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Current AI frameworks for brain decoding and encoding, typically train and test models within the same datasets. This limits their utility for brain computer interfaces (BCI) or neurofeedback, for which it would be useful to pool experiences across individuals to better simulate stimuli not sampled during training. A key obstacle to model generalisation is the degree of variability of inter-subject cortical organisation, which makes it difficult to align or compare cortical signals across participants. In this paper we address this through the use of surface vision transformers, which build a generalisable model of cortical functional dynamics, through encoding the topography of cortical networks and their interactions as a moving image across a surface. This is then combined with tri-modal self-supervised contrastive (CLIP) alignment of audio, video, and fMRI modalities to enable the retrieval of visual and auditory stimuli from patterns of cortical activity (and vice-versa). We validate our approach on 7T task-fMRI data from 174 healthy participants engaged in the movie-watching experiment from the Human Connectome Project (HCP). Results show that it is possible to detect which movie clips an individual is watching purely from their brain activity, even for individuals and movies not seen during training. Further analysis of attention maps reveals that our model captures individual patterns of brain activity that reflect semantic and visual systems. This opens the door to future personalised simulations of brain function. Code & pre-trained models will be made available at https://github.com/metrics-lab/sim, processed data for training will be available upon request at https://gin.g-node.org/Sdahan30/sim., Comment: 27 pages, accepted to ICLR 2025

Chronic rhinosinusitis (CRS) is a common and persistent sinus imflammation that affects 5 - 12\% of the general population. It significantly impacts quality of life and is often difficult to assess due to its subjective nature in clinical evaluation. We introduce PARASIDE, an automatic tool for segmenting air and soft tissue volumes of the structures of the sinus maxillaris, frontalis, sphenodalis and ethmoidalis in T1 MRI. By utilizing that segmentation, we can quantify feature relations that have been observed only manually and subjectively before. We performed an exemplary study and showed both volume and intensity relations between structures and radiology reports. While the soft tissue segmentation is good, the automated annotations of the air volumes are excellent. The average intensity over air structures are consistently below those of the soft tissues, close to perfect separability. Healthy subjects exhibit lower soft tissue volumes and lower intensities. Our developed system is the first automated whole nasal segmentation of 16 structures, and capable of calculating medical relevant features such as the Lund-Mackay score.

Dark-field radiography of the human chest has been demonstrated to have promising potential for the analysis of the lung microstructure and the diagnosis of respiratory diseases. However, previous studies of dark-field chest radiographs evaluated the lung signal only in the inspiratory breathing state. Our work aims to add a new perspective to these previous assessments by locally comparing dark-field lung information between different respiratory states. To this end, we discuss suitable image registration methods for dark-field chest radiographs to enable consistent spatial alignment of the lung in distinct breathing states. Utilizing full inspiration and expiration scans from a clinical chronic obstructive pulmonary disease study, we assess the performance of the proposed registration framework and outline applicable evaluation approaches. Our regional characterization of lung dark-field signal changes between the breathing states provides a proof-of-principle that dynamic radiography-based lung function assessment approaches may benefit from considering registered dark-field images in addition to standard plain chest radiographs., Comment: 10 pages, 6 figures

Neural implicit k-space representations (NIK) have shown promising results for dynamic magnetic resonance imaging (MRI) at high temporal resolutions. Yet, reducing acquisition time, and thereby available training data, results in severe performance drops due to overfitting. To address this, we introduce a novel self-supervised k-space loss function $\mathcal{L}_\mathrm{PISCO}$, applicable for regularization of NIK-based reconstructions. The proposed loss function is based on the concept of parallel imaging-inspired self-consistency (PISCO), enforcing a consistent global k-space neighborhood relationship without requiring additional data. Quantitative and qualitative evaluations on static and dynamic MR reconstructions show that integrating PISCO significantly improves NIK representations. Particularly for high acceleration factors (R$\geq$54), NIK with PISCO achieves superior spatio-temporal reconstruction quality compared to state-of-the-art methods. Furthermore, an extensive analysis of the loss assumptions and stability shows PISCO's potential as versatile self-supervised k-space loss function for further applications and architectures. Code is available at: https://github.com/compai-lab/2025-pisco-spieker

Predicting future brain states is crucial for understanding healthy aging and neurodegenerative diseases. Longitudinal brain MRI registration, a cornerstone for such analyses, has long been limited by its inability to forecast future developments, reliance on extensive, dense longitudinal data, and the need to balance registration accuracy with temporal smoothness. In this work, we present \emph{TimeFlow}, a novel framework for longitudinal brain MRI registration that overcomes all these challenges. Leveraging a U-Net architecture with temporal conditioning inspired by diffusion models, TimeFlow enables accurate longitudinal registration and facilitates prospective analyses through future image prediction. Unlike traditional methods that depend on explicit smoothness regularizers and dense sequential data, TimeFlow achieves temporal consistency and continuity without these constraints. Experimental results highlight its superior performance in both future timepoint prediction and registration accuracy compared to state-of-the-art methods. Additionally, TimeFlow supports novel biological brain aging analyses, effectively differentiating neurodegenerative conditions from healthy aging. It eliminates the need for segmentation, thereby avoiding the challenges of non-trivial annotation and inconsistent segmentation errors. TimeFlow paves the way for accurate, data-efficient, and annotation-free prospective analyses of brain aging and chronic diseases.

Glioblastoma, a highly aggressive brain tumor, poses major challenges due to its poor prognosis and high morbidity rates. Partial differential equation-based models offer promising potential to enhance therapeutic outcomes by simulating patient-specific tumor behavior for improved radiotherapy planning. However, model calibration remains a bottleneck due to the high computational demands of optimization methods like Monte Carlo sampling and evolutionary algorithms. To address this, we recently introduced an approach leveraging a neural forward solver with gradient-based optimization to significantly reduce calibration time. This approach requires a highly accurate and fully differentiable forward model. We investigate multiple architectures, including (i) an enhanced TumorSurrogate, (ii) a modified nnU-Net, and (iii) a 3D Vision Transformer (ViT). The optimized TumorSurrogate achieved the best overall results, excelling in both tumor outline matching and voxel-level prediction of tumor cell concentration. It halved the MSE relative to the baseline model and achieved the highest Dice score across all tumor cell concentration thresholds. Our study demonstrates significant enhancement in forward solver performance and outlines important future research directions.

Modern deep learning-based clinical imaging workflows rely on accurate labels of the examined anatomical region. Knowing the anatomical region is required to select applicable downstream models and to effectively generate cohorts of high quality data for future medical and machine learning research efforts. However, this information may not be available in externally sourced data or generally contain data entry errors. To address this problem, we show the effectiveness of self-supervised methods such as SimCLR and BYOL as well as supervised contrastive deep learning methods in assigning one of 14 anatomical region classes in our in-house dataset of 48,434 skeletal radiographs. We achieve a strong linear evaluation accuracy of 96.6% with a single model and 97.7% using an ensemble approach. Furthermore, only a few labeled instances (1% of the training set) suffice to achieve an accuracy of 92.2%, enabling usage in low-label and thus low-resource scenarios. Our model can be used to correct data entry mistakes: a follow-up analysis of the test set errors of our best-performing single model by an expert radiologist identified 35% incorrect labels and 11% out-of-domain images. When accounted for, the radiograph anatomical region labelling performance increased -- without and with an ensemble, respectively -- to a theoretical accuracy of 98.0% and 98.8%., Comment: 12 pages, 4 figures, 2 supplementary figures

Image registration is fundamental in medical imaging applications, such as disease progression analysis or radiation therapy planning. The primary objective of image registration is to precisely capture the deformation between two or more images, typically achieved by minimizing an optimization problem. Due to its inherent ill-posedness, regularization is a key component in driving the solution toward anatomically meaningful deformations. A wide range of regularization methods has been proposed for both conventional and deep learning-based registration. However, the appropriate application of regularization techniques often depends on the specific registration problem, and no one-fits-all method exists. Despite its importance, regularization is often overlooked or addressed with default approaches, assuming existing methods are sufficient. A comprehensive and structured review remains missing. This review addresses this gap by introducing a novel taxonomy that systematically categorizes the diverse range of proposed regularization methods. It highlights the emerging field of learned regularization, which leverages data-driven techniques to automatically derive deformation properties from the data. Moreover, this review examines the transfer of regularization methods from conventional to learning-based registration, identifies open challenges, and outlines future research directions. By emphasizing the critical role of regularization in image registration, we hope to inspire the research community to reconsider regularization strategies in modern registration algorithms and to explore this rapidly evolving field further., Comment: Submitted to Medical Image Analysis

Topological correctness, i.e., the preservation of structural integrity and specific characteristics of shape, is a fundamental requirement for medical imaging tasks, such as neuron or vessel segmentation. Despite the recent surge in topology-aware methods addressing this challenge, their real-world applicability is hindered by flawed benchmarking practices. In this paper, we identify critical pitfalls in model evaluation that include inadequate connectivity choices, overlooked topological artifacts in ground truth annotations, and inappropriate use of evaluation metrics. Through detailed empirical analysis, we uncover these issues' profound impact on the evaluation and ranking of segmentation methods. Drawing from our findings, we propose a set of actionable recommendations to establish fair and robust evaluation standards for topology-aware medical image segmentation methods., Comment: Code is available at https://github.com/AlexanderHBerger/topo-pitfalls

Dynamic fetal heart magnetic resonance imaging (MRI) presents unique challenges due to the fast heart rate of the fetus compared to adult subjects and uncontrolled fetal motion. This requires high temporal and spatial resolutions over a large field of view, in order to encompass surrounding maternal anatomy. In this work, we introduce Dynamic Cardiac Reconstruction Attention Network (DCRA-Net) - a novel deep learning model that employs attention mechanisms in spatial and temporal domains and temporal frequency representation of data to reconstruct the dynamics of the fetal heart from highly accelerated free-running (non-gated) MRI acquisitions. DCRA-Net was trained on retrospectively undersampled complex-valued cardiac MRIs from 42 fetal subjects and separately from 153 adult subjects, and evaluated on data from 14 fetal and 39 adult subjects respectively. Its performance was compared to L+S and k-GIN methods in both fetal and adult cases for an undersampling factor of 8x. The proposed network performed better than the comparators for both fetal and adult data, for both regular lattice and centrally weighted random undersampling. Aliased signals due to the undersampling were comprehensively resolved, and both the spatial details of the heart and its temporal dynamics were recovered with high fidelity. The highest performance was achieved when using lattice undersampling, data consistency and temporal frequency representation, yielding PSNR of 38 for fetal and 35 for adult cases. Our method is publicly available at https://github.com/denproc/DCRA-Net.

Biophysical modeling of brain tumors has emerged as a promising strategy for personalizing radiotherapy planning by estimating the otherwise hidden distribution of tumor cells within the brain. However, many existing state-of-the-art methods are computationally intensive, limiting their widespread translation into clinical practice. In this work, we propose an efficient and direct method that utilizes soft physical constraints to estimate the tumor cell concentration from preoperative MRI of brain tumor patients. Our approach optimizes a 3D tumor concentration field by simultaneously minimizing the difference between the observed MRI and a physically informed loss function. Compared to existing state-of-the-art techniques, our method significantly improves predicting tumor recurrence on two public datasets with a total of 192 patients while maintaining a clinically viable runtime of under one minute - a substantial reduction from the 30 minutes required by the current best approach. Furthermore, we showcase the generalizability of our framework by incorporating additional imaging information and physical constraints, highlighting its potential to translate to various medical diffusion phenomena with imperfect data.

Data-driven deformable image registration methods predominantly rely on operations that process grid-like inputs. However, applying deformable transformations to an image results in a warped space that deviates from a rigid grid structure. Consequently, data-driven approaches with sequential deformations have to apply grid resampling operations between each deformation step. While artifacts caused by resampling are negligible in high-resolution images, the resampling of sparse, high-dimensional feature grids introduces errors that affect the deformation modeling process. Taking inspiration from Lagrangian reference frames of deformation fields, our work introduces a novel paradigm for data-driven deformable image registration that utilizes geometric deep-learning principles to model deformations without grid requirements. Specifically, we model image features as a set of nodes that freely move in Euclidean space, update their coordinates under graph operations, and dynamically readjust their local neighborhoods. We employ this formulation to construct a multi-resolution deformable registration model, where deformation layers iteratively refine the overall transformation at each resolution without intermediate resampling operations on the feature grids. We investigate our method's ability to fully deformably capture large deformations across a number of medical imaging registration tasks. In particular, we apply our approach (GeoReg) to the registration of inter-subject brain MR images and inhale-exhale lung CT images, showing on par performance with the current state-of-the-art methods. We believe our contribution open up avenues of research to reduce the black-box nature of current learned registration paradigms by explicitly modeling the transformation within the architecture., Comment: 22 Pages

Conventional cardiac cine MRI methods rely on retrospective gating, which limits temporal resolution and the ability to capture continuous cardiac dynamics, particularly in patients with arrhythmias and beat-to-beat variations. To address these challenges, we propose a reconstruction framework based on subspace implicit neural representations for real-time cardiac cine MRI of continuously sampled radial data. This approach employs two multilayer perceptrons to learn spatial and temporal subspace bases, leveraging the low-rank properties of cardiac cine MRI. Initialized with low-resolution reconstructions, the networks are fine-tuned using spoke-specific loss functions to recover spatial details and temporal fidelity. Our method directly utilizes the continuously sampled radial k-space spokes during training, thereby eliminating the need for binning and non-uniform FFT. This approach achieves superior spatial and temporal image quality compared to conventional binned methods at the acceleration rate of 10 and 20, demonstrating potential for high-resolution imaging of dynamic cardiac events and enhancing diagnostic capability.

As early as 1949, Weaver defined communication in a very broad sense to include all procedures by which one mind or technical system can influence another, thus establishing the idea of semantic communication. With the recent success of machine learning in expert assistance systems where sensed information is wirelessly provided to a human to assist task execution, the need to design effective and efficient communications has become increasingly apparent. In particular, semantic communication aims to convey the meaning behind the sensed information relevant for Human Decision-Making (HDM). Regarding the interplay between semantic communication and HDM, many questions remain, such as how to model the entire end-to-end sensing-decision-making process, how to design semantic communication for the HDM and which information should be provided to the HDM. To address these questions, we propose to integrate semantic communication and HDM into one probabilistic end-to-end sensing-decision framework that bridges communications and psychology. In our interdisciplinary framework, we model the human through a HDM process, allowing us to explore how feature extraction from semantic communication can best support human decision-making. In this sense, our study provides new insights for the design/interaction of semantic communication with models of HDM. Our initial analysis shows how semantic communication can balance the level of detail with human cognitive capabilities while demanding less bandwidth, power, and latency.

Machine unlearning refers to removing the influence of a specified subset of training data from a machine learning model, efficiently, after it has already been trained. This is important for key applications, including making the model more accurate by removing outdated, mislabeled, or poisoned data. In this work, we study localized unlearning, where the unlearning algorithm operates on a (small) identified subset of parameters. Drawing inspiration from the memorization literature, we propose an improved localization strategy that yields strong results when paired with existing unlearning algorithms. We also propose a new unlearning algorithm, Deletion by Example Localization (DEL), that resets the parameters deemed-to-be most critical according to our localization strategy, and then finetunes them. Our extensive experiments on different datasets, forget sets and metrics reveal that DEL sets a new state-of-the-art for unlearning metrics, against both localized and full-parameter methods, while modifying a small subset of parameters, and outperforms the state-of-the-art localized unlearning in terms of test accuracy too.

Employing pre-trained Large Language Models (LLMs) has become the de facto standard in Natural Language Processing (NLP) despite their extensive data requirements. Motivated by the recent surge in research focused on training LLMs with limited data, particularly in low-resource domains and languages, this paper surveys recent transfer learning approaches to optimize model performance in downstream tasks where data is scarce. We first address initial and continued pre-training strategies to better leverage prior knowledge in unseen domains and languages. We then examine how to maximize the utility of limited data during fine-tuning and few-shot learning. The final section takes a task-specific perspective, reviewing models and methods suited for different levels of data scarcity. Our goal is to provide practitioners with practical guidelines for overcoming the challenges posed by constrained data while also highlighting promising directions for future research.

Topological correctness plays a critical role in many image segmentation tasks, yet most networks are trained using pixel-wise loss functions, such as Dice, neglecting topological accuracy. Existing topology-aware methods often lack robust topological guarantees, are limited to specific use cases, or impose high computational costs. In this work, we propose a novel, graph-based framework for topologically accurate image segmentation that is both computationally efficient and generally applicable. Our method constructs a component graph that fully encodes the topological information of both the prediction and ground truth, allowing us to efficiently identify topologically critical regions and aggregate a loss based on local neighborhood information. Furthermore, we introduce a strict topological metric capturing the homotopy equivalence between the union and intersection of prediction-label pairs. We formally prove the topological guarantees of our approach and empirically validate its effectiveness on binary and multi-class datasets. Our loss demonstrates state-of-the-art performance with up to fivefold faster loss computation compared to persistent homology methods.

To ensure the efficiency of robot autonomy under diverse real-world conditions, a high-quality heterogeneous dataset is essential to benchmark the operating algorithms' performance and robustness. Current benchmarks predominantly focus on urban terrains, specifically for on-road autonomous driving, leaving multi-degraded, densely vegetated, dynamic and feature-sparse environments, such as underground tunnels, natural fields, and modern indoor spaces underrepresented. To fill this gap, we introduce EnvoDat, a large-scale, multi-modal dataset collected in diverse environments and conditions, including high illumination, fog, rain, and zero visibility at different times of the day. Overall, EnvoDat contains 26 sequences from 13 scenes, 10 sensing modalities, over 1.9TB of data, and over 89K fine-grained polygon-based annotations for more than 82 object and terrain classes. We post-processed EnvoDat in different formats that support benchmarking SLAM and supervised learning algorithms, and fine-tuning multimodal vision models. With EnvoDat, we contribute to environment-resilient robotic autonomy in areas where the conditions are extremely challenging. The datasets and other relevant resources can be accessed through https://linusnep.github.io/EnvoDat/.

In Magnetic Resonance Imaging (MRI), high temporal-resolved motion can be useful for image acquisition and reconstruction, MR-guided radiotherapy, dynamic contrast-enhancement, flow and perfusion imaging, and functional assessment of motion patterns in cardiovascular, abdominal, peristaltic, fetal, or musculoskeletal imaging. Conventionally, these motion estimates are derived through image-based registration, a particularly challenging task for complex motion patterns and high dynamic resolution. The accelerated scans in such applications result in imaging artifacts that compromise the motion estimation. In this work, we propose a novel self-supervised deep learning-based framework, dubbed the Local-All Pass Attention Network (LAPANet), for non-rigid motion estimation directly from the acquired accelerated Fourier space, i.e. k-space. The proposed approach models non-rigid motion as the cumulative sum of local translational displacements, following the Local All-Pass (LAP) registration technique. LAPANet was evaluated on cardiac motion estimation across various sampling trajectories and acceleration rates. Our results demonstrate superior accuracy compared to prior conventional and deep learning-based registration methods, accommodating as few as 2 lines/frame in a Cartesian trajectory and 3 spokes/frame in a non-Cartesian trajectory. The achieved high temporal resolution (less than 5 ms) for non-rigid motion opens new avenues for motion detection, tracking and correction in dynamic and real-time MRI applications.

Deep learning has made significant strides in medical imaging, leveraging the use of large datasets to improve diagnostics and prognostics. However, large datasets often come with inherent errors through subject selection and acquisition. In this paper, we investigate the use of Diffusion Autoencoder (DAE) embeddings for uncovering and understanding data characteristics and biases, including biases for protected variables like sex and data abnormalities indicative of unwanted protocol variations. We use sagittal T2-weighted magnetic resonance (MR) images of the neck, chest, and lumbar region from 11186 German National Cohort (NAKO) participants. We compare DAE embeddings with existing generative models like StyleGAN and Variational Autoencoder. Evaluations on a large-scale dataset consisting of sagittal T2-weighted MR images of three spine regions show that DAE embeddings effectively separate protected variables such as sex and age. Furthermore, we used t-SNE visualization to identify unwanted variations in imaging protocols, revealing differences in head positioning. Our embedding can identify samples where a sex predictor will have issues learning the correct sex. Our findings highlight the potential of using advanced embedding techniques like DAEs to detect data quality issues and biases in medical imaging datasets. Identifying such hidden relations can enhance the reliability and fairness of deep learning models in healthcare applications, ultimately improving patient care and outcomes., Comment: This paper was accepted in the "Workshop on Interpretability of Machine Intelligence in Medical Image Computing" (iMIMIC) at MICCAI 2024

Recent breakthroughs in natural language processing and computer vision, driven by efficient pre-training on large datasets, have enabled foundation models to excel on a wide range of tasks. However, this potential has not yet been fully realised in time series analysis, as existing methods fail to address the heterogeneity in large time series corpora. Prevalent in domains ranging from medicine to finance, time series vary substantially in characteristics such as variate count, inter-variate relationships, temporal patterns, and sampling frequency. To address this, we introduce a novel pre-training paradigm specifically designed to handle time series heterogeneity. We propose a tokeniser with learnable domain signatures, a dual masking strategy, and a normalised cross-correlation loss, enabling our open model for general time series analysis (OTiS) to efficiently learn from large time series corpora. Extensive benchmarking on diverse tasks, such as classification, regression, and forecasting, demonstrates that OTiS outperforms state-of-the-art baselines. Our code and pre-trained weights are available at https://github.com/oetu/otis.

Cardiac magnetic resonance imaging (CMR), considered the gold standard for noninvasive cardiac assessment, is a diverse and complex modality requiring a wide variety of image processing tasks for comprehensive assessment of cardiac morphology and function. Advances in deep learning have enabled the development of state-of-the-art (SoTA) models for these tasks. However, model training is challenging due to data and label scarcity, especially in the less common imaging sequences. Moreover, each model is often trained for a specific task, with no connection between related tasks. In this work, we introduce a vision foundation model trained for CMR assessment, that is trained in a self-supervised fashion on 36 million CMR images. We then finetune the model in supervised way for 9 clinical tasks typical to a CMR workflow, across classification, segmentation, landmark localization, and pathology detection. We demonstrate improved accuracy and robustness across all tasks, over a range of available labeled dataset sizes. We also demonstrate improved few-shot learning with fewer labeled samples, a common challenge in medical image analyses. We achieve an out-of-box performance comparable to SoTA for most clinical tasks. The proposed method thus presents a resource-efficient, unified framework for CMR assessment, with the potential to accelerate the development of deep learning-based solutions for image analysis tasks, even with few annotated data available., Comment: 11 pages, 3 figures, 4 tables

Active learning (AL) is a widely used technique for optimizing data labeling in machine learning by iteratively selecting, labeling, and training on the most informative data. However, its integration with formal privacy-preserving methods, particularly differential privacy (DP), remains largely underexplored. While some works have explored differentially private AL for specialized scenarios like online learning, the fundamental challenge of combining AL with DP in standard learning settings has remained unaddressed, severely limiting AL's applicability in privacy-sensitive domains. This work addresses this gap by introducing differentially private active learning (DP-AL) for standard learning settings. We demonstrate that naively integrating DP-SGD training into AL presents substantial challenges in privacy budget allocation and data utilization. To overcome these challenges, we propose step amplification, which leverages individual sampling probabilities in batch creation to maximize data point participation in training steps, thus optimizing data utilization. Additionally, we investigate the effectiveness of various acquisition functions for data selection under privacy constraints, revealing that many commonly used functions become impractical. Our experiments on vision and natural language processing tasks show that DP-AL can improve performance for specific datasets and model architectures. However, our findings also highlight the limitations of AL in privacy-constrained environments, emphasizing the trade-offs between privacy, model accuracy, and data selection accuracy., Comment: This work has been accepted for publication in the IEEE Conference on Secure and Trustworthy Machine Learning (SaTML). The final version will be available on IEEE Xplore

Predicting future disease progression risk from medical images is challenging due to patient heterogeneity, and subtle or unknown imaging biomarkers. Moreover, deep learning (DL) methods for survival analysis are susceptible to image domain shifts across scanners. We tackle these issues in the task of predicting late dry Age-related Macular Degeneration (dAMD) onset from retinal OCT scans. We propose a novel DL method for survival prediction to jointly predict from the current scan a risk score, inversely related to time-to-conversion, and the probability of conversion within a time interval $t$. It uses a family of parallel hyperplanes generated by parameterizing the bias term as a function of $t$. In addition, we develop unsupervised losses based on intra-subject image pairs to ensure that risk scores increase over time and that future conversion predictions are consistent with AMD stage prediction using actual scans of future visits. Such losses enable data-efficient fine-tuning of the trained model on new unlabeled datasets acquired with a different scanner. Extensive evaluation on two large datasets acquired with different scanners resulted in a mean AUROCs of 0.82 for Dataset-1 and 0.83 for Dataset-2, across prediction intervals of 6,12 and 24 months., Comment: accepted in MICCAI 2024

Although existing medical image segmentation methods provide impressive pixel-wise accuracy, they often neglect topological correctness, making their segmentations unusable for many downstream tasks. One option is to retrain such models whilst including a topology-driven loss component. However, this is computationally expensive and often impractical. A better solution would be to have a versatile plug-and-play topology refinement method that is compatible with any domain-specific segmentation pipeline. Directly training a post-processing model to mitigate topological errors often fails as such models tend to be biased towards the topological errors of a target segmentation network. The diversity of these errors is confined to the information provided by a labelled training set, which is especially problematic for small datasets. Our method solves this problem by training a model-agnostic topology refinement network with synthetic segmentations that cover a wide variety of topological errors. Inspired by the Stone-Weierstrass theorem, we synthesize topology-perturbation masks with randomly sampled coefficients of orthogonal polynomial bases, which ensures a complete and unbiased representation. Practically, we verified the efficiency and effectiveness of our methods as being compatible with multiple families of polynomial bases, and show evidence that our universal plug-and-play topology refinement network outperforms both existing topology-driven learning-based and post-processing methods. We also show that combining our method with learning-based models provides an effortless add-on, which can further improve the performance of existing approaches., Comment: Accepted by the 27th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2024)

The Orientation Distribution Function (ODF) characterizes key brain microstructural properties and plays an important role in understanding brain structural connectivity. Recent works introduced Implicit Neural Representation (INR) based approaches to form a spatially aware continuous estimate of the ODF field and demonstrated promising results in key tasks of interest when compared to conventional discrete approaches. However, traditional INR methods face difficulties when scaling to large-scale images, such as modern ultra-high-resolution MRI scans, posing challenges in learning fine structures as well as inefficiencies in training and inference speed. In this work, we propose HashEnc, a grid-hash-encoding-based estimation of the ODF field and demonstrate its effectiveness in retaining structural and textural features. We show that HashEnc achieves a 10% enhancement in image quality while requiring 3x less computational resources than current methods. Our code can be found at https://github.com/MunzerDw/NODF-HashEnc., Comment: 16 pages, 8 figures, conference: Medical Image Computing and Computer-Assisted Intervention (MICCAI)

Real-time computational speed and a high degree of precision are requirements for computer-assisted interventions. Applying a segmentation network to a medical video processing task can introduce significant inter-frame prediction noise. Existing approaches can reduce inconsistencies by including temporal information but often impose requirements on the architecture or dataset. This paper proposes a method to include temporal information in any segmentation model and, thus, a technique to improve video segmentation performance without alterations during training or additional labeling. With Motion-Corrected Moving Average, we refine the exponential moving average between the current and previous predictions. Using optical flow to estimate the movement between consecutive frames, we can shift the prior term in the moving-average calculation to align with the geometry of the current frame. The optical flow calculation does not require the output of the model and can therefore be performed in parallel, leading to no significant runtime penalty for our approach. We evaluate our approach on two publicly available segmentation datasets and two proprietary endoscopic datasets and show improvements over a baseline approach.

Accurate calibration of finite element (FE) models is essential across various biomechanical applications, including human intervertebral discs (IVDs), to ensure their reliability and use in diagnosing and planning treatments. However, traditional calibration methods are computationally intensive, requiring iterative, derivative-free optimization algorithms that often take days to converge. This study addresses these challenges by introducing a novel, efficient, and effective calibration method demonstrated on a human L4-L5 IVD FE model as a case study using a neural network (NN) surrogate. The NN surrogate predicts simulation outcomes with high accuracy, outperforming other machine learning models, and significantly reduces the computational cost associated with traditional FE simulations. Next, a Projected Gradient Descent (PGD) approach guided by gradients of the NN surrogate is proposed to efficiently calibrate FE models. Our method explicitly enforces feasibility with a projection step, thus maintaining material bounds throughout the optimization process. The proposed method is evaluated against SOTA Genetic Algorithm and inverse model baselines on synthetic and in vitro experimental datasets. Our approach demonstrates superior performance on synthetic data, achieving an MAE of 0.06 compared to the baselines' MAE of 0.18 and 0.54, respectively. On experimental specimens, our method outperforms the baseline in 5 out of 6 cases. While our approach requires initial dataset generation and surrogate training, these steps are performed only once, and the actual calibration takes under three seconds. In contrast, traditional calibration time scales linearly with the number of specimens, taking up to 8 days in the worst-case. Such efficiency paves the way for applying more complex FE models, potentially extending beyond IVDs, and enabling accurate patient-specific simulations., Comment: In review. Project code: https://github.com/matanat/IVD-CalibNN/

Counterfactual explanations (CEs) aim to enhance the interpretability of machine learning models by illustrating how alterations in input features would affect the resulting predictions. Common CE approaches require an additional model and are typically constrained to binary counterfactuals. In contrast, we propose a novel method that operates directly on the latent space of a generative model, specifically a Diffusion Autoencoder (DAE). This approach offers inherent interpretability by enabling the generation of CEs and the continuous visualization of the model's internal representation across decision boundaries. Our method leverages the DAE's ability to encode images into a semantically rich latent space in an unsupervised manner, eliminating the need for labeled data or separate feature extraction models. We show that these latent representations are helpful for medical condition classification and the ordinal regression of severity pathologies, such as vertebral compression fractures (VCF) and diabetic retinopathy (DR). Beyond binary CEs, our method supports the visualization of ordinal CEs using a linear model, providing deeper insights into the model's decision-making process and enhancing interpretability. Experiments across various medical imaging datasets demonstrate the method's advantages in interpretability and versatility. The linear manifold of the DAE's latent space allows for meaningful interpolation and manipulation, making it a powerful tool for exploring medical image properties. Our code is available at https://doi.org/10.5281/zenodo.13859266., Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org/2024:024. arXiv admin note: text overlap with arXiv:2303.12031

Cardiac Magnetic Resonance Imaging (CMR) is the gold standard for diagnosing cardiovascular diseases. Clinical diagnoses predominantly rely on magnitude-only Digital Imaging and Communications in Medicine (DICOM) images, omitting crucial phase information that might provide additional diagnostic benefits. In contrast, k-space is complex-valued and encompasses both magnitude and phase information, while humans cannot directly perceive. In this work, we propose KMAE, a Transformer-based model specifically designed to process k-space data directly, eliminating conventional intermediary conversion steps to the image domain. KMAE can handle critical cardiac disease classification, relevant phenotype regression, and cardiac morphology segmentation tasks. We utilize this model to investigate the potential of k-space-based diagnosis in cardiac MRI. Notably, this model achieves competitive classification and regression performance compared to image-domain methods e.g. Masked Autoencoders (MAEs) and delivers satisfactory segmentation performance with a myocardium dice score of 0.884. Last but not least, our model exhibits robust performance with consistent results even when the k-space is 8* undersampled. We encourage the MR community to explore the untapped potential of k-space and pursue end-to-end, automated diagnosis with reduced human intervention.

Our findings indicate that adopting "advanced" computational elements fails to significantly improve registration accuracy. Instead, well-established registration-specific designs offer fair improvements, enhancing results by a marginal 1.5\% over the baseline. Our findings emphasize the importance of rigorous, unbiased evaluation and contribution disentanglement of all low- and high-level registration components, rather than simply following the computer vision trends with "more advanced" computational blocks. We advocate for simpler yet effective solutions and novel evaluation metrics that go beyond conventional registration accuracy, warranting further research across diverse organs and modalities. The code is available at \url{https://github.com/BailiangJ/rethink-reg}., Comment: WBIR 2024 Workshop on Biomedical Imaging Registration

General vision encoders like DINOv2 and SAM have recently transformed computer vision. Even though they are trained on natural images, such encoder models have excelled in medical imaging, e.g., in classification, segmentation, and registration. However, no in-depth comparison of different state-of-the-art general vision encoders for medical registration is available. In this work, we investigate how well general vision encoder features can be used in the dissimilarity metrics for medical image registration. We explore two encoders that were trained on natural images as well as one that was fine-tuned on medical data. We apply the features within the well-established B-spline FFD registration framework. In extensive experiments on cardiac cine MRI data, we find that using features as additional guidance for conventional metrics improves the registration quality. The code is available at github.com/compai-lab/2024-miccai-koegl., Comment: Accepted at WBIR MICCAI 2024

In this article, we propose a novel standalone hybrid Spiking-Convolutional Neural Network (SC-NN) model and test on using image inpainting tasks. Our approach uses the unique capabilities of SNNs, such as event-based computation and temporal processing, along with the strong representation learning abilities of CNNs, to generate high-quality inpainted images. The model is trained on a custom dataset specifically designed for image inpainting, where missing regions are created using masks. The hybrid model consists of SNNConv2d layers and traditional CNN layers. The SNNConv2d layers implement the leaky integrate-and-fire (LIF) neuron model, capturing spiking behavior, while the CNN layers capture spatial features. In this study, a mean squared error (MSE) loss function demonstrates the training process, where a training loss value of 0.015, indicates accurate performance on the training set and the model achieved a validation loss value as low as 0.0017 on the testing set. Furthermore, extensive experimental results demonstrate state-of-the-art performance, showcasing the potential of integrating temporal dynamics and feature extraction in a single network for image inpainting., Comment: 7 Pages, 3 figures, and 2 tables

Clinicians spend a significant amount of time reviewing medical images and transcribing their findings regarding patient diagnosis, referral and treatment in text form. Vision-language models (VLMs), which automatically interpret images and summarize their findings as text, have enormous potential to alleviate clinical workloads and increase patient access to high-quality medical care. While foundational models have stirred considerable interest in the medical community, it is unclear whether their general capabilities translate to real-world clinical utility. In this work, we show that foundation VLMs markedly underperform compared to practicing ophthalmologists on specialist tasks crucial to the care of patients with age-related macular degeneration (AMD). To address this, we initially identified the essential capabilities required for image-based clinical decision-making, and then developed a curriculum to selectively train VLMs in these skills. The resulting model, RetinaVLM, can be instructed to write reports that significantly outperform those written by leading foundation medical VLMs in disease staging (F1 score of 0.63 vs. 0.11) and patient referral (0.67 vs. 0.39), and approaches the diagnostic performance of junior ophthalmologists (who achieve 0.77 and 0.78 on the respective tasks). Furthermore, in a reader study involving two senior ophthalmologists with up to 32 years of experience, RetinaVLM's reports were found to be similarly correct (78.6% vs. 82.1%) and complete (both 78.6%) as reports written by junior ophthalmologists with up to 10 years of experience. These results demonstrate that our curriculum-based approach provides a blueprint for specializing generalist foundation medical VLMs to handle real-world clinical tasks., Comment: Submitted to Nature Medicine

Machine unlearning is the process of removing the impact of a particular set of training samples from a pretrained model. It aims to fulfill the "right to be forgotten", which grants the individuals such as patients the right to reconsider their contribution in models including medical imaging models. In this study, we evaluate the effectiveness (performance) and computational efficiency of different unlearning algorithms in medical imaging domain. Our evaluations demonstrate that the considered unlearning algorithms perform well on the retain set (samples whose influence on the model is allowed to be retained) and forget set (samples whose contribution to the model should be eliminated), and show no bias against male or female samples. They, however, adversely impact the generalization of the model, especially for larger forget set sizes. Moreover, they might be biased against easy or hard samples, and need additional computational overhead for hyper-parameter tuning. In conclusion, machine unlearning seems promising for medical imaging, but the existing unlearning algorithms still needs further improvements to become more practical for medical applications.

Traditional Variational Autoencoders (VAEs) are constrained by the limitations of the Evidence Lower Bound (ELBO) formulation, particularly when utilizing simplistic, non-analytic, or unknown prior distributions. These limitations inhibit the VAE's ability to generate high-quality samples and provide clear, interpretable latent representations. This work introduces the Entropy Decomposed Variational Autoencoder (ED-VAE), a novel re-formulation of the ELBO that explicitly includes entropy and cross-entropy components. This reformulation significantly enhances model flexibility, allowing for the integration of complex and non-standard priors. By providing more detailed control over the encoding and regularization of latent spaces, ED-VAE not only improves interpretability but also effectively captures the complex interactions between latent variables and observed data, thus leading to better generative performance.

With the increasing incidence of neurodegenerative diseases such as Alzheimer's Disease (AD), there is a need for further research that enhances detection and monitoring of the diseases. We present MORPHADE (Morphological Autoencoders for Alzheimer's Disease Detection), a novel unsupervised learning approach which uses deformations to allow the analysis of 3D T1-weighted brain images. To the best of our knowledge, this is the first use of deformations with deep unsupervised learning to not only detect, but also localize and assess the severity of structural changes in the brain due to AD. We obtain markedly higher anomaly scores in clinically important areas of the brain in subjects with AD compared to healthy controls, showcasing that our method is able to effectively locate AD-related atrophy. We additionally observe a visual correlation between the severity of atrophy highlighted in our anomaly maps and medial temporal lobe atrophy scores evaluated by a clinical expert. Finally, our method achieves an AUROC of 0.80 in detecting AD, out-performing several supervised and unsupervised baselines. We believe our framework shows promise as a tool towards improved understanding, monitoring and detection of AD. To support further research and application, we have made our code publicly available at github.com/ci-ber/MORPHADE., Comment: 11 pages, 5 figures

Cardiac Cine Magnetic Resonance Imaging (MRI) provides an accurate assessment of heart morphology and function in clinical practice. However, MRI requires long acquisition times, with recent deep learning-based methods showing great promise to accelerate imaging and enhance reconstruction quality. Existing networks exhibit some common limitations that constrain further acceleration possibilities, including single-domain learning, reliance on a single regularization term, and equal feature contribution. To address these limitations, we propose to embed information from multiple domains, including low-rank, image, and k-space, in a novel deep learning network for MRI reconstruction, which we denote as A-LIKNet. A-LIKNet adopts a parallel-branch structure, enabling independent learning in the k-space and image domain. Coupled information sharing layers realize the information exchange between domains. Furthermore, we introduce attention mechanisms into the network to assign greater weights to more critical coils or important temporal frames. Training and testing were conducted on an in-house dataset, including 91 cardiovascular patients and 38 healthy subjects scanned with 2D cardiac Cine using retrospective undersampling. Additionally, we evaluated A-LIKNet on the real-time 8x prospectively undersampled data from the OCMR dataset. The results demonstrate that our proposed A-LIKNet outperforms existing methods and provides high-quality reconstructions. The network can effectively reconstruct highly retrospectively undersampled dynamic MR images up to 24x accelerations, indicating its potential for single breath-hold imaging.

Segmentation is often the first step in many medical image analyses workflows. Deep learning approaches, while giving state-of-the-art accuracies, are data intensive and do not scale well to low data regimes. We introduce Deep Conditional Shape Models 2.0, which uses an edge detector, along with an implicit shape function conditioned on edge maps, to leverage cross-modality shape information. The shape function is trained exclusively on a source domain (contrasted CT) and applied to the target domain of interest (3D echocardiography). We demonstrate data efficiency in the target domain by varying the amounts of training data used in the edge detection stage. We observe that DCSM 2.0 outperforms the baseline at all data levels in terms of Hausdorff distances, and while using 50% or less of the training data in terms of average mesh distance, and at 10% or less of the data with the dice coefficient. The method scales well to low data regimes, with gains of up to 5% in dice coefficient, 2.58 mm in average surface distance and 21.02 mm in Hausdorff distance when using just 2% (22 volumes) of the training data., Comment: Best oral paper award at ISBI 2024

Since the Transformer architecture emerged, language model development has grown, driven by their promising potential. Releasing these models into production requires properly understanding their behavior, particularly in sensitive domains like medicine. Despite this need, the medical literature still lacks practical assessment of pre-trained language models, which are especially valuable in settings where only consumer-grade computational resources are available. To address this gap, we have conducted a comprehensive survey of language models in the medical field and evaluated a subset of these for medical text classification and conditional text generation. The subset includes 53 models with 110 million to 13 billion parameters, spanning the Transformer-based model families and knowledge domains. Different approaches are employed for text classification, including zero-shot learning, enabling tuning without the need to train the model. These approaches are helpful in our target settings, where many users of language models find themselves. The results reveal remarkable performance across the tasks and datasets evaluated, underscoring the potential of certain models to contain medical knowledge, even without domain specialization. This study thus advocates for further exploration of model applications in medical contexts, particularly in computational resource-constrained settings, to benefit a wide range of users. The code is available on https://github.com/anpoc/Language-models-in-medicine.

Existing learning-based cortical surface reconstruction approaches heavily rely on the supervision of pseudo ground truth (pGT) cortical surfaces for training. Such pGT surfaces are generated by traditional neuroimage processing pipelines, which are time consuming and difficult to generalize well to low-resolution brain MRI, e.g., from fetuses and neonates. In this work, we present CoSeg, a learning-based cortical surface reconstruction framework weakly supervised by brain segmentations without the need for pGT surfaces. CoSeg introduces temporal attention networks to learn time-varying velocity fields from brain MRI for diffeomorphic surface deformations, which fit an initial surface to target cortical surfaces within only 0.11 seconds for each brain hemisphere. A weakly supervised loss is designed to reconstruct pial surfaces by inflating the white surface along the normal direction towards the boundary of the cortical gray matter segmentation. This alleviates partial volume effects and encourages the pial surface to deform into deep and challenging cortical sulci. We evaluate CoSeg on 1,113 adult brain MRI at 1mm and 2mm resolution. CoSeg achieves superior geometric and morphological accuracy compared to existing learning-based approaches. We also verify that CoSeg can extract high-quality cortical surfaces from fetal brain MRI on which traditional pipelines fail to produce acceptable results., Comment: Accepted by the 27th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2024)

In differentially private (DP) machine learning, the privacy guarantees of DP mechanisms are often reported and compared on the basis of a single $(\varepsilon, \delta)$-pair. This practice overlooks that DP guarantees can vary substantially even between mechanisms sharing a given $(\varepsilon, \delta)$, and potentially introduces privacy vulnerabilities which can remain undetected. This motivates the need for robust, rigorous methods for comparing DP guarantees in such cases. Here, we introduce the $\Delta$-divergence between mechanisms which quantifies the worst-case excess privacy vulnerability of choosing one mechanism over another in terms of $(\varepsilon, \delta)$, $f$-DP and in terms of a newly presented Bayesian interpretation. Moreover, as a generalisation of the Blackwell theorem, it is endowed with strong decision-theoretic foundations. Through application examples, we show that our techniques can facilitate informed decision-making and reveal gaps in the current understanding of privacy risks, as current practices in DP-SGD often result in choosing mechanisms with high excess privacy vulnerabilities., Comment: ICML 2024

Field-of-view (FOV) recovery of truncated chest CT scans is crucial for accurate body composition analysis, which involves quantifying skeletal muscle and subcutaneous adipose tissue (SAT) on CT slices. This, in turn, enables disease prognostication. Here, we present a method for recovering truncated CT slices using generative image outpainting. We train a diffusion model and apply it to truncated CT slices generated by simulating a small FOV. Our model reliably recovers the truncated anatomy and outperforms the previous state-of-the-art despite being trained on 87% less data., Comment: Shared last authorship: Florian J. Fintelmann and Philip M\"uller

Visual prompting infuses visual information into the input image to adapt models toward specific predictions and tasks. Recently, manually crafted markers such as red circles are shown to guide the model to attend to a target region on the image. However, these markers only work on models trained with data containing those markers. Moreover, finding these prompts requires guesswork or prior knowledge of the domain on which the model is trained. This work circumvents manual design constraints by proposing to learn the visual prompts for guiding the attention of vision transformers. The learned visual prompt, added to any input image would redirect the attention of the pre-trained vision transformer to its spatial location on the image. Specifically, the prompt is learned in a self-supervised manner without requiring annotations and without fine-tuning the vision transformer. Our experiments demonstrate the effectiveness of the proposed optimization-based visual prompting strategy across various pre-trained vision encoders., Comment: Short version (4-pages) accepted as a spotlight paper at T4V workshop, CVPR 2024

Cardiac Magnetic Resonance (CMR) imaging serves as the gold-standard for evaluating cardiac morphology and function. Typically, a multi-view CMR stack, covering short-axis (SA) and 2/3/4-chamber long-axis (LA) views, is acquired for a thorough cardiac assessment. However, efficiently streamlining the complex, high-dimensional 3D+T CMR data and distilling compact, coherent representation remains a challenge. In this work, we introduce a whole-heart self-supervised learning framework that utilizes masked imaging modeling to automatically uncover the correlations between spatial and temporal patches throughout the cardiac stacks. This process facilitates the generation of meaningful and well-clustered heart representations without relying on the traditionally required, and often costly, labeled data. The learned heart representation can be directly used for various downstream tasks. Furthermore, our method demonstrates remarkable robustness, ensuring consistent representations even when certain CMR planes are missing/flawed. We train our model on 14,000 unlabeled CMR data from UK BioBank and evaluate it on 1,000 annotated data. The proposed method demonstrates superior performance to baselines in tasks that demand comprehensive 3D+T cardiac information, e.g. cardiac phenotype (ejection fraction and ventricle volume) prediction and multi-plane/multi-frame CMR segmentation, highlighting its effectiveness in extracting comprehensive cardiac features that are both anatomically and pathologically relevant.