Comparative Benchmarking of Failure Detection Methods in Medical Image Segmentation: Unveiling the Role of Confidence Aggregation

Semantic segmentation is an essential component of medical image analysis research, with recent deep learning algorithms offering out-of-the-box applicability across diverse datasets. Despite these advancements, segmentation failures remain a significant concern for real-world clinical applications, necessitating reliable detection mechanisms. This paper introduces a comprehensive benchmarking framework aimed at evaluating failure detection methodologies within medical image segmentation. Through our analysis, we identify the strengths and limitations of current failure detection metrics, advocating for the risk-coverage analysis as a holistic evaluation approach. Utilizing a collective dataset comprising five public 3D medical image collections, we assess the efficacy of various failure detection strategies under realistic test-time distribution shifts. Our findings highlight the importance of pixel confidence aggregation and we observe superior performance of the pairwise Dice score (Roy et al., 2019) between ensemble predictions, positioning it as a simple and robust baseline for failure detection in medical image segmentation. To promote ongoing research, we make the benchmarking framework available to the community.

Real-World Federated Learning in Radiology: Hurdles to overcome and Benefits to gain

Objective: Federated Learning (FL) enables collaborative model training while keeping data locally. Currently, most FL studies in radiology are conducted in simulated environments due to numerous hurdles impeding its translation into practice. The few existing real-world FL initiatives rarely communicate specific measures taken to overcome these hurdles, leaving behind a significant knowledge gap. Minding efforts to implement real-world FL, there is a notable lack of comprehensive assessment comparing FL to less complex alternatives. Materials & Methods: We extensively reviewed FL literature, categorizing insights along with our findings according to their nature and phase while establishing a FL initiative, summarized to a comprehensive guide. We developed our own FL infrastructure within the German Radiological Cooperative Network (RACOON) and demonstrated its functionality by training FL models on lung pathology segmentation tasks across six university hospitals. We extensively evaluated FL against less complex alternatives in three distinct evaluation scenarios. Results: The proposed guide outlines essential steps, identified hurdles, and proposed solutions for establishing successful FL initiatives conducting real-world experiments. Our experimental results show that FL outperforms less complex alternatives in all evaluation scenarios, justifying the effort required to translate FL into real-world applications. Discussion & Conclusion: Our proposed guide aims to aid future FL researchers in circumventing pitfalls and accelerating translation of FL into radiological applications. Our results underscore the value of efforts needed to translate FL into real-world applications by demonstrating advantageous performance over alternatives, and emphasize the importance of strategic organization, robust management of distributed data and infrastructure in real-world settings.

Mitigating False Predictions In Unreasonable Body Regions

Despite considerable strides in developing deep learning models for 3D medical image segmentation, the challenge of effectively generalizing across diverse image distributions persists. While domain generalization is acknowledged as vital for robust application in clinical settings, the challenges stemming from training with a limited Field of View (FOV) remain unaddressed. This limitation leads to false predictions when applied to body regions beyond the FOV of the training data. In response to this problem, we propose a novel loss function that penalizes predictions in implausible body regions, applicable in both single-dataset and multi-dataset training schemes. It is realized with a Body Part Regression model that generates axial slice positional scores. Through comprehensive evaluation using a test set featuring varying FOVs, our approach demonstrates remarkable improvements in generalization capabilities. It effectively mitigates false positive tumor predictions up to 85% and significantly enhances overall segmentation performance.

Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures

Accurately segmenting thin tubular structures, such as vessels, nerves, roads or concrete cracks, is a crucial task in computer vision. Standard deep learning-based segmentation loss functions, such as Dice or Cross-Entropy, focus on volumetric overlap, often at the expense of preserving structural connectivity or topology. This can lead to segmentation errors that adversely affect downstream tasks, including flow calculation, navigation, and structural inspection. Although current topology-focused losses mark an improvement, they introduce significant computational and memory overheads. This is particularly relevant for 3D data, rendering these losses infeasible for larger volumes as well as increasingly important multi-class segmentation problems. To mitigate this, we propose a novel Skeleton Recall Loss, which effectively addresses these challenges by circumventing intensive GPU-based calculations with inexpensive CPU operations. It demonstrates overall superior performance to current state-of-the-art approaches on five public datasets for topology-preserving segmentation, while substantially reducing computational overheads by more than 90%. In doing so, we introduce the first multi-class capable loss function for thin structure segmentation, excelling in both efficiency and efficacy for topology-preservation.

ValUES: A Framework for Systematic Validation of Uncertainty Estimation in Semantic Segmentation

Uncertainty estimation is an essential and heavily-studied component for the reliable application of semantic segmentation methods. While various studies exist claiming methodological advances on the one hand, and successful application on the other hand, the field is currently hampered by a gap between theory and practice leaving fundamental questions unanswered: Can data-related and model-related uncertainty really be separated in practice? Which components of an uncertainty method are essential for real-world performance? Which uncertainty method works well for which application? In this work, we link this research gap to a lack of systematic and comprehensive evaluation of uncertainty methods. Specifically, we identify three key pitfalls in current literature and present an evaluation framework that bridges the research gap by providing 1) a controlled environment for studying data ambiguities as well as distribution shifts, 2) systematic ablations of relevant method components, and 3) test-beds for the five predominant uncertainty applications: OoD-detection, active learning, failure detection, calibration, and ambiguity modeling. Empirical results on simulated as well as real-world data demonstrate how the proposed framework is able to answer the predominant questions in the field revealing for instance that 1) separation of uncertainty types works on simulated data but does not necessarily translate to real-world data, 2) aggregation of scores is a crucial but currently neglected component of uncertainty methods, 3) While ensembles are performing most robustly across the different downstream tasks and settings, test-time augmentation often constitutes a light-weight alternative. Code is at: https://github.com/IML-DKFZ/values

Why is the winner the best?

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.

MultiTalent: A Multi-Dataset Approach to Medical Image Segmentation

The medical imaging community generates a wealth of datasets, many of which are openly accessible and annotated for specific diseases and tasks such as multi-organ or lesion segmentation. Current practices continue to limit model training and supervised pre-training to one or a few similar datasets, neglecting the synergistic potential of other available annotated data. We propose MultiTalent, a method that leverages multiple CT datasets with diverse and conflicting class definitions to train a single model for a comprehensive structure segmentation. Our results demonstrate improved segmentation performance compared to previous related approaches, systematically, also compared to single dataset training using state-of-the-art methods, especially for lesion segmentation and other challenging structures. We show that MultiTalent also represents a powerful foundation model that offers a superior pre-training for various segmentation tasks compared to commonly used supervised or unsupervised pre-training baselines. Our findings offer a new direction for the medical imaging community to effectively utilize the wealth of available data for improved segmentation performance. The code and model weights will be published here: [tba]

Biomedical image analysis competitions: The state of current participation practice

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.

Federated Learning Enables Big Data for Rare Cancer Boundary Detection

Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data. This is currently addressed by centrally sharing ample, and importantly diverse, data from multiple sites. However, such centralization is challenging to scale (or even not feasible) due to various limitations. Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here we present findings from the largest FL study to-date, involving data from 71 healthcare institutions across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, utilizing the largest dataset of such patients ever used in the literature (25,256 MRI scans from 6,314 patients). We demonstrate a 33% improvement over a publicly trained model to delineate the surgically targetable tumor, and 23% improvement over the tumor's entire extent. We anticipate our study to: 1) enable more studies in healthcare informed by large and diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further quantitative analyses for glioblastoma via performance optimization of our consensus model for eventual public release, and 3) demonstrate the effectiveness of FL at such scale and task complexity as a paradigm shift for multi-site collaborations, alleviating the need for data sharing.

The Federated Tumor Segmentation (FeTS) Challenge

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often remains unclear, as the data included in challenges are usually acquired in very controlled settings at few institutions. The seemingly obvious solution of just collecting increasingly more data from more institutions in such challenges does not scale well due to privacy and ownership hurdles. Towards alleviating these concerns, we are proposing the FeTS challenge 2021 to cater towards both the development and the evaluation of models for the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. Specifically, the FeTS 2021 challenge uses clinically acquired, multi-institutional magnetic resonance imaging (MRI) scans from the BraTS 2020 challenge, as well as from various remote independent institutions included in the collaborative network of a real-world federation (https://www.fets.ai/). The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i.e. on data from institutional distributions that were not part of the training datasets.