Görkem Polat

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al. · utoronto

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.

Ümit Mert Çağlar, Alperen İnci, Oğuz Hanoğlu et al.

Endoscopic imaging is commonly used to diagnose Ulcerative Colitis (UC) and classify its severity. It has been shown that deep learning based methods are effective in automated analysis of these images and can potentially be used to aid medical doctors. Unleashing the full potential of these methods depends on the availability of large amount of labeled images; however, obtaining and labeling these images are quite challenging. In this paper, we propose a active learning based generative augmentation method. The method involves generating a large number of synthetic samples by training using a small dataset consisting of real endoscopic images. The resulting data pool is narrowed down by using active learning methods to select the most informative samples, which are then used to train a classifier. We demonstrate the effectiveness of our method through experiments on a publicly available endoscopic image dataset. The results show that using synthesized samples in conjunction with active learning leads to improved classification performance compared to using only the original labeled examples and the baseline classification performance of 68.1% increases to 74.5% in terms of Quadratic Weighted Kappa (QWK) Score. Another observation is that, attaining equivalent performance using only real data necessitated three times higher number of images.

Gorkem Polat, Ümit Mert Çağlar, Alptekin Temizel

Assessing disease severity with ordinal classes, where each class reflects increasing severity levels, benefits from loss functions designed for this ordinal structure. Traditional categorical loss functions, like Cross-Entropy (CE), often perform suboptimally in these scenarios. To address this, we propose a novel loss function, Class Distance Weighted Cross-Entropy (CDW-CE), which penalizes misclassifications more severely when the predicted and actual classes are farther apart. We evaluated CDW-CE using various deep architectures, comparing its performance against several categorical and ordinal loss functions. To assess the quality of latent representations, we used t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) visualizations, quantified the clustering quality using the Silhouette Score, and compared Class Activation Maps (CAM) generated by models trained with CDW-CE and CE loss. Feedback from domain experts was incorporated to evaluate how well model attention aligns with expert opinion. Our results show that CDW-CE consistently improves performance in ordinal image classification tasks. It achieves higher Silhouette Scores, indicating better class discrimination capability, and its CAM visualizations show a stronger focus on clinically significant regions, as validated by domain experts. Receiver operator characteristics (ROC) curves and the area under the curve (AUC) scores highlight that CDW-CE outperforms other loss functions, including prominent ordinal loss functions from the literature.

Sharib Ali, Noha Ghatwary, Debesh Jha et al.

Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, location, and surface largely affect identification, localisation, and characterisation. Moreover, colonoscopic surveillance and removal of polyps (referred to as polypectomy ) are highly operator-dependent procedures. There exist a high missed detection rate and incomplete removal of colonic polyps due to their variable nature, the difficulties to delineate the abnormality, the high recurrence rates, and the anatomical topography of the colon. There have been several developments in realising automated methods for both detection and segmentation of these polyps using machine learning. However, the major drawback in most of these methods is their ability to generalise to out-of-sample unseen datasets that come from different centres, modalities and acquisition systems. To test this hypothesis rigorously we curated a multi-centre and multi-population dataset acquired from multiple colonoscopy systems and challenged teams comprising machine learning experts to develop robust automated detection and segmentation methods as part of our crowd-sourcing Endoscopic computer vision challenge (EndoCV) 2021. In this paper, we analyse the detection results of the four top (among seven) teams and the segmentation results of the five top teams (among 16). Our analyses demonstrate that the top-ranking teams concentrated on accuracy (i.e., accuracy > 80% on overall Dice score on different validation sets) over real-time performance required for clinical applicability. We further dissect the methods and provide an experiment-based hypothesis that reveals the need for improved generalisability to tackle diversity present in multi-centre datasets.

Ece Isik-Polat, Gorkem Polat, Altan Kocyigit et al.

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.

Gorkem Polat, Ilkay Ergenc, Haluk Tarik Kani et al.

In scoring systems used to measure the endoscopic activity of ulcerative colitis, such as Mayo endoscopic score or Ulcerative Colitis Endoscopic Index Severity, levels increase with severity of the disease activity. Such relative ranking among the scores makes it an ordinal regression problem. On the other hand, most studies use categorical cross-entropy loss function to train deep learning models, which is not optimal for the ordinal regression problem. In this study, we propose a novel loss function, 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 the cost. Experimental evaluations show that models trained with CDW-CE outperform the models trained with conventional categorical cross-entropy and other commonly used loss functions which are designed for the ordinal regression problems. In addition, the class activation maps of models trained with CDW-CE loss are more class-discriminative and they are found to be more reasonable by the domain experts.

Ece Isik-Polat, Gorkem Polat, Altan Kocyigit

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.

Sharib Ali, Mariia Dmitrieva, Noha Ghatwary et al.

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. The out-of-sample generalization 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.

Gorkem Polat, Ugur Halici, Yesim Serinagaoglu Dogrusoz

Recent studies have shown that lung cancer screening using annual low-dose computed tomography (CT) reduces lung cancer mortality by 20% compared to traditional chest radiography. Therefore, CT lung screening has started to be used widely all across the world. However, analyzing these images is a serious burden for radiologists. In this study, we propose a novel and simple framework that analyzes CT lung screenings using convolutional neural networks (CNNs) and reduces false positives. Our framework shows that even non-complex architectures are very powerful to classify 3D nodule data when compared to traditional methods. We also use different fusions in order to show their power and effect on the overall score. 3D CNNs are preferred over 2D CNNs because data are in 3D, and 2D convolutional operations may result in information loss. Mini-batch is used in order to overcome class-imbalance. Proposed framework has been validated according to the LUNA16 challenge evaluation and got score of 0.786, which is the average sensitivity values at seven predefined false positive (FP) points.