1 code implementation • 6 Dec 2022 • Vajira Thambawita, Steven A. Hicks, Andrea M. Storås, Thu Nguyen, Jorunn M. Andersen, Oliwia Witczak, Trine B. Haugen, Hugo L. Hammer, Pål Halvorsen, Michael A. Riegler
A manual assessment of sperm motility requires microscopy observation, which is challenging due to the fast-moving spermatozoa in the field of view.
We proposed two approaches; one using only the CT scans to make predictions and another using a combination of the CT and PET scans.
For many use cases, combining information from different datasets can be of interest to improve a machine learning model's performance, especially when the number of samples from at least one of the datasets is small.
We evaluate a method to evolve a biologically-inspired artificial neural network that learns from environment reactions named Neuroevolution of Artificial General Intelligence (NAGI), a framework for low-level AGI.
Generalizability is seen as one of the major challenges in deep learning, in particular in the domain of medical imaging, where a change of hospital or in imaging routines can lead to a complete failure of a model.
In this paper, we explore the capabilities of the Hierarchical Temporal Memory (HTM) algorithm to perform anomaly detection in videos, as it has favorable properties such as noise tolerance and online learning which combats concept drift.
Early identification of a polyp in the lower gastrointestinal (GI) tract can lead to prevention of life-threatening colorectal cancer.
Missing data is a commonly occurring problem in practice.
Tacrolimus is one of the cornerstone immunosuppressive drugs in most transplantation centers worldwide following solid organ transplantation.
Deep learning has in recent years achieved immense success in all areas of computer vision and has the potential of assisting medical doctors in analyzing visual content for disease and other abnormalities.
The experiments show that our method can produce a small set of features in a fraction of the amount of time by the other methods under comparison.
no code implementations • 24 Feb 2022 • Sharib Ali, Noha Ghatwary, Debesh Jha, Ece Isik-Polat, Gorkem Polat, Chen Yang, Wuyang Li, Adrian Galdran, Miguel-Ángel González Ballester, Vajira Thambawita, Steven Hicks, Sahadev Poudel, Sang-Woong Lee, Ziyi Jin, Tianyuan Gan, Chenghui Yu, Jiangpeng Yan, Doyeob Yeo, Hyunseok Lee, Nikhil Kumar Tomar, Mahmood Haithmi, Amr Ahmed, Michael A. Riegler, Christian Daul, Pål Halvorsen, Jens Rittscher, Osama E. Salem, Dominique Lamarque, Renato Cannizzaro, Stefano Realdon, Thomas de Lange, James E. East
Polyps are well-known cancer precursors identified by colonoscopy.
We develop progressive alternating attention dense (PAAD) blocks, which construct a guiding attention map (GAM) after every convolutional layer in the dense blocks using features from all scales.
1 code implementation • • Steven Hicks, Debesh Jha, Vajira Thambawita, Pål Halvorsen, Bjørn-Jostein Singstad, Sachin Gaur, Klas Pettersen, Morten Goodwin, Sravanthi Parasa, Thomas de Lange, Michael Riegler
MedAI: Transparency in Medical Image Segmentation is a challenge held for the first time at the Nordic AI Meet that focuses on medical image segmentation and transparency in machine learning (ML)-based systems.
no code implementations • 2 Sep 2021 • Andrea M. Storås, Inga Strümke, Michael A. Riegler, Jakob Grauslund, Hugo L. Hammer, Anis Yazidi, Pål Halvorsen, Kjell G. Gundersen, Tor P. Utheim, Catherine Jackson
Although the term `AI' is commonly used, recent success in its applications to medicine is mainly due to advancements in the sub-field of machine learning, which has been used to automatically classify images and predict medical outcomes.
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.
Ranked #1 on Medical Image Segmentation on CVC-ColonDB (using extra training data)
Minimally invasive surgery is a surgical intervention used to examine the organs inside the abdomen and has been widely used due to its effectiveness over open surgery.
Ranked #1 on Medical Image Segmentation on ROBUST-MIS
For our contribution to the EndoCV 2021 segmentation challenge, we propose two separate approaches.
The pipeline is evaluated using qualitative and quantitative comparisons between real and synthetic data to show that the style transfer technique used in our pipeline significantly improves the quality of the generated data and our method is better than other state-of-the-art GANs to prepare synthetic images when the size of training datasets are limited.
2 code implementations • 8 Jun 2021 • Sharib Ali, Debesh Jha, Noha Ghatwary, Stefano Realdon, Renato Cannizzaro, Osama E. Salem, Dominique Lamarque, Christian Daul, Michael A. Riegler, Kim V. Anonsen, Andreas Petlund, Pål Halvorsen, Jens Rittscher, Thomas de Lange, James E. East
To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset curated by a team of computational scientists and expert gastroenterologists.
To our knowledge, this is the first work that exploits iMAML for medical image segmentation and explores the strength of the model on scenarios such as meta-training on unique and mixed instances of lesion datasets.
The proposed MSRF-Net allows to capture object variabilities and provides improved results on different biomedical datasets.
Ranked #3 on Medical Image Segmentation on 2018 Data Science Bowl
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.
Ranked #1 on Medical Image Segmentation on KvasirCapsule-SEG
We propose a novel architecture called feedback attention network (FANet) that unifies the previous epoch mask with the feature map of the current training epoch.
Ranked #1 on Medical Image Segmentation on EM
Deep Neural Networks (DNNs) have become the de-facto standard in computer vision, as well as in many other pattern recognition tasks.
Colorectal cancer is the third most common cause of cancer worldwide.
Colonoscopy is the gold standard for examination and detection of colorectal polyps.
Segmentation of findings in the gastrointestinal tract is a challenging but also an important task which is an important building stone for sufficient automatic decision support systems.
Benchmarking of novel methods can provide a direction to the development of automated polyp detection and segmentation tasks.
1 code implementation • 23 Oct 2020 • Debesh Jha, Sharib Ali, Krister Emanuelsen, Steven A. Hicks, VajiraThambawita, Enrique Garcia-Ceja, Michael A. Riegler, Thomas de Lange, Peter T. Schmidt, Håvard D. Johansen, Dag Johansen, Pål Halvorsen
Additionally, we provide a baseline for the segmentation of the GI tools to promote research and algorithm development.
Ranked #2 on Medical Image Segmentation on Kvasir-Instrument
The encouraging results, produced on various medical image segmentation datasets, show that DoubleU-Net can be used as a strong baseline for both medical image segmentation and cross-dataset evaluation testing to measure the generalizability of Deep Learning (DL) models.
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.
no code implementations • 23 Mar 2020 • Tobias Ross, Annika Reinke, Peter M. Full, Martin Wagner, Hannes Kenngott, Martin Apitz, Hellena Hempe, Diana Mindroc Filimon, Patrick Scholz, Thuy Nuong Tran, Pierangela Bruno, Pablo Arbeláez, Gui-Bin Bian, Sebastian Bodenstedt, Jon Lindström Bolmgren, Laura Bravo-Sánchez, Hua-Bin Chen, Cristina González, Dong Guo, Pål Halvorsen, Pheng-Ann Heng, Enes Hosgor, Zeng-Guang Hou, Fabian Isensee, Debesh Jha, Tingting Jiang, Yueming Jin, Kadir Kirtac, Sabrina Kletz, Stefan Leger, Zhixuan Li, Klaus H. Maier-Hein, Zhen-Liang Ni, Michael A. Riegler, Klaus Schoeffmann, Ruohua Shi, Stefanie Speidel, Michael Stenzel, Isabell Twick, Gutai Wang, Jiacheng Wang, Liansheng Wang, Lu Wang, Yu-Jie Zhang, Yan-Jie Zhou, Lei Zhu, Manuel Wiesenfarth, Annette Kopp-Schneider, Beat P. Müller-Stich, Lena Maier-Hein
The validation of the competing methods for the three tasks (binary segmentation, multi-instance detection and multi-instance segmentation) was performed in three different stages with an increasing domain gap between the training and the test data.
In this paper, we present Kvasir-SEG: an open-access dataset of gastrointestinal polyp images and corresponding segmentation masks, manually annotated by a medical doctor and then verified by an experienced gastroenterologist.
Ranked #1 on Polyp Segmentation on Kvasir-SEG (DSC metric)
In this paper, we present a two-step deep learning method that is used to predict sperm motility and morphology-based on video recordings of human spermatozoa.
To solve this regression task of predicting motility and morphology, stacked dense optical flows and extracted original frames from sperm videos were used with the modified state of the art convolution neural networks.
In this paper, we present our approach for the 2018 Medico Task classifying diseases in the gastrointestinal tract.