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Structure-aware machine learning for medical image analysis
Umeå University, Faculty of Science and Technology, Department of Computing Science.ORCID iD: 0009-0001-9691-6042
2026 (English)Doctoral thesis, comprehensive summary (Other academic)Alternative title
Strukturmedveten maskininlärning för medicinsk bildanalys (Swedish)
Abstract [en]

Machine learning (ML) has become a powerful tool, with remarkable success across a wide range of areas. In medical image analysis, ML has shown great potential for supporting diagnosis, treatment planning, and disease monitoring by extracting patterns from complex imaging data.

This thesis focuses on structure-aware ML methods for medical image analysis. Medical images exhibit strong spatial structure rather than consisting of independent pixel or voxel intensities. The central idea in the work is to incorporate this prior knowledge into the learning process. The work combines theoretical method development with empirical evaluation on medical imaging applications. The work begins by introducing mathematical morphology as a form of regularization, encouraging the selection of spatially coherent features while also controlling the size of the selected structures (Paper I). The proposed methods are further developed for the multi-class classification task, with particular emphasis on identifying spatially coherent and interpretable image regions associated with disease progression (Paper II).

The work then develops a structured prior distribution based on total variation (TV) within a Bayesian regression framework. Specifically, a well-defined family of structured priors that combines TV with an lp norm is constructed and proven to be proper. The resulting Bayesian formulation enables the estimation of tissue-specific parameter maps together with the quantification of their associated uncertainty (Paper III & Paper IV).

Finally, an input-dependent model is developed in which a neural network generates sample-specific regression coefficients. The Fisher information is used to quantify uncertainty in these coefficients, providing both interpretable predictions and uncertainty estimates (Paper V).

These contributions demonstrate how incorporating prior structure knowledge can guide models toward anatomically plausible solutions. By additionally quantifying uncertainty in estimated parameters, the developed methods provide information about how certain a model is in its outputs, thereby improving the reliability and interpretability of ML methods for medical image analysis.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2026. , p. 58
Series
Report / UMINF, ISSN 0348-0542 ; 26.07
Keywords [en]
Machine learning, Structured regularization, MRI, Bayesian approaches, Interpretability, Uncertainty
National Category
Computer Sciences
Identifiers
URN: urn:nbn:se:umu:diva-257244ISBN: 978-91-6850-109-3 (print)ISBN: 978-91-6850-110-9 (electronic)OAI: oai:DiVA.org:umu-257244DiVA, id: diva2:2090423
Public defence
2026-09-04, AUR.B.330 – Castor, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2026-08-14 Created: 2026-08-06 Last updated: 2026-08-07Bibliographically approved
List of papers
1. Structured regularization with object size selection using mathematical morphology
Open this publication in new window or tab >>Structured regularization with object size selection using mathematical morphology
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2025 (English)In: Pattern Analysis and Applications, ISSN 1433-7541, E-ISSN 1433-755X, Vol. 28, article id 70Article in journal (Refereed) Published
Abstract [en]

We propose a novel way to incorporate morphology operators through structured regularization of machine learning models. Specifically, we introduce a feature map in the models that performs structured variable selection. The feature map is automatically processed by approximate morphology operators and is learned together with the model coefficients. Experiments were conducted with linear regression on both synthetic data, demonstrating that the proposed methods are effective in selecting groups of parameters with much less noise than baseline models, and on three-dimensional T1-weighted brain magnetic resonance images (MRI) for age prediction, demonstrating that the proposed methods enforce sparsity and select homogeneous regions of non-zero and relevant regression coefficients. The proposed methods improve interpretability in pattern analysis. The minimum size of features in the structured variable selection can be controlled by adjusting the structuring element in the approximate morphology operator, tailored to the specific study of interest. With these added benefits, the proposed methods still perform on par with commonly used variable selection and structured variable selection methods in terms of the coefficient of determination and the Pearson correlation coefficient.

Place, publisher, year, edition, pages
Springer Nature, 2025
Keywords
Structured regularization, Approximate morphology operators, Feature selection, fW-mean filters
National Category
Artificial Intelligence Computer graphics and computer vision
Identifiers
urn:nbn:se:umu:diva-236995 (URN)10.1007/s10044-025-01444-7 (DOI)001455367400002 ()2-s2.0-105001489397 (Scopus ID)
Funder
Swedish Research Council, 2021-04810Lions Cancerforskningsfond i Norr, LP 24-2367
Available from: 2025-03-27 Created: 2025-03-27 Last updated: 2026-08-06Bibliographically approved
2. Structured regularization using approximate morphology for Alzheimer's disease classification
Open this publication in new window or tab >>Structured regularization using approximate morphology for Alzheimer's disease classification
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2025 (English)In: 2025 IEEE 22nd International Symposium on Biomedical Imaging (ISBI), 2025, p. 1-4Conference paper, Published paper (Refereed)
Abstract [en]

Structured regularization allows machine learning models to consider spatial relationships among parameters, leading to results that generalize better and are more interpretable compared to norm penalties. In this study, we evaluated a novel structured regularization method that incorporates approximate morphology operators defined using harmonic mean-based fW-filters. We extended this method to multiclass classification and conducted experiments aimed at classifying magnetic resonance images (MRI) of subjects into four stages of Alzheimer's disease progression. The experimental results demonstrate that the novel structured regularization method not only performs better than standard sparse and structured regularization methods in terms of prediction accuracy (ACC), F1 scores, and the area under the receiver operating characteristic curve (AUC), but also produces interpretable coefficient maps.

Series
Proceedings (International Symposium on Biomedical Imaging), ISSN 1945-7928, E-ISSN 1945-8452
Keywords
Structured regularization, MRI, Alzheimer’s disease, Classification, Interpretation
National Category
Computer graphics and computer vision Neurosciences Artificial Intelligence
Identifiers
urn:nbn:se:umu:diva-239040 (URN)10.1109/ISBI60581.2025.10981098 (DOI)2-s2.0-105005824554 (Scopus ID)979-8-3315-2052-6 (ISBN)979-8-3315-2053-3 (ISBN)
Conference
2025 IEEE 22nd International Symposium on Biomedical Imaging (ISBI), Houston, TX, USA, April 11-17, 2025
Funder
Swedish Research Council, 2021-04810Lions Cancerforskningsfond i Norr, LP 24-2367
Available from: 2025-05-21 Created: 2025-05-21 Last updated: 2026-08-06Bibliographically approved
3. A proper structured prior for Bayesian T1 mapping
Open this publication in new window or tab >>A proper structured prior for Bayesian T1 mapping
2025 (English)In: Uncertainty for safe utilization of machine learning in medical imaging: 7th International workshop, UNSURE 2025, held in conjunction with MICCAI 2025, Daejeon, South Korea, September 27, 2025, Proceedings / [ed] Carole H. Sudre, Mobarak I. Hoque, Raghav Mehta, Cheng Ouyang, Chen Qin, Marianne Rakic, William M. Wells, Cham: Springer, 2025, Vol. 16166, p. 224-233Conference paper, Published paper (Refereed)
Abstract [en]

This work proposes a structured prior integrated within the Bayesian framework for variable flip angle T1 mapping. The proposed structured prior combines total variation (TV) and L1 norm functions, and is proven to be a proper prior. The TV–L1 prior promotes sparsity in the spatial gradients of the parametric maps, resulting in smooth and coherent image reconstructions. Embedding the prior within the Bayesian framework enables uncertainty quantification for both T1 and M0 estimates. Posterior inference was performed using the No-U-Turn Sampler (NUTS). The proposed method is compared to maximum likelihood estimation and to alternative Bayesian models that employ uniform, Laplace, and bounded TV priors. The results show that the proposed method yields narrower probability density functions, indicating reduced uncertainty. The proposed method also achieves lower variance and exhibits a smaller negative bias, reflecting more stable estimates. Overall, the integration of TV and L1 functions in a prior within the Bayesian framework enhances spatial coherence in T1 mapping and delivers improved uncertainty quantification, making it a promising tool for robust quantitative MRI parameter estimation.

Place, publisher, year, edition, pages
Cham: Springer, 2025
Series
Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 16166
Keywords
Bayesian inference, T1 Mapping, Uncertainty quantification, Structured prior, Total variation
National Category
Artificial Intelligence Computer graphics and computer vision Probability Theory and Statistics Radiology and Medical Imaging
Identifiers
urn:nbn:se:umu:diva-244790 (URN)10.1007/978-3-032-06593-3_21 (DOI)978-3-032-06592-6 (ISBN)978-3-032-06593-3 (ISBN)
Conference
7th International Workshop, UNSURE 2025, Daejeon, South Korea, September 27, 2025
Funder
Swedish Research Council, 2021-04810Lions Cancerforskningsfond i Norr, LP 24-2367
Available from: 2025-09-30 Created: 2025-09-30 Last updated: 2026-08-06Bibliographically approved
4. Generalized TV–ℓp Structured Priors for Bayesian T1 Mapping
Open this publication in new window or tab >>Generalized TV–ℓp Structured Priors for Bayesian T1 Mapping
2026 (English)In: Machine Learning for Biomedical Imaging, E-ISSN 2766-905X, Vol. 2026, no UNSURE2025, p. 297-312, article id 2026:015Article in journal (Refereed) Published
Abstract [en]

We propose an extended family of structured spatial priors that incorporates the total variation (TV) function with ℓp norms. The prior is proven to be proper and incorporated into a Bayesian regression framework to enable uncertainty quantification in T1 mapping, with posterior inference performed using the No-U-Turn Sampler (NUTS). This TV– ℓp construction is proven to constitute a well-defined family of prior distributions, and it naturally enforces spatial consistency and smooth variations in the estimated parameter maps. The method was evaluated in comparison to maximum-likelihood estimation and several Bayesian alternative priors based on the uniform, Gamma, and bounded TV priors. The evaluation includes experiments on synthetic brain and cardiac T1 mapping datasets, as well as a real in-vivo breast T1 mapping dataset. The results show that the TV–ℓp prior yields more concentrated posterior densities, indicating reduced uncertainty. It also consistently achieves lower variance and smaller (negative) bias, leading to more reliable estimates. Overall, embedding a TV-based structured penalty along with ℓp norms in a prior in a Bayesian model improves spatial coherence in T1 maps and enhances uncertainty quantification, offering a robust approach for T1 mapping with uncertainties.

Place, publisher, year, edition, pages
Machine Learning for Biomedical Imaging, 2026
Keywords
Bayesian Inference, T1 Mapping, Uncertainty Quantification, Structured Prior, Total Variation, ℓp Norms
National Category
Computational Mathematics
Identifiers
urn:nbn:se:umu:diva-257242 (URN)10.59275/j.melba.2026-g41g (DOI)
Funder
Swedish Research Council, 2021-04810Cancerforskningsfonden i Norrland, LP 22-2319Cancerforskningsfonden i Norrland, LP 24-2367Cancerforskningsfonden i Norrland, AMP 26-1265
Available from: 2026-08-06 Created: 2026-08-06 Last updated: 2026-08-07Bibliographically approved
5. Large-scale local regression models with uncertainty quantification
Open this publication in new window or tab >>Large-scale local regression models with uncertainty quantification
(English)Manuscript (preprint) (Other academic)
National Category
Computational Mathematics
Identifiers
urn:nbn:se:umu:diva-257243 (URN)
Available from: 2026-08-06 Created: 2026-08-06 Last updated: 2026-08-07Bibliographically approved

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