@inproceedings {28020,
	title = {Exploring Deep Learning Methods for Real-Time Surgical Instrument Segmentation in Laparoscopy},
	journal = {2021 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI)},
	year = {2021},
	pages = {1-4},
	publisher = {IEEE},
	abstract = {Minimally Invasive Surgery (MIS) is a surgical intervention used to examine the organs inside the abdomen and has been widely used due to its effectiveness over open surgery. Due to the hardware improvements such as high definition cameras, this procedure has significantly improved and new software methods have open potential for computer-assisted procedures. However, there exists challenges and requirement to improve detection and tracking of the position of the instruments during these surgical procedures. To this end, we evaluate and compare some popular deep learning methods that can potentially be explored for the automated segmentation of surgical instruments in laparoscopy, an important step towards tool tracking. Our experimental results demonstrate that the Dual decoder attention network (DDANet) produces a superior result compared to other recent deep learning methods. DDANet produces a dice coefficient of 0.8739 and mean intersection over union of 0.8183 for the Robust Medical Instrument Segmentation (ROBUST-MIS) Challenge 2019 dataset, at a real-time speed of 101.36 frames per second which is critical for such procedures.},
	keywords = {Real-time segmentation, minimally invasive surgery, surgical instruments,  laparoscopy, deep learning},
	author = {Jha, Debesh and Ali, Sharib and Nikhil Kumar {Tomar} and Riegler, Michael and Johansen, Dag and H{\r a}vard D {Johansen} and Halvorsen, P{\r a}l}
}
@inproceedings {27856,
	title = {NanoNet: Real-Time Polyp Segmentation in Video Capsule Endoscopy and Colonoscopy},
	journal = {34th IEEE CBMS International Symposium on Computer-Based Medical Systems},
	year = {2021},
	publisher = { IEEE},
	abstract = {Deep learning in gastrointestinal endoscopy can assist to improve clinical performance and be helpful to assess lesions more accurately. To this extent, semantic segmentation methods that can perform automated real-time delineation of a region-of-interest, e.g., boundary identification of cancer or precancerous lesions, can benefit both diagnosis and interventions. However, accurate and real-time segmentation of endoscopic images is extremely challenging due to its high operator dependence and high-definition image quality. To utilize automated methods in clinical settings, it is crucial to design lightweight models with low latency such that they can be integrated with low-end endoscope hardware devices. In this work, we propose NanoNet, a novel architecture for the segmentation of video capsule endoscopy and colonoscopy images. Our proposed architecture allows real-time performance and has higher segmentation accuracy compared to other more complex ones. We use video capsule endoscopy and standard colonoscopy datasets with polyps, and a dataset consisting of endoscopy biopsies and surgical instruments, to evaluate the effectiveness of our approach. Our experiments demonstrate the increased performance of our architecture in terms of a trade-off between model complexity, speed, model parameters, and metric performances. Moreover, the resulting model size is relatively tiny, with only nearly 36,000 parameters compared to traditional deep learning approaches having millions of parameters.},
	keywords = {colonoscopy, deep learning, segmentation, tool  segmentation, Video capsule endoscopy},
	author = {Jha, Debesh and Nikhil Kumar {Tomar} and Ali, Sharib and Riegler, Michael and H{\r a}vard D {Johansen} and Johansen, Dag and de Lange, Thomas and Halvorsen, P{\r a}l}
}
@article {27773,
	title = {Real-Time Polyp Detection, Localization and Segmentation in Colonoscopy Using Deep Learning},
	journal = {IEEE Access},
	volume = {9},
	year = {2021},
	pages = {40496-40510},
	publisher = { IEEE},
	abstract = {Computer-aided detection, localization, and segmentation methods can help improve colonoscopy procedures. Even though many methods have been built to tackle automatic detection and segmentation of polyps, benchmarking of state-of-the-art methods still remains an open problem. This is due to the increasing number of researched computer vision methods that can be applied to polyp datasets. Benchmarking of novel methods can provide a direction to the development of automated polyp detection and segmentation tasks. Furthermore, it ensures that the produced results in the community are reproducible and provide a fair comparison of developed methods. In this paper, we benchmark several recent state-of-the-art methods using Kvasir-SEG, an open-access dataset of colonoscopy images for polyp detection, localization, and segmentation evaluating both method accuracy and speed. Whilst, most methods in literature have competitive performance over accuracy, we show that the proposed ColonSegNet achieved a better trade-off between an average precision of 0.8000 and mean IoU of 0.8100, and the fastest speed of 180 frames per second for the detection and localization task. Likewise, the proposed ColonSegNetachieved a competitive dice coefficient of 0.8206 and the best average speed of 182.38 frames per second for the segmentation task. Our comprehensive comparison with various state-of-the-art methods reveals the importance of benchmarking the deep learning methods for automated real-time polyp identification and delineations that can potentially transform current clinical practices and minimize miss-detection rates.},
	keywords = {Medical image segmentation,  ColonSegNet, colonoscopy, polyps, deep learning, detection, localization, benchmarking, Kvasir-SEG},
	doi = {10.1109/ACCESS.2021.3063716},
	author = {Jha, Debesh and Ali, Sharib and Nikhil Kumar {Tomar} and H{\r a}vard D {Johansen} and Johansen, Dag and Rittscher, Jens and Riegler, Michael and Halvorsen, P{\r a}l}
}
@inproceedings {27324,
	title = {DoubleU-Net: A Deep Convolutional Neural Network for Medical Image Segmentation},
	journal = {CBMS 2020: International Symposium on Computer-Based Medical Systems},
	year = {2020},
	note = {This paper was nominated for the best paper award at CBMS 2020.\&nbsp;},
	publisher = { IEEE},
	author = {Jha, Debesh and Riegler, Michael and Johansen, Dag and Halvorsen, P{\r a}l and H{\r a}vard D {Johansen}}
}
@article {27265,
	title = {An Extensive Study on Cross-Dataset Bias and Evaluation Metrics Interpretation for Machine Learning applied to Gastrointestinal Tract Abnormality Classification},
	journal = {ACM Transactions on Computing for Healthcare},
	volume = {1},
	number = {3},
	year = {2020},
	pages = {1-29},
	publisher = {ACM},
	abstract = {Precise and efficient automated identification of Gastrointestinal (GI) tract diseases can help doctors treat more patients and improve the rate of disease detection and identification. Currently, automatic analysis of diseases in the GI tract is a hot topic in both computer science and medical-related journals. Nevertheless, the evaluation of such an automatic analysis is often incomplete or simply wrong. Algorithms are often only tested on small and biased datasets, and cross-dataset evaluations are rarely performed. A clear understanding of evaluation metrics and machine learning models with cross datasets is crucial to bring research in the field to a new quality level. Towards this goal, we present comprehensive evaluations of five distinct machine learning models using Global Features and Deep Neural Networks that can classify 16 different key types of GI tract conditions, including pathological findings, anatomical landmarks, polyp removal conditions, and normal findings from images captured by common GI tract examination instruments. Inour evaluation, we introduce performance hexagons using six performance metrics such as recall, precision, specificity, accuracy, F1-score, and Matthews Correlation Coefficient to demonstrate how to determine the real capabilities of models rather than evaluatingthem shallowly. Furthermore, we perform cross-dataset evaluations using different datasets for training and testing. With these cross-dataset evaluations, we demonstrate the challenge of actually building a generalizable model that could be used across different hospitals. Our experiments clearly show that more sophisticated performance metrics and evaluation methods need to be applied to get reliable models rather than depending on evaluations of the splits of the same dataset, i.e., the performance metrics should always be interpreted together rather than relying on a single metric.},
	author = {Thambawita, Vajira and Jha, Debesh and Hugo Lewi {Hammer} and H{\r a}vard D {Johansen} and Johansen, Dag and Halvorsen, P{\r a}l and Riegler, Michael}
}
@inproceedings {39534,
	title = {Kvasir-instrument: Diagnostic and therapeutic tool segmentation dataset in gastrointestinal endoscopy},
	journal = {International Conference on Multimedia Modeling},
	year = {2020},
	publisher = { Springer},
	abstract = {Gastrointestinal\&nbsp;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,\&nbsp; 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\&nbsp;annotated frames containing GI\&nbsp;procedure tools such as snares, balloons, and biopsy forceps, etc. Besides the images, the dataset includes ground truth masks and bounding boxes and has been verified by two expert GI\&nbsp;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\&nbsp;and a Jaccard index of 0.8578\&nbsp;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 tools, 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 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\&nbsp;endoscopy.},
	keywords = {Benchmarking, Convolutional  neural network, Gastrointestinal endoscopy, Tool segmentation},
	url = {https://www.springerprofessional.de/en/kvasir-instrument-diagnostic-and-therapeutic-tool-segmentation-d/18788368},
	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 {26630,
	title = {Predicting Peek Readiness-to-Train of Soccer Players Using Long Short-Term Memory Recurrent Neural Networks},
	journal = {2019 International Conference on Content-Based Multimedia Indexing (CBMI)},
	year = {2019},
	publisher = {IEEE},
	abstract = {We are witnessing the emergence of a myriad of hardware and software systems that quantifies sport and physical activities. These are frequently touted as game changers and important for future sport developments. The vast amount of generated data is often visualized in graphs and dashboards, for use by coaches and other sports professionals to make decisions on training and match strategies. Modern machine- learning methods have the potential to further fuel this process by deriving useful insights that are not easily observable in the raw data streams.This paper tackles the problem of deriving peaks in soccer players{\textquoteright} ability to perform from subjective self-reported wellness data collected using the PMSys system. For this, we train a long short-term memory recurrent neural network model using data from two professional Norwegian soccer teams. We show that our model can predict performance peaks in most scenarios with a precision and recall of at least 90\%. Equipped with such insight, coaches and trainers can better plan individual and team training sessions, and perhaps avoid over training and injuries.},
	doi = {10.1109/CBMI.2019.8877406},
	author = {Wiik, Theodor and H{\r a}vard D {Johansen} and Svein Arne {Pettersen} and Baptista, Ivan and Kupka, Tomas and Johansen, Dag and Riegler, Michael and Halvorsen, P{\r a}l}
}
@inproceedings {26812,
	title = {ResUNet++: An Advanced Architecture for Medical Image Segmentation},
	journal = {2019 IEEE International Symposium on Multimedia (ISM)},
	year = {2019},
	publisher = {IEEE},
	address = {San Diego, California, USA},
	abstract = {Accurate computer-aided polyp detection and segmentation during colonoscopy examinations can help endoscopists resect abnormal tissue and thereby decrease chances of polyps growing into cancer. Towards developing a fully automated model for pixel-wise polyp segmentation, we propose ResUNet++, which is an improved ResUNet architecture for colonoscopic image segmentation. Our experimental evaluations show that the suggested architecture produces good segmentation results on publicly available datasets. Furthermore, ResUNet++ significantly outperforms U-Net and ResUNet, two key state-of-the-art deep learning architectures, by achieving high evaluation scores with a dice coefficient of 81.33\%, and a mean Intersection over Union (mIoU) of 79.27\% for the Kvasir-SEG dataset and a dice coefficient of 79.55\%, and a mIoU of 79.62\% with CVC-612 dataset.},
	keywords = {colonoscopy, deep learning, health informatics, Medical image segmentation, Polyp segmentation, Semantic segmentation},
	author = {Jha, Debesh and Pia H. {Smedsrud} and Riegler, Michael and Johansen, Dag and de Lange, Thomas and Halvorsen, P{\r a}l and H{\r a}vard D {Johansen}}
}
