Failure detection in biomedical image classification under realistic distribution shifts: insights from a large-scale evaluation
Open accessAbstract
Biomedical images (BMI) exhibit variability due to different acquisition protocols, devices, and patient populations, making failure detection at inference time essential for reliable deployment of clinical classifiers. As existing evaluations of failure detection methods use different settings, it is difficult to compare results and identify the best strategy, if any. We present a comprehensive evaluation of eight confidence scoring functions and two score-aggregation strategies across eight BMI tasks spanning diverse modalities, backbone architectures, training setups, and failure sources. The confidence ranking ability and classification error mitigation are jointly evaluated. While no single method systematically dominated across settings, aggregation of confidence scores consistently matched or approached the best individual method and substantially reduced silent failure rate. The failure detection performance was strongly correlated with classifier accuracy for all tested settings. These findings provide large-scale evidence of the strengths and limitations of confidence scoring strategies and offer actionable guidance for mitigating silent failures under realistic distribution shifts in BMI. Graphical Abstract: Highlights: Failure detection performance is independent of biomedical image modality but strongly correlated with classifier accuracy. Monte Carlo Dropout does not outperform simple margin-based scores despite substantially higher computational costs. Aggregating standardized confidence scores provides more robust performance than individual methods and reduces mean silent failure rates from 24% down to 8% for realistic distribution shifts. Cross-validation ensembling improves both classification accuracy and failure detection performance.
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Cites
Identifying Medical Diagnoses and Treatable Diseases by Image-Based Deep Learning
Kermany, D. S., Goldbaum, M., Cai, W., Valentim, C. C. S., Liang, H., Baxter, S. L., McKeown, A., Yang, G., Wu, X., Yan, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.010 · Cited by 4,842 · see citing works
Randaugment: Practical automated data augmentation with a reduced search space
Cubuk, E. D., Zoph, B., Shlens, J., & Le, Q. V. (2020) · 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) · doi:10.1109/cvprw50498.2020.00359 · Cited by 3,223 · see citing works
Dataset of breast ultrasound images
Al-Dhabyani, W., Gomaa, M., Khaled, H., & Fahmy, A. (2020) · Data in Brief · doi:10.1016/j.dib.2019.104863 · Cited by 2,405 · see citing works
The Liver Tumor Segmentation Benchmark (LiTS)
Bilic, P., Christ, P., Li, H. B., Vorontsov, E., Ben-Cohen, A., Kaissis, G., Szeskin, A., Jacobs, C., Mamani, G. E. H., Chartrand, G., et al. (2023) · Medical Image Analysis · doi:10.1016/j.media.2022.102680 · Cited by 1,412 · see citing works
Kather, J. N., Krisam, J., Charoentong, P., Luedde, T., Herpel, E., Weis, C.-A., Gaiser, T., Marx, A., Valous, N. A., Ferber, D., et al. (2019) · PLOS Medicine · doi:10.1371/journal.pmed.1002730 · Cited by 1,082 · see citing works
MedMNIST v2 - A large-scale lightweight benchmark for 2D and 3D biomedical image classification
Yang, J., Shi, R., Wei, D., Liu, Z., Zhao, L., Ke, B., Pfister, H., & Ni, B. (2023) · Scientific Data · doi:10.1038/s41597-022-01721-8 · Cited by 1,043 · see citing works
Generalized Out-of-Distribution Detection: A Survey
Yang, J., Zhou, K., Li, Y., & Liu, Z. (2024) · International Journal of Computer Vision · doi:10.1007/s11263-024-02117-4 · Cited by 884 · see citing works
Annotated high-throughput microscopy image sets for validation
Ljosa, V., Sokolnicki, K. L., & Carpenter, A. E. (2012) · Nature Methods · doi:10.1038/nmeth.2083 · Cited by 601 · see citing works
The need for uncertainty quantification in machine-assisted medical decision making
Begoli, E., Bhattacharya, T., & Kusnezov, D. (2019) · Nature Machine Intelligence · doi:10.1038/s42256-018-0004-1 · Cited by 597 · see citing works
Acevedo, A., Merino, A., Alférez, S., Molina, Á., Boldú, L., & Rodellar, J. (2020) · Data in Brief · doi:10.1016/j.dib.2020.105474 · Cited by 344 · see citing works
Lambert, B., Forbes, F., Doyle, S., Dehaene, H., & Dojat, M. (2024) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2024.102830 · Cited by 318 · see citing works
100,000 Histological Images Of Human Colorectal Cancer And Healthy Tissue
Kather, J. N., Halama, N., & Marx, A. (2018) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.1214455 · Cited by 194 · see citing works
100,000 Histological Images Of Human Colorectal Cancer And Healthy Tissue
Kather, J. N., Halama, N., & Marx, A. (2018) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.1214456 · Cited by 180 · see citing works
Large Dataset of Labeled Optical Coherence Tomography (OCT) and Chest X-Ray Images
Kermany, D. (2018) · Mendeley · doi:10.17632/rscbjbr9sj.3 · Cited by 172 · see citing works
Dvijotham, K., Winkens, J., Barsbey, M., Ghaisas, S., Stanforth, R., Pawlowski, N., Strachan, P., Ahmed, Z., Azizi, S., Bachrach, Y., et al. (2023) · Nature Medicine · doi:10.1038/s41591-023-02437-x · Cited by 136 · see citing works
Huang, L., Ruan, S., Xing, Y.-C., & Feng, M.-L. (2024) · Medical Image Anal. · doi:10.1016/j.media.2024.103223 · Cited by 90 · see citing works
Predictive uncertainty estimation for out-of-distribution detection in digital pathology
Linmans, J., Elfwing, S., van der Laak, J., & Litjens, G. (2023) · Medical Image Analysis · doi:10.1016/j.media.2022.102655 · Cited by 75 · see citing works
A comprehensive multi-domain dataset for mitotic figure detection
Aubreville, M., Wilm, F., Stathonikos, N., Breininger, K., Donovan, T., Jabari, S., Veta, M., Ganz, J., Ammeling, J., van Diest, P. J., et al. (2023) · Scientific Data · doi:10.1038/s41597-023-02327-4 · Cited by 72 · see citing works
Implementing vision transformer for classifying 2D biomedical images
Halder, A., Gharami, S., Sadhu, P., Singh, P. K., Woźniak, M., & Ijaz, M. F. (2024) · Scientific Reports · doi:10.1038/s41598-024-63094-9 · Cited by 72 · see citing works
Tschandl, P. (2018) · Harvard Dataverse · doi:10.7910/dvn/dbw86t · Cited by 71 · see citing works
Physical imaging parameter variation drives domain shift
Kilim, O., Olar, A., Joó, T., Palicz, T., Pollner, P., & Csabai, I. (2022) · Scientific Reports · doi:10.1038/s41598-022-23990-4 · Cited by 36 · see citing works
Investigating the Quality of DermaMNIST and Fitzpatrick17k Dermatological Image Datasets
Abhishek, K., Jain, A., & Hamarneh, G. (2025) · Scientific Data · doi:10.1038/s41597-025-04382-5 · Cited by 32 · see citing works
In Situ Classification of Cell Types in Human Kidney Tissue Using 3D Nuclear Staining
Woloshuk, A., Khochare, S., Almulhim, A., McNutt, A. T., Dean, D. F., Barwinska, D., Ferkowicz, M. J., Eadon, M. T., Kelly, K. J., Dunn, K. W., et al. (2020) · Cytometry Part A · doi:10.1002/cyto.a.24274 · Cited by 25 · see citing works
Zenk, M., Zimmerer, D., Isensee, F., Traub, J., Norajitra, T., Jäger, P. F., & Maier-Hein, K. H. (2024) · Medical Image Analysis · doi:10.1016/j.media.2024.103392 · Cited by 22 · see citing works
Mehrtens, H. A., Kurz, A., Bucher, T.-C., & Brinker, T. J. (2023) · Medical Image Analysis · doi:10.1016/j.media.2023.102914 · Cited by 18 · see citing works
Xia, G., & Bouganis, C.-S. (2024) · International Journal of Computer Vision · doi:10.1007/s11263-024-02029-3 · Cited by 17 · see citing works
Rethinking model prototyping through the MedMNIST+ dataset collection
Doerrich, S., Salvo, F. D., Brockmann, J., & Ledig, C. (2025) · Scientific Reports · doi:10.1038/s41598-025-92156-9 · Cited by 14 · see citing works
OpenMIBOOD: Open Medical Imaging Benchmarks for Out-Of-Distribution Detection
Gutbrod, M., Rauber, D., Nunes, D. W., et al. (2025) · IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings · doi:10.1109/cvpr52734.2025.02410 · Cited by 10 · see citing works
Understanding Silent Failures in Medical Image Classification
Bungert, T. J., Kobelke, L., & Jäger, P. F. (2023) · Lecture notes in computer science · doi:10.1007/978-3-031-43898-1_39 · Cited by 9 · see citing works
Large-Scale Histological Image Dataset with Metadata for Colorectal Cancer Microenvironment
Wang, H., Li, H., Xue, J., Jiang, Y., Ma, K., Du, F., Mo, G., Li, H. R., Huang, Y., Xie, H., et al. (2026) · Scientific Data · doi:10.1038/s41597-026-06675-9
Flagged first, then by citations
Research works printed but not linked: 17
- 2019, Skin lesion analysis toward melanoma detection 2018: A challenge hosted by the international skin imaging collaboration (isic), arXiv preprint
- 2024, Medmnist-c: Comprehensive benchmark and improved classifier robustness by simulating realistic image corruptions, arXiv preprint
- Gal, Y. , Ghahramani, Z. , 2016. Dropout as a bayesian approximation: Representing model uncertainty in deep learning, in: international conference on machine learning, PMLR. pp. 1050–1059.
- Guo, C. , Pleiss, G. , Sun, Y. , Weinberger, K.Q. , 2017. On calibration of modern neural networks, in: International conference on machine learning, PMLR. pp. 1321–1330.
- 2019, Scaling out-of-distribution detection for real-world settings, arXiv preprint
- 2016, A baseline for detecting misclassified and out-of-distribution examples in neural networks, arXiv preprint
- 2022, A call to reflect on evaluation practices for failure detection in image classification, arXiv preprint
- 2022, Amos: A large-scale abdominal multi-organ benchmark for versatile medical image segmentation, arXiv preprint
- Lakshminarayanan, B. , Pritzel, A. , Blundell, C. , 2017. Simple and scalable predictive uncertainty estimation using deep ensembles. Advances in neural information processing systems 30.
- 2017, Leveraging uncertainty information from deep neural networks for disease detection, Scientific reports, 7, 1
- Lyzhov, A. , Molchanova, Y. , Ashukha, A. , Molchanov, D. , Vetrov, D. , 2020. Greedy policy search: A simple baseline for learnable test-time augmentation, in: Conference on uncertainty in artificial intelligence, PMLR. pp. 1308–1317.
- 2025, A systematic analysis of out-of-distribution detection under representation and training paradigm shifts, arXiv preprint
- Sun, Y. , Ming, Y. , Zhu, X. , Li, Y. , 2022. Out-of-distribution detection with deep nearest neighbors, in: International conference on machine learning, PMLR. pp. 20827–20840.
- 2024, Overcoming common flaws in the evaluation of selective classification systems, Advances in Neural Information Processing Systems, 37, 2323
- 2018, The ham10000 dataset, a large collection of multi-source dermatoscopic images of common pigmented skin lesions, Scientific data, 5, 1
- 2021, A fine-grained analysis on distribution shift, arXiv preprint
- 2022, Openood: Benchmarking generalized out-of-distribution detection, Advances in Neural Information Processing Systems, 35, 32598
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- Authors
- Steinmetz, P., Frouin, F., Morard, V., & Buvat, I.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Université Paris-Saclay (FR)
- GE HealthCare, Buc, 78530, France
- Venue
- medRxiv
- Publisher
- openRxiv
- Published
- 2026-05-05
- OpenAlex
- W7160306460
- Semantic Scholar
- bb46cc54507e46389150c9dc442fc464e1c2a6d8
- Cited by
- 0
- References
- 30
- Type
- posted content
- Open access
- green
- doi.org
- Licence
- Locations
- medRxiv (acceptedVersion, cc-by-nc)
- Topics
- Health Sciences › Medicine › Health Informatics › Artificial Intelligence in Healthcare and Education
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
- Physical Sciences › Computer Science › Artificial Intelligence › Adversarial Robustness in Machine Learning
- Keywords
- fault detection, biomedical image classification, distribution shift, confidence scores, silent failures, Monte Carlo dropout, evaluation benchmark
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