Kristoffer Wickstrøm

Kristoffer Wickstrøm, Michael Kampffmeyer, Karl Øyvind Mikalsen et al.

The lack of labeled data is a key challenge for learning useful representation from time series data. However, an unsupervised representation framework that is capable of producing high quality representations could be of great value. It is key to enabling transfer learning, which is especially beneficial for medical applications, where there is an abundance of data but labeling is costly and time consuming. We propose an unsupervised contrastive learning framework that is motivated from the perspective of label smoothing. The proposed approach uses a novel contrastive loss that naturally exploits a data augmentation scheme in which new samples are generated by mixing two data samples with a mixing component. The task in the proposed framework is to predict the mixing component, which is utilized as soft targets in the loss function. Experiments demonstrate the framework's superior performance compared to other representation learning approaches on both univariate and multivariate time series and illustrate its benefits for transfer learning for clinical time series.

Solveig Thrun, Stine Hansen, Zijun Sun et al.

Regular mammography screening is crucial for early breast cancer detection. By leveraging deep learning-based risk models, screening intervals can be personalized, especially for high-risk individuals. While recent methods increasingly incorporate longitudinal information from prior mammograms, accurate spatial alignment across time points remains a key challenge. Misalignment can obscure meaningful tissue changes and degrade model performance. In this study, we provide insights into various alignment strategies, image-based registration, feature-level (representation space) alignment with and without regularization, and implicit alignment methods, for their effectiveness in longitudinal deep learning-based risk modeling. Using two large-scale mammography datasets, we assess each method across key metrics, including predictive accuracy, precision, recall, and deformation field quality. Our results show that image-based registration consistently outperforms the more recently favored feature-based and implicit approaches across all metrics, enabling more accurate, temporally consistent predictions and generating smooth, anatomically plausible deformation fields. Although regularizing the deformation field improves deformation quality, it reduces the risk prediction performance of feature-level alignment. Applying image-based deformation fields within the feature space yields the best risk prediction performance. These findings underscore the importance of image-based deformation fields for spatial alignment in longitudinal risk modeling, offering improved prediction accuracy and robustness. This approach has strong potential to enhance personalized screening and enable earlier interventions for high-risk individuals. The code is available at https://github.com/sot176/Mammogram_Alignment_Study_Risk_Prediction.git, allowing full reproducibility of the results.

Kristoffer Wickstrøm, J. Emmanuel Johnson, Sigurd Løkse et al.

This paper presents the kernelized Taylor diagram, a graphical framework for visualizing similarities between data populations. The kernelized Taylor diagram builds on the widely used Taylor diagram, which is used to visualize similarities between populations. However, the Taylor diagram has several limitations such as not capturing non-linear relationships and sensitivity to outliers. To address such limitations, we propose the kernelized Taylor diagram. Our proposed kernelized Taylor diagram is capable of visualizing similarities between populations with minimal assumptions of the data distributions. The kernelized Taylor diagram relates the maximum mean discrepancy and the kernel mean embedding in a single diagram, a construction that, to the best of our knowledge, have not been devised prior to this work. We believe that the kernelized Taylor diagram can be a valuable tool in data visualization.

Kristoffer Wickstrøm, Teresa Dorszewski, Siyan Chen et al.

Current approaches for designing self-explainable models (SEMs) require complicated training procedures and specific architectures which makes them impractical. With the advance of general purpose foundation models based on Vision Transformers (ViTs), this impracticability becomes even more problematic. Therefore, new methods are necessary to provide transparency and reliability to ViT-based foundation models. In this work, we present a new method for turning any well-trained ViT-based model into a SEM without retraining, which we call Keypoint Counting Classifiers (KCCs). Recent works have shown that ViTs can automatically identify matching keypoints between images with high precision, and we build on these results to create an easily interpretable decision process that is inherently visualizable in the input. We perform an extensive evaluation which show that KCCs improve the human-machine communication compared to recent baselines. We believe that KCCs constitute an important step towards making ViT-based foundation models more transparent and reliable.

Solveig Thrun, Stine Hansen, Zijun Sun et al.

Regular mammography screening is essential for early breast cancer detection. Deep learning-based risk prediction methods have sparked interest to adjust screening intervals for high-risk groups. While early methods focused only on current mammograms, recent approaches leverage the temporal aspect of screenings to track breast tissue changes over time, requiring spatial alignment across different time points. Two main strategies for this have emerged: explicit feature alignment through deformable registration and implicit learned alignment using techniques like transformers, with the former providing more control. However, the optimal approach for explicit alignment in mammography remains underexplored. In this study, we provide insights into where explicit alignment should occur (input space vs. representation space) and if alignment and risk prediction should be jointly optimized. We demonstrate that jointly learning explicit alignment in representation space while optimizing risk estimation performance, as done in the current state-of-the-art approach, results in a trade-off between alignment quality and predictive performance and show that image-level alignment is superior to representation-level alignment, leading to better deformation field quality and enhanced risk prediction accuracy. The code is available at https://github.com/sot176/Longitudinal_Mammogram_Alignment.git.

Suaiba Amina Salahuddin, Teresa Dorszewski, Marit Almenning Martiniussen et al.

Understanding what deep learning (DL) models learn is essential for the safe deployment of artificial intelligence (AI) in clinical settings. While previous work has focused on pixel-based explainability methods, less attention has been paid to the textual concepts learned by these models, which may better reflect the reasoning used by clinicians. We introduce Mammo-CLIP Dissect, the first concept-based explainability framework for systematically dissecting DL vision models trained for mammography. Leveraging a mammography-specific vision-language model (Mammo-CLIP) as a "dissector," our approach labels neurons at specified layers with human-interpretable textual concepts and quantifies their alignment to domain knowledge. Using Mammo-CLIP Dissect, we investigate three key questions: (1) how concept learning differs between DL vision models trained on general image datasets versus mammography-specific datasets; (2) how fine-tuning for downstream mammography tasks affects concept specialisation; and (3) which mammography-relevant concepts remain underrepresented. We show that models trained on mammography data capture more clinically relevant concepts and align more closely with radiologists' workflows than models not trained on mammography data. Fine-tuning for task-specific classification enhances the capture of certain concept categories (e.g., benign calcifications) but can reduce coverage of others (e.g., density-related features), indicating a trade-off between specialisation and generalisation. Our findings show that Mammo-CLIP Dissect provides insights into how convolutional neural networks (CNNs) capture mammography-specific knowledge. By comparing models across training data and fine-tuning regimes, we reveal how domain-specific training and task-specific adaptation shape concept learning. Code and concept set are available: https://github.com/Suaiba/Mammo-CLIP-Dissect.

Valentina Corbetta, Floris Six Dijkstra, Regina Beets-Tan et al.

Deep learning models in medical imaging often achieve strong in-distribution performance but struggle to generalise under distribution shifts, frequently relying on spurious correlations instead of clinically meaningful features. We introduce LCRReg, a novel regularisation approach that leverages Latent Concept Representations (LCRs) (e.g., Concept Activation Vectors (CAVs)) to guide models toward semantically grounded representations. LCRReg requires no concept labels in the main training set and instead uses a small auxiliary dataset to synthesise high-quality, disentangled concept examples. We extract LCRs for predefined relevant features, and incorporate a regularisation term that guides a Convolutional Neural Network (CNN) to activate within latent subspaces associated with those concepts. We evaluate LCRReg across synthetic and real-world medical tasks. On a controlled toy dataset, it significantly improves robustness to injected spurious correlations and remains effective even in multi-concept and multiclass settings. On the diabetic retinopathy binary classification task, LCRReg enhances performance under both synthetic spurious perturbations and out-of-distribution (OOD) generalisation. Compared to baselines, including multitask learning, linear probing, and post-hoc concept-based models, LCRReg offers a lightweight, architecture-agnostic strategy for improving model robustness without requiring dense concept supervision. Code is available at the following link: https://github.com/Trustworthy-AI-UU-NKI/lcr\_regularization

Kristoffer Wickstrøm, Marina Marie-Claire Höhne, Anna Hedström

The lack of ground truth explanation labels is a fundamental challenge for quantitative evaluation in explainable artificial intelligence (XAI). This challenge becomes especially problematic when evaluation methods have numerous hyperparameters that must be specified by the user, as there is no ground truth to determine an optimal hyperparameter selection. It is typically not feasible to do an exhaustive search of hyperparameters so researchers typically make a normative choice based on similar studies in the literature, which provides great flexibility for the user. In this work, we illustrate how this flexibility can be exploited to manipulate the evaluation outcome. We frame this manipulation as an adversarial attack on the evaluation where seemingly innocent changes in hyperparameter setting significantly influence the evaluation outcome. We demonstrate the effectiveness of our manipulation across several datasets with large changes in evaluation outcomes across several explanation methods and models. Lastly, we propose a mitigation strategy based on ranking across hyperparameters that aims to provide robustness towards such manipulation. This work highlights the difficulty of conducting reliable XAI evaluation and emphasizes the importance of a holistic and transparent approach to evaluation in XAI.

Christian Salomonsen, Samuel Kuttner, Michael Kampffmeyer et al.

Tracer kinetic modeling serves a vital role in diagnosis, treatment planning, tracer development and oncology, but burdens practitioners with complex and invasive arterial input function estimation (AIF). We adopt a physics-informed CycleGAN showing promise in DCE-MRI quantification to dynamic PET quantification. Our experiments demonstrate sound AIF predictions and parameter maps closely resembling the reference.

Kristoffer Wickstrøm, Karl Øyvind Mikalsen, Michael Kampffmeyer et al.

Deep learning-based support systems have demonstrated encouraging results in numerous clinical applications involving the processing of time series data. While such systems often are very accurate, they have no inherent mechanism for explaining what influenced the predictions, which is critical for clinical tasks. However, existing explainability techniques lack an important component for trustworthy and reliable decision support, namely a notion of uncertainty. In this paper, we address this lack of uncertainty by proposing a deep ensemble approach where a collection of DNNs are trained independently. A measure of uncertainty in the relevance scores is computed by taking the standard deviation across the relevance scores produced by each model in the ensemble, which in turn is used to make the explanations more reliable. The class activation mapping method is used to assign a relevance score for each time step in the time series. Results demonstrate that the proposed ensemble is more accurate in locating relevant time steps and is more consistent across random initializations, thus making the model more trustworthy. The proposed methodology paves the way for constructing trustworthy and dependable support systems for processing clinical time series for healthcare related tasks.

Kristoffer Wickstrøm, Sigurd Løkse, Michael Kampffmeyer et al.

Analyzing deep neural networks (DNNs) via information plane (IP) theory has gained tremendous attention recently as a tool to gain insight into, among others, their generalization ability. However, it is by no means obvious how to estimate mutual information (MI) between each hidden layer and the input/desired output, to construct the IP. For instance, hidden layers with many neurons require MI estimators with robustness towards the high dimensionality associated with such layers. MI estimators should also be able to naturally handle convolutional layers, while at the same time being computationally tractable to scale to large networks. None of the existing IP methods to date have been able to study truly deep Convolutional Neural Networks (CNNs), such as the e.g.\ VGG-16. In this paper, we propose an IP analysis using the new matrix--based Rényi's entropy coupled with tensor kernels over convolutional layers, leveraging the power of kernel methods to represent properties of the probability distribution independently of the dimensionality of the data. The obtained results shed new light on the previous literature concerning small-scale DNNs, however using a completely new approach. Importantly, the new framework enables us to provide the first comprehensive IP analysis of contemporary large-scale DNNs and CNNs, investigating the different training phases and providing new insights into the training dynamics of large-scale neural networks.

Kristoffer Wickstrøm, Michael Kampffmeyer, Robert Jenssen

Convolutional Neural Networks (CNNs) are propelling advances in a range of different computer vision tasks such as object detection and object segmentation. Their success has motivated research in applications of such models for medical image analysis. If CNN-based models are to be helpful in a medical context, they need to be precise, interpretable, and uncertainty in predictions must be well understood. In this paper, we develop and evaluate recent advances in uncertainty estimation and model interpretability in the context of semantic segmentation of polyps from colonoscopy images. We evaluate and enhance several architectures of Fully Convolutional Networks (FCNs) for semantic segmentation of colorectal polyps and provide a comparison between these models. Our highest performing model achieves a 76.06\% mean IOU accuracy on the EndoScene dataset, a considerable improvement over the previous state-of-the-art.

Shujian Yu, Kristoffer Wickstrøm, Robert Jenssen et al.

The matrix-based Renyi's α-entropy functional and its multivariate extension were recently developed in terms of the normalized eigenspectrum of a Hermitian matrix of the projected data in a reproducing kernel Hilbert space (RKHS). However, the utility and possible applications of these new estimators are rather new and mostly unknown to practitioners. In this paper, we first show that our estimators enable straightforward measurement of information flow in realistic convolutional neural networks (CNN) without any approximation. Then, we introduce the partial information decomposition (PID) framework and develop three quantities to analyze the synergy and redundancy in convolutional layer representations. Our results validate two fundamental data processing inequalities and reveal some fundamental properties concerning the training of CNN.