@article {27774,
	title = {A comprehensive analysis of classification methods in gastrointestinal endoscopy imaging},
	journal = {Medical Image Analysis},
	volume = {70},
	year = {2021},
	pages = {102007},
	publisher = {Elsevier},
	abstract = {Gastrointestinal endoscopy has\&nbsp;been\&nbsp;an\&nbsp;active field\&nbsp;of research motivated by the large number of highly lethal GI cancers. Early GI cancer precursors are often missed during the endoscopic surveillance. \&nbsp; The high missed rate of such abnormalities during endoscopy is thus a\&nbsp; critical bottleneck. Lack of attentiveness due to tiring procedures, and requirement of training are few contributing factors. An automatic\&nbsp; GI\&nbsp; disease classification system can help reduce such risks by flagging suspicious frames and lesions. GI endoscopy consists of several multi-organ surveillance, therefore, there is need to develop methods that can generalize to various endoscopic findings. In this realm, we present a comprehensive analysis of the\&nbsp; Medico\&nbsp; GI\&nbsp; challenges:\&nbsp; Medical\&nbsp; Multimedia Task at MediaEval 2017, Medico Multimedia Task at MediaEval 2018,\&nbsp; and\&nbsp; BioMedia\&nbsp; ACM\&nbsp; MM\&nbsp; Grand\&nbsp; Challenge\&nbsp; 2019.\&nbsp; These challenges are initiative to set-up\&nbsp; a\&nbsp; benchmark for different computer vision methods applied to the multi-class endoscopic images and promote to build new approaches that could reliably be used in clinics. We report the performance of 21 participating teams over a\&nbsp; period of three consecutive years and provide a\&nbsp; detailed analysis of the methods used by the participants, highlighting the challenges and shortcomings of the current approaches and dissect their credibility for the use in clinical settings.\&nbsp; Our analysis revealed that the participants achieved an improvement on maximum\&nbsp; Mathew correlation coefficient\&nbsp; (MCC)\&nbsp; from\&nbsp; 82.68\%\&nbsp; in\&nbsp; 2017\&nbsp; to\&nbsp; 93.98\%\&nbsp; in\&nbsp; 2018\&nbsp; and 95.20\% in 2019 challenges, and a significant increase in computational speed over consecutive years.},
	keywords = {Artificial intelligence, BioMedia 2019 Grand Challenge, Computer-aided detection and diagnosis, Gastrointestinal endoscopy challenges, Medical imaging, Medico Task 2017, Medico Task 2018},
	doi = {https://doi.org/10.1016/j.media.2021.102007},
	author = {Jha, Debesh and Ali, Sharib and Hicks, Steven and Thambawita, Vajira and Borgli, Hanna and Pia H. {Smedsrud} and de Lange, Thomas and Pogorelov, Konstantin and Wang, Xiaowei and Harzig, Philipp and Tran, Minh-Triet and Meng, Wenhua and Hoang, Trung-Hieu and Dias, Danielle and Tobey H. {Ko} and Agrawal, Taruna and Ostroukhova, Olga and Khan, Zeshan and Muhammad Atif {Tahir} and Liu, Yang and Chang, Yuan and Kirker{\o}d, Mathias and Johansen, Dag and Lux, Mathias and H{\r a}vard D. {Johansen} and Riegler, Michael and Halvorsen, P{\r a}l}
}
@article {27640,
	title = {A Comprehensive Study on Colorectal Polyp Segmentation with ResUNet++, Conditional Random Field and Test-Time Augmentation},
	journal = {IEEE Journal of Biomedical and Health Informatics},
	volume = {25},
	year = {2021},
	pages = {2029 - 2040},
	publisher = { IEEE},
	abstract = {Colonoscopy is considered the gold standard for detection of colorectal cancer and its precursors. Existing examination methods are, however, hampered by high overall miss-rate, and many abnormalities are left undetected. Computer-Aided Diagnosis systems based on advanced machine learning algorithms are touted as a game-changer that can identify regions in the colon overlooked by the physicians during endoscopic examinations, and help detect and characterize lesions. In previous work, we have proposed the ResUNet++ architecture and demonstrated that it produces more efficient results compared with its counterparts U-Net and ResUNet. In this paper, we demonstrate that further improvements to the overall prediction performance of the ResUNet++ architecture can be achieved by using Conditional Random Field (CRF) and Test-Time Augmentation (TTA). We have performed extensive evaluations and validated the improvements using six publicly available datasets: Kvasir-SEG, CVC-ClinicDB, CVC-ColonDB, ETIS-Larib PolypDB, ASU-Mayo Clinic Colonoscopy Video Database, and CVC-VideoClinicDB. Moreover, we compare our proposed architecture and resulting model with other State-of-the-art methods. To explore the generalization capability of ResUNet++ on different publicly available polyp datasets, so that it could be used in a real-world setting, we performed an extensive cross-dataset evaluation. The experimental results show that applying CRF andTTA improves the performance on various polyp segmentation datasets both on the same dataset and cross-dataset. To check the model{\textquoteright}s performance on difficult to detect polyps, we selected, with the help of an expert gastroenterologist,196sessile or flat polyps that are less than ten millimeters in size. This additional data has been made available as a subset of Kvasir-SEG. Our approaches showed good results for flat or sessile and smaller polyps, which are known to be one of the major reasons for high polyp miss-rates. This is one of the significant strengths of our work and indicates that our methods should be investigated further for use in clinical practice.},
	keywords = {colonoscopy, conditional random field, generalization, Polyp segmentation, ResUNet++, test-time augmentation},
	doi = {10.1109/JBHI.2021.3049304},
	author = {Jha, Debesh and Pia H. {Smedsrud} and Johansen, Dag and de Lange, Thomas and H{\r a}vard D. {Johansen} and Halvorsen, P{\r a}l and Riegler, Michael}
}
@inproceedings {27635,
	title = {DDANet: Dual Decoder Attention Network for Automatic Polyp Segmentation},
	journal = {25th International Conference on Pattern Recognition},
	year = {2021},
	pages = {307-314},
	publisher = { Springer},
	abstract = {Colonoscopy is the gold standard for examination and detection of colorectal polyps. Localization and delineation of polyps can play a vital role in treatment (e.g., surgical planning) and prognostic decision making. Polyp segmentation can provide detailed boundary information for clinical analysis. Convolutional neural networks have improved the performance in colonoscopy. However, polyps usually possess various challenges, such as intra-and inter-class variation and noise. While manual labeling for polyp assessment requires time from experts and is prone to human error (e.g., missed lesions), an automated, accurate, and fast segmentation can improve the quality of delineated lesion boundaries and reduce missed rate. The Endotect challenge provides an opportunity to benchmark computer vision methods by training on the publicly available Hyperkvasir and testing on a separate unseen dataset. In this paper, we propose a novel architecture called {\textquoteleft}{\textquoteleft}DDANet{\textquoteright}{\textquoteright} based on a dual decoder attention network. Our experiments demonstrate that the model trained on the Kvasir-SEG dataset and tested on an unseen dataset achieves a dice coefficient of 0.7874, mIoU of 0.7010, recall of 0.7987, and a precision of 0.8577, demonstrating the generalization ability of our model.},
	keywords = {Benchmarking, Convolutional neural network, deep learning, Polyp segmentation},
	author = {Nikhil Kumar {Tomar} and Jha, Debesh and Ali, Sharib and H{\r a}vard D. {Johansen} and Johansen, Dag and Riegler, Michael and Halvorsen, P{\r a}l}
}
@inproceedings {27834,
	title = {DeepSynthBody: the beginning of the end for data deficiency in medicine},
	journal = {The International Conference on Applied Artificial Intelligence (ICAPAI)},
	year = {2021},
	publisher = {IEEE},
	abstract = {Limited access to medical data is a barrier on developing new and efficient machine learning solutions in medicine such as computer-aided diagnosis, risk assessments, predicting optimal treatments and home-based personal healthcare systems. This paper presents DeepSynthBody: a novel framework that overcomes some of the inherent restrictions and limitations of medical data by using deep generative adversarial networks to produce synthetic data with characteristics similar to the real data, so-called DeepSynth (deep synthetic) data. We show that DeepSynthBody can address two key issues commonly associated with medical data, namely privacy concerns (as a result of data protection rules and regulations) and the high costs of annotations. To demonstrate the full pipeline of applying DeepSynthBody concepts and user-friendly functionalities, we also describe a synthetic medical dataset generated and published using our framework. DeepSynthBody opens a new era of machine learning applications in medicine with a synthetic model of the human body.},
	doi = {10.1109/ICAPAI49758.2021.9462062},
	author = {Thambawita, Vajira and Hicks, Steven and Isaksen, Jonas and Mette Haug {Stensen} and Trine B {Haugen} and Kanters, J{\o}rgen and Parasa, Sravanthi and de Lange, Thomas and H{\r a}vard D. {Johansen} and Johansen, Dag and Hugo Lewi {Hammer} and Halvorsen, P{\r a}l and Riegler, Michael}
}
@inproceedings {27511,
	title = {Kvasir-Instrument: Diagnostic and therapeutic tool segmentation dataset in gastrointestinal endoscopy},
	journal = {27th International Conference on Multimedia Modeling},
	volume = {LNCS, volume 12573},
	year = {2021},
	pages = {218-229},
	publisher = {Springer},
	abstract = {Gastrointestinal (GI) pathologies are periodically screened, biopsied, and resected using surgical tools. Usually the procedures and the treated or resected areas are not specifically tracked or analysed during or after colonoscopies. Information regarding disease borders, development and amount and size of the resected area get lost. This can lead to poor follow-up and bothersome reassessment difficulties post-treatment. To improve the current standard and also to foster more research on the topic we have released the\&nbsp; {\textquoteleft}{\textquoteleft}Kvasir Instrument{\textquoteright}{\textquoteright} dataset which consists of $590$ annotated frames containing GI procedure tools such as snares, balloons and biopsy forceps, etc. Beside of the images, the dataset includes ground truth masks and bounding boxes and has been verified by two expert GI endoscopists. Additionally, we provide a baseline for the segmentation of the GI tools to promote research and algorithm development. We obtained a dice coefficient score of 0.9158 and a Jaccard index of 0.8578 using a classical U-Net architecture. A similar dice coefficient score was observed for DoubleUNet. The qualitative results showed that the model did not work for the images with specularity and the frames with multiple instruments, while the best result for both methods was observed on all other types of images. Both, qualitative and quantitative results show that the model performs reasonably good, but there is a large potential for further improvements.\&nbsp; Benchmarking using the dataset provides an opportunity for researchers to contribute to the field of automatic endoscopic diagnostic and therapeutic tool segmentation for GI endoscopy.\&nbsp;},
	author = {Jha, Debesh and Ali, Sharib and Emanuelsen, Krister and Hicks, Steven and Thambawita, Vajira and Garcia-Ceja, Enrique and Riegler, Michael and de Lange, Thomas and Peter T. {Schmidt} and H{\r a}vard D. {Johansen} and Johansen, Dag and Halvorsen, P{\r a}l}
}
@inproceedings {26811,
	title = {Kvasir-SEG: A Segmented Polyp Dataset},
	journal = {International Conference on Multimedia Modeling},
	year = {2020},
	pages = {451-462},
	publisher = {Springer},
	address = {Daejeon, Korea},
	abstract = {Pixel-wise image segmentation is a highly demanding task in medical image analysis. In practice, it is difficult to find annotated medical images with corresponding segmentation masks. In this paper, we present\&nbsp; Kvasir-SEG: an open-access dataset of gastrointestinal polyp images and corresponding segmentation masks, manually annotated and verified by an experienced gastroenterologist. We demonstrate the use of our dataset with a traditional segmentation approach and a modern deep learning based CNN approach. This work will be valuable for researchers to reproduce results and compare their methods in the future.\&nbsp;By adding segmentation masks to the Kvasir dataset, which until today only consisted of framewise annotations, we enable multimedia and computer vision researchers to contribute in the field of polyp segmentation and automatic analysis of colonoscopy videos.\&nbsp;\&nbsp;},
	keywords = {Kvasir-SEG dataset, Medical images, Polyp segmentation, ResUNet  Fuzzy c-mean clustering, Semantic segmentation},
	author = {Jha, Debesh and Pia H. {Smedsrud} and Riegler, Michael and Halvorsen, P{\r a}l and H{\r a}vard D. {Johansen} and de Lange, Thomas and Johansen, Dag}
}
@inproceedings {27639,
	title = {LightLayers: Parameter Efficient Dense and Convolutional Layers for Image Classification},
	journal = {The Joint International Conference PDCAT-PAAP 2020},
	year = {2020},
	publisher = { Springer},
	abstract = {Deep Neural Networks (DNNs) have become the de-facto standard in computer vision, as well as in many other pattern recognition tasks. A key drawback of DNNs is that the training phase can be very computationally expensive. Organizations or individuals that cannot afford purchasing state-of-the-art hardware or tapping into cloud-hosted infrastructures may face a long waiting time before the training completes or might not be able to train a model at all. Investigating novel ways to reduce the training time could be a potential solution to alleviate this drawback, and thus enabling more rapid development of new algorithms and models. In this paper, we propose LightLayers, a method for reducing the number of trainable parameters in deep neural networks (DNN). The proposed LightLayers consists of LightDense andLightConv2D layer that are as efficient as regular Conv2D and Dense layers, but uses less parameters. We resort to Matrix Factorization to reduce the complexity of the DNN models resulting into lightweight DNNmodels that require less computational power, without much loss in the accuracy. We have tested LightLayers on MNIST, Fashion MNIST, CI-FAR 10, and CIFAR 100 datasets. Promising results are obtained for MNIST, Fashion MNIST, CIFAR-10 datasets whereas CIFAR 100 shows acceptable performance by using fewer parameters.},
	keywords = {CIFAR-10, Convolutional  neural network, Deep  Learning, Fashion MNIST, Lightweight  model, MNIST, Weight decomposition},
	author = {Jha, Debesh and Yazidi, Anis and Riegler, Michael and Johansen, Dag and H{\r a}vard D. {Johansen} and Halvorsen, P{\r a}l}
}
@inproceedings {27637,
	title = {Medico Multimedia Task at MediaEval 2020: Automatic Polyp Segmentation},
	journal = {Medico MediaEval 2020},
	year = {2020},
	publisher = {CEUR},
	abstract = {Colorectal cancer is the third most common cause of cancer worldwide. According to Global cancer statistics 2018, the incidence of colorectal cancer is increasing in both developing and developed countries. Early detection of colon anomalies such as polyps is important for cancer prevention, and automatic polyp segmentation can play a crucial role for this. Regardless of the recent advancement in early detection and treatment options, the estimated polyp miss rate is still around 20\%. Support via an automated computer-aided diagnosis system could be one of the potential solutions for the overlooked polyps. Such detection systems can help low-cost design solutions and save doctors time, which they could for example use to perform more patient examinations. In this paper, we introduce the 2020 Medico challenge, provide some information on related work and the dataset, describe the task and evaluation metrics, and discuss the necessity of organizing the Medico challenge.},
	author = {Jha, Debesh and Hicks, Steven and Emanuelsen, Krister and H{\r a}vard D. {Johansen} and Johansen, Dag and de Lange, Thomas and Riegler, Michael and Halvorsen, P{\r a}l}
}
@inproceedings {26205,
	title = {The Medico-Task 2018: Disease Detection in the Gastrointestinal Tract using Global Features and Deep Learning},
	journal = {MediaEval 2018},
	year = {2018},
	month = {10/2018},
	publisher = {MediaEval},
	address = {Nice, France},
	abstract = {In this paper, we present our approach for the 2018 Medico Task classifying diseases in the gastrointestinal tract. We have proposed a system based on global features and deep neural networks. The best approach combines two neural networks and the reproducible experimental results signify the efficiency of the proposed model with an accuracy rate of 95.80\%, a precision of 95.87\%, and an F1-score of 95.80\%.},
	keywords = {CNN, deep learning, Gastrointestinal Disease Detection, Global Features, Medico-Task 2018, Transfer Learning},
	author = {Thambawita, Vajira and Jha, Debesh and Riegler, Michael and Halvorsen, P{\r a}l and Hugo Lewi {Hammer} and H{\r a}vard D. {Johansen} and Johansen, Dag}
}
