The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

In federated learning, each participant trains its local model with its own data and a global model is formed at a trusted server by aggregating model updates coming from these participants. Since the server has no effect and visibility on the training procedure of the participants to ensure privacy, the global model becomes vulnerable to attacks such as data poisoning and model poisoning. Although many defense algorithms have recently been proposed to address these attacks, they often make strong assumptions that do not agree with the nature of federated learning, such as assuming Non-IID datasets. Moreover, they mostly lack comprehensive experimental analyses. In this work, we propose a defense algorithm called ARFED that does not make any assumptions about data distribution, update similarity of participants, or the ratio of the malicious participants. ARFED mainly considers the outlier status of participant updates for each layer of the model architecture based on the distance to the global model. Hence, the participants that do not have any outlier layer are involved in model aggregation. We have performed extensive experiments on diverse scenarios and shown that the proposed approach provides a robust defense against different attacks. To test the defense capability of the ARFED in different conditions, we considered label flipping, Byzantine, and partial knowledge attacks for both IID and Non-IID settings in our experimental evaluations. Moreover, we proposed a new attack, called organized partial knowledge attack, where malicious participants use their training statistics collaboratively to define a common poisoned model. We have shown that organized partial knowledge attacks are more effective than independent attacks.

Availability of large, diverse, and multi-national datasets is crucial for the development of effective and clinically applicable AI systems in the medical imaging domain. However, forming a global model by bringing these datasets together at a central location, comes along with various data privacy and ownership problems. To alleviate these problems, several recent studies focus on the federated learning paradigm, a distributed learning approach for decentralized data. Federated learning leverages all the available data without any need for sharing collaborators' data with each other or collecting them on a central server. Studies show that federated learning can provide competitive performance with conventional central training, while having a good generalization capability. In this work, we have investigated several federated learning approaches on the brain tumor segmentation problem. We explore different strategies for faster convergence and better performance which can also work on strong Non-IID cases.

Endoscopic Mayo score and Ulcerative Colitis Endoscopic Index of Severity are commonly used scoring systems for the assessment of endoscopic severity of ulcerative colitis. They are based on assigning a score in relation to the disease activity, which creates a rank among the levels, making it an ordinal regression problem. On the other hand, most studies use categorical cross-entropy loss function, which is not optimal for the ordinal regression problem, to train the deep learning models. In this study, we propose a novel loss function called class distance weighted cross-entropy (CDW-CE) that respects the order of the classes and takes the distance of the classes into account in calculation of cost. Experimental evaluations show that CDW-CE outperforms the conventional categorical cross-entropy and CORN framework, which is designed for the ordinal regression problems. In addition, CDW-CE does not require any modifications at the output layer and is compatible with the class activation map visualization techniques.

The Endoscopy Computer Vision Challenge (EndoCV) is a crowd-sourcing initiative to address eminent problems in developing reliable computer aided detection and diagnosis endoscopy systems and suggest a pathway for clinical translation of technologies. Whilst endoscopy is a widely used diagnostic and treatment tool for hollow-organs, there are several core challenges often faced by endoscopists, mainly: 1) presence of multi-class artefacts that hinder their visual interpretation, and 2) difficulty in identifying subtle precancerous precursors and cancer abnormalities. Artefacts often affect the robustness of deep learning methods applied to the gastrointestinal tract organs as they can be confused with tissue of interest. EndoCV2020 challenges are designed to address research questions in these remits. In this paper, we present a summary of methods developed by the top 17 teams and provide an objective comparison of state-of-the-art methods and methods designed by the participants for two sub-challenges: i) artefact detection and segmentation (EAD2020), and ii) disease detection and segmentation (EDD2020). Multi-center, multi-organ, multi-class, and multi-modal clinical endoscopy datasets were compiled for both EAD2020 and EDD2020 sub-challenges. An out-of-sample generalisation ability of detection algorithms was also evaluated. Whilst most teams focused on accuracy improvements, only a few methods hold credibility for clinical usability. The best performing teams provided solutions to tackle class imbalance, and variabilities in size, origin, modality and occurrences by exploring data augmentation, data fusion, and optimal class thresholding techniques.