Alexandros Karargyris

Lena Maier-Hein, Annika Reinke, Patrick Godau et al. · utoronto

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases.

Sanat Ramesh, Vinkle Srivastav, Deepak Alapatt et al.

The field of surgical computer vision has undergone considerable breakthroughs in recent years with the rising popularity of deep neural network-based methods. However, standard fully-supervised approaches for training such models require vast amounts of annotated data, imposing a prohibitively high cost; especially in the clinical domain. Self-Supervised Learning (SSL) methods, which have begun to gain traction in the general computer vision community, represent a potential solution to these annotation costs, allowing to learn useful representations from only unlabeled data. Still, the effectiveness of SSL methods in more complex and impactful domains, such as medicine and surgery, remains limited and unexplored. In this work, we address this critical need by investigating four state-of-the-art SSL methods (MoCo v2, SimCLR, DINO, SwAV) in the context of surgical computer vision. We present an extensive analysis of the performance of these methods on the Cholec80 dataset for two fundamental and popular tasks in surgical context understanding, phase recognition and tool presence detection. We examine their parameterization, then their behavior with respect to training data quantities in semi-supervised settings. Correct transfer of these methods to surgery, as described and conducted in this work, leads to substantial performance gains over generic uses of SSL - up to 7.4% on phase recognition and 20% on tool presence detection - as well as state-of-the-art semi-supervised phase recognition approaches by up to 14%. Further results obtained on a highly diverse selection of surgical datasets exhibit strong generalization properties. The code is available at https://github.com/CAMMA-public/SelfSupSurg.

Hasan Kassem, Orion Banks, Omar Benjelloun et al.

Decentralized AI systems, such as federated learning, can play a critical role in further unlocking AI asset marketplaces (e.g., healthcare data marketplaces) thanks to increased asset privacy protection. Unlocking this big potential necessitates governance mechanisms that are transparent, scalable, and verifiable. However current governance approaches rely on bespoke, infrastructure-specific policies that hinder asset interoperability and trust among systems. We are proposing a Technical Policy Blueprint that encodes governance requirements as policy-as-code objects and separates asset policy verification from asset policy enforcement. In this architecture the Policy Engine verifies evidence (e.g., identities, signatures, payments, trusted-hardware attestations) and issues capability packages. Asset Guardians (e.g. data guardians, model guardians, computation guardians, etc.) enforce access or execution solely based on these capability packages. This core concept of decoupling policy processing from capabilities enables governance to evolve without reconfiguring AI infrastructure, thus creating an approach that is transparent, auditable, and resilient to change.

Annika Reinke, Minu D. Tizabi, Michael Baumgartner et al.

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu et al.

Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children. The five-year survival rate for high-grade glioma in children is less than 20%. The development of new treatments is dependent upon multi-institutional collaborative clinical trials requiring reproducible and accurate centralized response assessment. We present the results of the BraTS-PEDs 2023 challenge, the first Brain Tumor Segmentation (BraTS) challenge focused on pediatric brain tumors. This challenge utilized data acquired from multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. BraTS-PEDs 2023 aimed to evaluate volumetric segmentation algorithms for pediatric brain gliomas from magnetic resonance imaging using standardized quantitative performance evaluation metrics employed across the BraTS 2023 challenges. The top-performing AI approaches for pediatric tumor analysis included ensembles of nnU-Net and Swin UNETR, Auto3DSeg, or nnU-Net with a self-supervised framework. The BraTSPEDs 2023 challenge fostered collaboration between clinicians (neuro-oncologists, neuroradiologists) and AI/imaging scientists, promoting faster data sharing and the development of automated volumetric analysis techniques. These advancements could significantly benefit clinical trials and improve the care of children with brain tumors.

Hasan Kassem, Deepak Alapatt, Pietro Mascagni et al.

Recent advancements in deep learning methods bring computer-assistance a step closer to fulfilling promises of safer surgical procedures. However, the generalizability of such methods is often dependent on training on diverse datasets from multiple medical institutions, which is a restrictive requirement considering the sensitive nature of medical data. Recently proposed collaborative learning methods such as Federated Learning (FL) allow for training on remote datasets without the need to explicitly share data. Even so, data annotation still represents a bottleneck, particularly in medicine and surgery where clinical expertise is often required. With these constraints in mind, we propose FedCy, a federated semi-supervised learning (FSSL) method that combines FL and self-supervised learning to exploit a decentralized dataset of both labeled and unlabeled videos, thereby improving performance on the task of surgical phase recognition. By leveraging temporal patterns in the labeled data, FedCy helps guide unsupervised training on unlabeled data towards learning task-specific features for phase recognition. We demonstrate significant performance gains over state-of-the-art FSSL methods on the task of automatic recognition of surgical phases using a newly collected multi-institutional dataset of laparoscopic cholecystectomy videos. Furthermore, we demonstrate that our approach also learns more generalizable features when tested on data from an unseen domain.

Annika Reinke, Evangelia Christodoulou, Sthuthi Sadananda et al.

Benchmarking competitions are central to the development of artificial intelligence (AI) in medical imaging, defining performance standards and shaping methodological progress. However, it remains unclear whether these benchmarks provide data that are sufficiently representative, accessible, and reusable to support clinically meaningful AI. In this work, we assess fairness along two complementary dimensions: (1) whether challenge datasets are representative of real-world clinical diversity, and (2) whether they are accessible and legally reusable in line with the FAIR principles. To address this question, we conducted a large-scale systematic study of 241 biomedical image analysis challenges comprising 458 tasks across 19 imaging modalities. Our findings show substantial biases in dataset composition, including geographic location, modality-, and problem type-related biases, indicating that current benchmarks do not adequately reflect real-world clinical diversity. Despite their widespread influence, challenge datasets were frequently constrained by restrictive or ambiguous access conditions, inconsistent or non-compliant licensing practices, and incomplete documentation, limiting reproducibility and long-term reuse. Together, these shortcomings expose foundational fairness limitations in our benchmarking ecosystem and highlight a disconnect between leaderboard success and clinical relevance.

Idris Hamoud, Alexandros Karargyris, Aidean Sharghi et al.

Semantic segmentation and activity classification are key components to creating intelligent surgical systems able to understand and assist clinical workflow. In the Operating Room, semantic segmentation is at the core of creating robots aware of clinical surroundings, whereas activity classification aims at understanding OR workflow at a higher level. State-of-the-art semantic segmentation and activity recognition approaches are fully supervised, which is not scalable. Self-supervision can decrease the amount of annotated data needed. We propose a new 3D self-supervised task for OR scene understanding utilizing OR scene images captured with ToF cameras. Contrary to other self-supervised approaches, where handcrafted pretext tasks are focused on 2D image features, our proposed task consists of predicting the relative 3D distance of image patches by exploiting the depth maps. Learning 3D spatial context generates discriminative features for our downstream tasks. Our approach is evaluated on two tasks and datasets containing multi-view data captured from clinical scenarios. We demonstrate a noteworthy improvement of performance on both tasks, specifically on low-regime data where utility of self-supervised learning is the highest.

Tanveer Syeda-Mahmood, Hassan M. Ahmad, Nadeem Ansari et al.

Chest X-rays are the most common diagnostic exams in emergency rooms and hospitals. There has been a surge of work on automatic interpretation of chest X-rays using deep learning approaches after the availability of large open source chest X-ray dataset from NIH. However, the labels are not sufficiently rich and descriptive for training classification tools. Further, it does not adequately address the findings seen in Chest X-rays taken in anterior-posterior (AP) view which also depict the placement of devices such as central vascular lines and tubes. In this paper, we present a new chest X-ray benchmark database of 73 rich sentence-level descriptors of findings seen in AP chest X-rays. We describe our method of obtaining these findings through a semi-automated ground truth generation process from crowdsourcing of clinician annotations. We also present results of building classifiers for these findings that show that such higher granularity labels can also be learned through the framework of deep learning classifiers.

Dominic LaBella, Ujjwal Baid, Omaditya Khanna et al.

We describe the design and results from the BraTS 2023 Intracranial Meningioma Segmentation Challenge. The BraTS Meningioma Challenge differed from prior BraTS Glioma challenges in that it focused on meningiomas, which are typically benign extra-axial tumors with diverse radiologic and anatomical presentation and a propensity for multiplicity. Nine participating teams each developed deep-learning automated segmentation models using image data from the largest multi-institutional systematically expert annotated multilabel multi-sequence meningioma MRI dataset to date, which included 1000 training set cases, 141 validation set cases, and 283 hidden test set cases. Each case included T2, FLAIR, T1, and T1Gd brain MRI sequences with associated tumor compartment labels delineating enhancing tumor, non-enhancing tumor, and surrounding non-enhancing FLAIR hyperintensity. Participant automated segmentation models were evaluated and ranked based on a scoring system evaluating lesion-wise metrics including dice similarity coefficient (DSC) and 95% Hausdorff Distance. The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0.976, 0.976, and 0.964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0.899, 0.904, and 0.871, respectively. These results serve as state-of-the-art benchmarks for future pre-operative meningioma automated segmentation algorithms. Additionally, we found that 1286 of 1424 cases (90.3%) had at least 1 compartment voxel abutting the edge of the skull-stripped image edge, which requires further investigation into optimal pre-processing face anonymization steps.

Spyridon Bakas, Siddhesh P. Thakur, Shahriar Faghani et al.

Glioblastoma is the most common primary adult brain tumor, with a grim prognosis - median survival of 12-18 months following treatment, and 4 months otherwise. Glioblastoma is widely infiltrative in the cerebral hemispheres and well-defined by heterogeneous molecular and micro-environmental histopathologic profiles, which pose a major obstacle in treatment. Correctly diagnosing these tumors and assessing their heterogeneity is crucial for choosing the precise treatment and potentially enhancing patient survival rates. In the gold-standard histopathology-based approach to tumor diagnosis, detecting various morpho-pathological features of distinct histology throughout digitized tissue sections is crucial. Such "features" include the presence of cellular tumor, geographic necrosis, pseudopalisading necrosis, areas abundant in microvascular proliferation, infiltration into the cortex, wide extension in subcortical white matter, leptomeningeal infiltration, regions dense with macrophages, and the presence of perivascular or scattered lymphocytes. With these features in mind and building upon the main aim of the BraTS Cluster of Challenges https://www.synapse.org/brats2024, the goal of the BraTS-Path challenge is to provide a systematically prepared comprehensive dataset and a benchmarking environment to develop and fairly compare deep-learning models capable of identifying tumor sub-regions of distinct histologic profile. These models aim to further our understanding of the disease and assist in the diagnosis and grading of conditions in a consistent manner.

Alexandros Karargyris, Renato Umeton, Micah J. Sheller et al.

Medical AI has tremendous potential to advance healthcare by supporting the evidence-based practice of medicine, personalizing patient treatment, reducing costs, and improving provider and patient experience. We argue that unlocking this potential requires a systematic way to measure the performance of medical AI models on large-scale heterogeneous data. To meet this need, we are building MedPerf, an open framework for benchmarking machine learning in the medical domain. MedPerf will enable federated evaluation in which models are securely distributed to different facilities for evaluation, thereby empowering healthcare organizations to assess and verify the performance of AI models in an efficient and human-supervised process, while prioritizing privacy. We describe the current challenges healthcare and AI communities face, the need for an open platform, the design philosophy of MedPerf, its current implementation status, and our roadmap. We call for researchers and organizations to join us in creating the MedPerf open benchmarking platform.

Annika Reinke, Minu D. Tizabi, Carole H. Sudre et al.

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide.

Sarthak Pati, Siddhesh P. Thakur, İbrahim Ethem Hamamcı et al.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

Alexandros Karargyris, Satyananda Kashyap, Ismini Lourentzou et al.

We developed a rich dataset of Chest X-Ray (CXR) images to assist investigators in artificial intelligence. The data were collected using an eye tracking system while a radiologist reviewed and reported on 1,083 CXR images. The dataset contains the following aligned data: CXR image, transcribed radiology report text, radiologist's dictation audio and eye gaze coordinates data. We hope this dataset can contribute to various areas of research particularly towards explainable and multimodal deep learning / machine learning methods. Furthermore, investigators in disease classification and localization, automated radiology report generation, and human-machine interaction can benefit from these data. We report deep learning experiments that utilize the attention maps produced by eye gaze dataset to show the potential utility of this data.

Sandesh Ghimire, Satyananda Kashyap, Joy T. Wu et al.

Chest radiography is the most common medical image examination for screening and diagnosis in hospitals. Automatic interpretation of chest X-rays at the level of an entry-level radiologist can greatly benefit work prioritization and assist in analyzing a larger population. Subsequently, several datasets and deep learning-based solutions have been proposed to identify diseases based on chest X-ray images. However, these methods are shown to be vulnerable to shift in the source of data: a deep learning model performing well when tested on the same dataset as training data, starts to perform poorly when it is tested on a dataset from a different source. In this work, we address this challenge of generalization to a new source by forcing the network to learn a source-invariant representation. By employing an adversarial training strategy, we show that a network can be forced to learn a source-invariant representation. Through pneumonia-classification experiments on multi-source chest X-ray datasets, we show that this algorithm helps in improving classification accuracy on a new source of X-ray dataset.

Satyananda Kashyap, Alexandros Karargyris, Joy Wu et al.

Deep learning has now become the de facto approach to the recognition of anomalies in medical imaging. Their 'black box' way of classifying medical images into anomaly labels poses problems for their acceptance, particularly with clinicians. Current explainable AI methods offer justifications through visualizations such as heat maps but cannot guarantee that the network is focusing on the relevant image region fully containing the anomaly. In this paper, we develop an approach to explainable AI in which the anomaly is assured to be overlapping the expected location when present. This is made possible by automatically extracting location-specific labels from textual reports and learning the association of expected locations to labels using a hybrid combination of Bi-Directional Long Short-Term Memory Recurrent Neural Networks (Bi-LSTM) and DenseNet-121. Use of this expected location to bias the subsequent attention-guided inference network based on ResNet101 results in the isolation of the anomaly at the expected location when present. The method is evaluated on a large chest X-ray dataset.

Tanveer Syeda-Mahmood, Ken C. L. Wong, Yaniv Gur et al.

Obtaining automated preliminary read reports for common exams such as chest X-rays will expedite clinical workflows and improve operational efficiencies in hospitals. However, the quality of reports generated by current automated approaches is not yet clinically acceptable as they cannot ensure the correct detection of a broad spectrum of radiographic findings nor describe them accurately in terms of laterality, anatomical location, severity, etc. In this work, we present a domain-aware automatic chest X-ray radiology report generation algorithm that learns fine-grained description of findings from images and uses their pattern of occurrences to retrieve and customize similar reports from a large report database. We also develop an automatic labeling algorithm for assigning such descriptors to images and build a novel deep learning network that recognizes both coarse and fine-grained descriptions of findings. The resulting report generation algorithm significantly outperforms the state of the art using established score metrics.

Deepta Rajan, Jayaraman J. Thiagarajan, Alexandros Karargyris et al.

Automated diagnostic assistants in healthcare necessitate accurate AI models that can be trained with limited labeled data, can cope with severe class imbalances and can support simultaneous prediction of multiple disease conditions. To this end, we present a deep learning framework that utilizes a number of key components to enable robust modeling in such challenging scenarios. Using an important use-case in chest X-ray classification, we provide several key insights on the effective use of data augmentation, self-training via distillation and confidence tempering for small data learning in medical imaging. Our results show that using 85% lesser labeled data, we can build predictive models that match the performance of classifiers trained in a large-scale data setting.

Alexandros Karargyris, Ken C. L. Wong, Joy T. Wu et al.

In many screening applications, the primary goal of a radiologist or assisting artificial intelligence is to rule out certain findings. The classifiers built for such applications are often trained on large datasets that derive labels from clinical notes written for patients. While the quality of the positive findings described in these notes is often reliable, lack of the mention of a finding does not always rule out the presence of it. This happens because radiologists comment on the patient in the context of the exam, for example focusing on trauma as opposed to chronic disease at emergency rooms. However, this disease finding ambiguity can affect the performance of algorithms. Hence it is critical to model the ambiguity during training. We propose a scheme to apply reasonable class weight modifiers to our loss function for the no mention cases during training. We experiment with two different deep neural network architectures and show that the proposed method results in a large improvement in the performance of the classifiers, specially on negated findings. The baseline performance of a custom-made dilated block network proposed in this paper shows an improvement in comparison with baseline DenseNet-201, while both architectures benefit from the new proposed loss function weighting scheme. Over 200,000 chest X-ray images and three highly common diseases, along with their negated counterparts, are included in this study.

Alexandros Karargyris, Satyananda Kashyap, Joy T Wu et al.

Age prediction based on appearances of different anatomies in medical images has been clinically explored for many decades. In this paper, we used deep learning to predict a persons age on Chest X-Rays. Specifically, we trained a CNN in regression fashion on a large publicly available dataset. Moreover, for interpretability, we explored activation maps to identify which areas of a CXR image are important for the machine (i.e. CNN) to predict a patients age, offering insight. Overall, amongst correctly predicted CXRs, we see areas near the clavicles, shoulders, spine, and mediastinum being most activated for age prediction, as one would expect biologically. Amongst incorrectly predicted CXRs, we have qualitatively identified disease patterns that could possibly make the anatomies appear older or younger than expected. A further technical and clinical evaluation would improve this work. As CXR is the most commonly requested imaging exam, a potential use case for estimating age may be found in the preventative counseling of patient health status compared to their age-expected average, particularly when there is a large discrepancy between predicted age and the real patient age.

Ken C. L. Wong, Alexandros Karargyris, Tanveer Syeda-Mahmood et al.

Although deep learning can provide promising results in medical image analysis, the lack of very large annotated datasets confines its full potential. Furthermore, limited positive samples also create unbalanced datasets which limit the true positive rates of trained models. As unbalanced datasets are mostly unavoidable, it is greatly beneficial if we can extract useful knowledge from negative samples to improve classification accuracy on limited positive samples. To this end, we propose a new strategy for building medical image analysis pipelines that target disease detection. We train a discriminative segmentation model only on normal images to provide a source of knowledge to be transferred to a disease detection classifier. We show that using the feature maps of a trained segmentation network, deviations from normal anatomy can be learned by a two-class classification network on an extremely unbalanced training dataset with as little as one positive for 17 negative samples. We demonstrate that even though the segmentation network is only trained on normal cardiac computed tomography images, the resulting feature maps can be used to detect pericardial effusion and cardiac septal defects with two-class convolutional classification networks.

Alexandros Karargyris

Deep networks have become very popular over the past few years. The main reason for this widespread use is their excellent ability to learn and predict knowledge in a very easy and efficient way. Convolutional neural networks and auto-encoders have become the normal in the area of imaging and computer vision achieving unprecedented accuracy levels in many applications. The most common strategy is to build and train networks with many layers by tuning their hyper-parameters. While this approach has proven to be a successful way to build robust deep learning schemes it suffers from high complexity. In this paper we introduce a module that learns color space transformations within a network. Given a large dataset of colored images the color space transformation module tries to learn color space transformations that increase overall classification accuracy. This module has shown to increase overall accuracy for the same network design and to achieve faster convergence. It is part of a broader family of image transformations (e.g. spatial transformer network).