Carlos Martín-Isla

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.

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al.

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

Joan Perramon-Llussà, Amelia Jiménez-Sánchez, Grzegorz Skorupko et al.

Foundation models (FMs) show great promise for robust downstream performance across medical imaging tasks and modalities, including cardiac magnetic resonance (CMR), following task-specific adaptation. However, adaptation using single-site data may lead to suboptimal performance and increased model bias, while centralized fine-tuning on clinical data is often infeasible due to privacy constraints. Federated fine-tuning offers a privacy-preserving alternative; yet conventional approaches struggle under heterogeneous, non-IID multi-center data and incur substantial communication overhead when adapting large models. In this work, we study federated FM fine-tuning for 3D CMR disease detection and propose Med-DualLoRA, a client-aware parameter-efficient fine-tuning (PEFT) federated framework that disentangles globally shared and local low-rank adaptations (LoRA) through additive decomposition. Global and local LoRA modules are trained locally, but only the global component is shared and aggregated across sites, keeping local adapters private. This design improves personalization while significantly reducing communication cost, and experiments show that adapting only two transformer blocks preserves performance while further improving efficiency. We evaluate our method on a multi-center state-of-the-art cine 3D CMR FM fine-tuned for disease detection using ACDC and combined M\&Ms datasets, treating each vendor as a federated client. Med-DualLoRA achieves statistically significant improved performance (balanced accuracy 0.768, specificity 0.612) compared to other federated PEFT baselines, while maintaining communication efficiency. Our approach provides a scalable solution for local federated adaptation of medical FMs under realistic clinical constraints.

Lidia Garrucho, Smriti Joshi, Kaisar Kushibar et al.

Breast cancer is the most frequently diagnosed malignancy among women worldwide and a leading cause of cancer-related mortality. Dynamic contrast-enhanced magnetic resonance imaging plays a central role in tumor characterization and treatment monitoring, particularly in patients receiving neoadjuvant chemotherapy. However, existing artificial intelligence models for breast magnetic resonance imaging are often developed using single-center data and evaluated using aggregate performance metrics, limiting their generalizability and obscuring potential performance disparities across demographic subgroups. The MAMA-MIA Challenge was designed to address these limitations by introducing a large-scale benchmark that jointly evaluates primary tumor segmentation and prediction of pathologic complete response using pre-treatment magnetic resonance imaging only. The training cohort comprised 1,506 patients from multiple institutions in the United States, while evaluation was conducted on an external test set of 574 patients from three independent European centers to assess cross-continental and cross-institutional generalization. A unified scoring framework combined predictive performance with subgroup consistency across age, menopausal status, and breast density. Twenty-six international teams participated in the final evaluation phase. Results demonstrate substantial performance variability under external testing and reveal trade-offs between overall accuracy and subgroup fairness. The challenge provides standardized datasets, evaluation protocols, and public resources to promote the development of robust and equitable artificial intelligence systems for breast cancer imaging.

Jorge Fabila, Víctor M. Campello, Carlos Martín-Isla et al.

Africa faces significant challenges in healthcare delivery due to limited infrastructure and access to advanced medical technologies. This study explores the use of federated learning to overcome these barriers, focusing on perinatal health. We trained a fetal plane classifier using perinatal data from five African countries: Algeria, Ghana, Egypt, Malawi, and Uganda, along with data from Spanish hospitals. To incorporate the lack of computational resources in the analysis, we considered a heterogeneous set of devices, including a Raspberry Pi and several laptops, for model training. We demonstrate comparative performance between a centralized and a federated model, despite the compute limitations, and a significant improvement in model generalizability when compared to models trained only locally. These results show the potential for a future implementation at a large scale of a federated learning platform to bridge the accessibility gap and improve model generalizability with very little requirements.

Jun Ma, Feifei Li, Sumin Kim et al.

Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.

Grzegorz Skorupko, Fotios Avgoustidis, Carlos Martín-Isla et al.

The nnU-Net framework has played a crucial role in medical image segmentation and has become the gold standard in multitudes of applications targeting different diseases, organs, and modalities. However, so far it has been used primarily in a centralized approach where the collected data is stored in the same location where nnU-Net is trained. This centralized approach has various limitations, such as potential leakage of sensitive patient information and violation of patient privacy. Federated learning has emerged as a key approach for training segmentation models in a decentralized manner, enabling collaborative development while prioritising patient privacy. In this paper, we propose FednnU-Net, a plug-and-play, federated learning extension of the nnU-Net framework. To this end, we contribute two federated methodologies to unlock decentralized training of nnU-Net, namely, Federated Fingerprint Extraction (FFE) and Asymmetric Federated Averaging (AsymFedAvg). We conduct a comprehensive set of experiments demonstrating high and consistent performance of our methods for breast, cardiac and fetal segmentation based on a multi-modal collection of 6 datasets representing samples from 18 different institutions. To democratize research as well as real-world deployments of decentralized training in clinical centres, we publicly share our framework at https://github.com/faildeny/FednnUNet .

Jorge Fabila, Lidia Garrucho, Víctor M. Campello et al.

This study explores the use of Federated Learning (FL) for tuberculosis (TB) diagnosis using chest X-rays in low-resource settings across Africa. FL allows hospitals to collaboratively train AI models without sharing raw patient data, addressing privacy concerns and data scarcity that hinder traditional centralized models. The research involved hospitals and research centers in eight African countries. Most sites used local datasets, while Ghana and The Gambia used public ones. The study compared locally trained models with a federated model built across all institutions to evaluate FL's real-world feasibility. Despite its promise, implementing FL in sub-Saharan Africa faces challenges such as poor infrastructure, unreliable internet, limited digital literacy, and weak AI regulations. Some institutions were also reluctant to share model updates due to data control concerns. In conclusion, FL shows strong potential for enabling AI-driven healthcare in underserved regions, but broader adoption will require improvements in infrastructure, education, and regulatory support.

Lidia Garrucho, Kaisar Kushibar, Claire-Anne Reidel et al.

Artificial Intelligence (AI) research in breast cancer Magnetic Resonance Imaging (MRI) faces challenges due to limited expert-labeled segmentations. To address this, we present a multicenter dataset of 1506 pre-treatment T1-weighted dynamic contrast-enhanced MRI cases, including expert annotations of primary tumors and non-mass-enhanced regions. The dataset integrates imaging data from four collections in The Cancer Imaging Archive (TCIA), where only 163 cases with expert segmentations were initially available. To facilitate the annotation process, a deep learning model was trained to produce preliminary segmentations for the remaining cases. These were subsequently corrected and verified by 16 breast cancer experts (averaging 9 years of experience), creating a fully annotated dataset. Additionally, the dataset includes 49 harmonized clinical and demographic variables, as well as pre-trained weights for a baseline nnU-Net model trained on the annotated data. This resource addresses a critical gap in publicly available breast cancer datasets, enabling the development, validation, and benchmarking of advanced deep learning models, thus driving progress in breast cancer diagnostics, treatment response prediction, and personalized care.

Carla Sendra-Balcells, Víctor M. Campello, Carlos Martín-Isla et al.

The domain generalization problem has been widely investigated in deep learning for non-contrast imaging over the last years, but it received limited attention for contrast-enhanced imaging. However, there are marked differences in contrast imaging protocols across clinical centers, in particular in the time between contrast injection and image acquisition, while access to multi-center contrast-enhanced image data is limited compared to available datasets for non-contrast imaging. This calls for new tools for generalizing single-domain, single-center deep learning models across new unseen domains and clinical centers in contrast-enhanced imaging. In this paper, we present an exhaustive evaluation of deep learning techniques to achieve generalizability to unseen clinical centers for contrast-enhanced image segmentation. To this end, several techniques are investigated, optimized and systematically evaluated, including data augmentation, domain mixing, transfer learning and domain adaptation. To demonstrate the potential of domain generalization for contrast-enhanced imaging, the methods are evaluated for ventricular segmentation in contrast-enhanced cardiac magnetic resonance imaging (MRI). The results are obtained based on a multi-center cardiac contrast-enhanced MRI dataset acquired in four hospitals located in three countries (France, Spain and China). They show that the combination of data augmentation and transfer learning can lead to single-center models that generalize well to new clinical centers not included during training. Single-domain neural networks enriched with suitable generalization procedures can reach and even surpass the performance of multi-center, multi-vendor models in contrast-enhanced imaging, hence eliminating the need for comprehensive multi-center datasets to train generalizable models.

Víctor M. Campello, Carlos Martín-Isla, Cristian Izquierdo et al.

Accurate segmentation of the cardiac boundaries in late gadolinium enhancement magnetic resonance images (LGE-MRI) is a fundamental step for accurate quantification of scar tissue. However, while there are many solutions for automatic cardiac segmentation of cine images, the presence of scar tissue can make the correct delineation of the myocardium in LGE-MRI challenging even for human experts. As part of the Multi-Sequence Cardiac MR Segmentation Challenge, we propose a solution for LGE-MRI segmentation based on two components. First, a generative adversarial network is trained for the task of modality-to-modality translation between cine and LGE-MRI sequences to obtain extra synthetic images for both modalities. Second, a deep learning model is trained for segmentation with different combinations of original, augmented and synthetic sequences. Our results based on three magnetic resonance sequences (LGE, bSSFP and T2) from 45 different patients show that the multi-sequence model training integrating synthetic images and data augmentation improves in the segmentation over conventional training with real datasets. In conclusion, the accuracy of the segmentation of LGE-MRI images can be improved by using complementary information provided by non-contrast MRI sequences.