable 2 summarises average precision performances on theisolated validation dataset (25 images with ground-truthmasks) to get an estimate of the test set performance. Class-wise precision values were presented for two IoU thresholds.For AP (50), only candidates over 50% region comparingground truth were counted and we achieved about 36.1%average precision for bounding box detection and 34.7% av-erage precision for pixel-to-pixel segmentation. For AP (75),only the candidates over 75% IoU value are counted. Av-erage precision values were counted for large (AP (l)) andmedium-sized (AP (m)) objects in the images and the accu-racy ranged from 32.27% to 45% respectively. To be noted,we omitted AP (s) for small object (area < 32pixel2) due tothe absence of such small objects in the test dataset. However,such low values are indicative of the model being overfit andwe applied parameter-tuning to the fully connected networklayers along with realistic and balanced augmentation. Thissignificantly improved the mAP for for both bounding boxand segmentation mask to 47.9% and 51.3% respectively(shown in row 3 and 4 on Table 2).Fig. 3. Semantic segmentation results on some of the images from the test dataset4.2. Results on the test dataset: Phase-I and Phase-IIFor phase-I, we received 24 images and Figure 3 shows detec-tion and segmentation output from some of the images fromthis test set. From the scores available on the leaderboard,for ’BE’, we achieved average precision value of 51.14%, for’HGD’ and ’polyp’ it is 50%. However, the score for ’suspi-cious’ and ’cancer’ areas were very low. We attained a dicecoefficient of 0.4562 and an F2 score of 0.4508. We noticedthe missed and mis-classification was due to the imbalancebetween classes. Hence, before phase-II submission, weretrained the model after applying a ’WeightedRandomSam-pler’ for selective and balanced sampling of the augmenteddataset. During phase-II, we received 43 images and weretrained the model with a balanced augmentation dataset.From the leader-board scores available at this stage, the fi-nal detection score scored and semantic segmentation scorescores is listed in Table 3. In the table, we observed an in-crease in detection score to 0.29 when a class balancing andinstance cropping is applied on the training dataset. We hada score of 0.24 on phase-I which we obtained with genericaugmentation techniques applied on the data. We achieved animproved semantic segmentation score of 0.62 as well fromour phase-I score 0f 0.52. The final model had an standarddeviation of 0.082 in the mAPd value and deviation was 0.33in the semantic score.5. DISCUSSION & CONCLUSIONAs balanced augmentation has improved both detection andsegmentation score in this task, application of generative ad-versarial network-based augmentation techniques in futurecan contribute to a more generalised and robust model. Ad-ditionally, we assumed that the detected object was spreaduniformly across a detected region as the patch was classi-fied as a specific disease type (cancer, polyp) depending onthe patch-specific feature. However, the idea of one uniformregion of cancer or polyp or BE is not always the case inpractice. Very often, multifocal patches of cancer, low-gradeand high-grade dysplasia are scattered across the surface ofthe lesion. Further improvements are required to deal withbubble, saturation, instrument and other visible artefacts inthe dataset [14, 15]. This will improve the model’s perfor-mance by avoiding false detection in these regions and willprovide more accurate and realistic solution for endoscopicdisease detection cases.6. REFERENCES[1] Sharib Ali, Noha Ghatwary, Barbara Braden, Do-minique Lamarque, Adam Bailey, Stefano Realdon, Re-nato Cannizzaro, Jens Rittscher, Christian Daul, andJames East. Endoscopy disease detection challenge2020. arXiv preprint arXiv:2003.03376, 2020.[2] Jun Ki Min, Min Seob Kwak, and Jae Myung Cha.Overview of deep learning in gastrointestinal en-doscopy. Gut and liver, 13(4):388, 2019.[3] Robert Mendel, Alanna Ebigbo, Andreas Probst, et al.Barretts esophagus analysis using convolutional neu-ral networks. In Image Processing for Medicine 2017,pages 80–85. Springer, 2017.[4] Yoshimasa Horie, Toshiyuki Yoshio, KazuharuAoyama, Yoshimizu, et al. Diagnostic outcomes ofesophageal cancer by artificial intelligence using convo-lutional neural networks. Gastrointestinal endoscopy,89(1):25–32, 2019.[5] Xiaohong W Gao, Barbara Braden, Stephen Taylor, andWei Pang. Towards real-time detection of squamouspre-cancers from oesophageal endoscopic videos. In2019 18th IEEE International Conference On MachineLearning And Applications (ICMLA), pages 1606–1612,Dec 2019.[6] Yoriaki Komeda, Hisashi Handa, et al. Computer-aideddiagnosis based on convolutional neural network systemfor colorectal polyp classification: preliminary experi-ence. Oncology, 93:30–34, 2017.[7] Teng Zhou, Guoqiang Han, Bing Nan Li, et al. Quan-titative analysis of patients with celiac disease by videocapsule endoscopy: A deep learning method. Comput-ers in biology and medicine, 85:1–6, 2017.[8] Lequan Yu, Hao Chen, Qi Dou, Jing Qin, andPheng Ann Heng. Integrating online and offline three-dimensional deep learning for automated polyp detec-tion in colonoscopy videos. IEEE journal of biomedicaland health informatics, 21(1):65–75, 2016.[9] Lianlian Wu, Wei Zhou, Xinyue Wan, Jun Zhang, et al.A deep neural network improves endoscopic detectionof early gastric cancer without blind spots. Endoscopy,51(06):522–531, 2019.[10] Yuichi Mori, Tyler M Berzin, and Shin-ei Kudo. Ar-tificial intelligence for early gastric cancer: earlypromise and the path ahead. Gastrointestinal endoscopy,89(4):816–817, 2019.[11] Connor Shorten and Taghi M Khoshgoftaar. A surveyon image data augmentation for deep learning. Journalof Big Data, 6(1):60, 2019.[12] Kaiming He, Georgia Gkioxari, Piotr Dollár, and RossGirshick. Mask r-cnn. In Proceedings of the IEEE in-ternational conference on computer vision, pages 2961–2969, 2017.[13] Francisco Massa and Ross Girshick. maskrcnn-benchmark: Fast, modular reference im-plementation of Instance Segmentation andObject Detection algorithms in PyTorch.https://github.com/facebookresearch/maskrcnn-benchmark, 2018.[14] Sharib Ali, Felix Zhou, Christian Daul, Barbara Braden,Adam Bailey, Stefano Realdon, James East, GeorgesWagnieres, Victor Loschenov, Enrico Grisan, et al. En-doscopy artifact detection (ead 2019) challenge dataset.arXiv preprint arXiv:1905.03209, 2019.[15] Sharib Ali, Felix Zhou, Barbara Braden, Adam Bai-ley, Suhui Yang, Guanju Cheng, Pengyi Zhang, Xiao-qiong Li, Maxime Kayser, Roger D. Soberanis-Mukul,Shadi Albarqouni, Xiaokang Wang, Chunqing Wang,Seiryo Watanabe, Ilkay Oksuz, Qingtian Ning, Shu-fan Yang, Mohammad Azam Khan, Xiaohong W. Gao,Stefano Realdon, Maxim Loshchenov, Julia A. Schn-abel, James E. East, Geroges Wagnieres, Victor B.Loschenov, Enrico Grisan, Christian Daul, Walter Blon-del, and Jens Rittscher. An objective comparison of de-tection and segmentation algorithms for artefacts in clin-ical endoscopy. Scientific Reports, 10, 2020.

Transfer learning for endoscopy disease detection and segmentation with mask-RCNN benchmark architecture

https://repository.mdx.ac.uk/download/f148ad257a2a94b7953cd074e10b8f6808169e0ab52c8b4758eb3d8b1d05c915/2218503/endoCV2020_paper_id_17.pdf

Transfer learning for endoscopy disease detection and segmentation with mask-RCNN benchmark architecture

Abstract

Similar works

Full text

Available Versions

Middlesex University Research Repository