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In natural language processing and computer vision, self-supervised pre-training on large datasets unlocks foundational model capabilities across domains and tasks. However, this potential has not yet been realised in time series analysis, where existing methods disregard the heterogeneous nature of time series characteristics. Time series are prevalent in many domains, including medicine, engineering, natural sciences, and finance, but their characteristics vary significantly in terms of variate count, inter-variate relationships, temporal dynamics, and sampling frequency. This inherent heterogeneity across domains prevents effective pre-training on large time series corpora. To address this issue, we introduce OTiS, an open model for general time series analysis, that has been specifically designed to handle multi-domain heterogeneity. We propose a novel pre-training paradigm including a tokeniser with learnable domain-specific signatures, a dual masking strategy to capture temporal causality, and a normalised cross-correlation loss to model long-range dependencies. Our model is pre-trained on a large corpus of 640,187 samples and 11 billion time points spanning 8 distinct domains, enabling it to analyse time series from any (unseen) domain. In comprehensive experiments across 15 diverse applications - including classification, regression, and forecasting - OTiS showcases its ability to accurately capture domain-specific data characteristics and demonstrates its competitiveness against state-of-the-art baselines. Our code and pre-trained weights are publicly available at https://github.com/oetu/otis.

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)

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

Since the emergence of the Transformer architecture, language model development has increased, driven by their promising potential. However, releasing these models into production requires properly understanding their behavior, particularly in sensitive domains such as medicine. Despite this need, the medical literature still lacks technical assessments of pre-trained language models, which are especially valuable in resource-constrained settings in terms of computational power or limited budget. To address this gap, we provide a comprehensive survey of language models in the medical domain. In addition, we selected a subset of these models for thorough evaluation, focusing on classification and text generation tasks. Our subset encompasses 53 models, ranging from 110 million to 13 billion parameters, spanning the three families of Transformer-based models and from diverse knowledge domains. This study employs a series of approaches for text classification together with zero-shot prompting instead of model training or fine-tuning, which closely resembles the limited resource setting in which many users of language models find themselves. Encouragingly, our findings reveal remarkable performance across various tasks and datasets, underscoring the latent potential of certain models to contain medical knowledge, even without domain specialization. Consequently, our study advocates for further exploration of model applications in medical contexts, particularly in resource-constrained settings. The code is available on https://github.com/anpoc/Language-models-in-medicine.

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

Report generation models offer fine-grained textual interpretations of medical images like chest X-rays, yet they often lack interactivity (i.e. the ability to steer the generation process through user queries) and localized interpretability (i.e. visually grounding their predictions), which we deem essential for future adoption in clinical practice. While there have been efforts to tackle these issues, they are either limited in their interactivity by not supporting textual queries or fail to also offer localized interpretability. Therefore, we propose a novel multitask architecture and training paradigm integrating textual prompts and bounding boxes for diverse aspects like anatomical regions and pathologies. We call this approach the Chest X-Ray Explainer (ChEX). Evaluations across a heterogeneous set of 9 chest X-ray tasks, including localized image interpretation and report generation, showcase its competitiveness with SOTA models while additional analysis demonstrates ChEX's interactive capabilities. Code: https://github.com/philip-mueller/chex, Comment: Accepted at ECCV 2024

This research explores the integration of language models and unsupervised anomaly detection in medical imaging, addressing two key questions: (1) Can language models enhance the interpretability of anomaly detection maps? and (2) Can anomaly maps improve the generalizability of language models in open-set anomaly detection tasks? To investigate these questions, we introduce a new dataset for multi-image visual question-answering on brain magnetic resonance images encompassing multiple conditions. We propose KQ-Former (Knowledge Querying Transformer), which is designed to optimally align visual and textual information in limited-sample contexts. Our model achieves a 60.81% accuracy on closed questions, covering disease classification and severity across 15 different classes. For open questions, KQ-Former demonstrates a 70% improvement over the baseline with a BLEU-4 score of 0.41, and achieves the highest entailment ratios (up to 71.9%) and lowest contradiction ratios (down to 10.0%) among various natural language inference models. Furthermore, integrating anomaly maps results in an 18% accuracy increase in detecting open-set anomalies, thereby enhancing the language model's generalizability to previously unseen medical conditions. The code and dataset are available at https://github.com/compai-lab/miccai-2024-junli?tab=readme-ov-file, Comment: 13 pages, 7 figures. 5th International Workshop on Multiscale Multimodal Medical Imaging (MMMI 2024)

Weakly supervised object detection (WSup-OD) increases the usefulness and interpretability of image classification algorithms without requiring additional supervision. The successes of multiple instance learning in this task for natural images, however, do not translate well to medical images due to the very different characteristics of their objects (i.e. pathologies). In this work, we propose Weakly Supervised ROI Proposal Networks (WSRPN), a new method for generating bounding box proposals on the fly using a specialized region of interest-attention (ROI-attention) module. WSRPN integrates well with classic backbone-head classification algorithms and is end-to-end trainable with only image-label supervision. We experimentally demonstrate that our new method outperforms existing methods in the challenging task of disease localization in chest X-ray images. Code: https://github.com/philip-mueller/wsrpn

Pathology detection and delineation enables the automatic interpretation of medical scans such as chest X-rays while providing a high level of explainability to support radiologists in making informed decisions. However, annotating pathology bounding boxes is a time-consuming task such that large public datasets for this purpose are scarce. Current approaches thus use weakly supervised object detection to learn the (rough) localization of pathologies from image-level annotations, which is however limited in performance due to the lack of bounding box supervision. We therefore propose anatomy-driven pathology detection (ADPD), which uses easy-to-annotate bounding boxes of anatomical regions as proxies for pathologies. We study two training approaches: supervised training using anatomy-level pathology labels and multiple instance learning (MIL) with image-level pathology labels. Our results show that our anatomy-level training approach outperforms weakly supervised methods and fully supervised detection with limited training samples, and our MIL approach is competitive with both baseline approaches, therefore demonstrating the potential of our approach., Comment: Accepted at MICCAI 2023

The electrocardiogram (ECG) is a widely available diagnostic tool that allows for a cost-effective and fast assessment of the cardiovascular health. However, more detailed examination with expensive cardiac magnetic resonance (CMR) imaging is often preferred for the diagnosis of cardiovascular diseases. While providing detailed visualization of the cardiac anatomy, CMR imaging is not widely available due to long scan times and high costs. To address this issue, we propose the first self-supervised contrastive approach that transfers domain-specific information from CMR images to ECG embeddings. Our approach combines multimodal contrastive learning with masked data modeling to enable holistic cardiac screening solely from ECG data. In extensive experiments using data from 40,044 UK Biobank subjects, we demonstrate the utility and generalizability of our method. We predict the subject-specific risk of various cardiovascular diseases and determine distinct cardiac phenotypes solely from ECG data. In a qualitative analysis, we demonstrate that our learned ECG embeddings incorporate information from CMR image regions of interest. We make our entire pipeline publicly available, including the source code and pre-trained model weights.

Training Artificial Intelligence (AI) models on 3D images presents unique challenges compared to the 2D case: Firstly, the demand for computational resources is significantly higher, and secondly, the availability of large datasets for pre-training is often limited, impeding training success. This study proposes a simple approach of adapting 2D networks with an intermediate feature representation for processing 3D images. Our method employs attention pooling to learn to assign each slice an importance weight and, by that, obtain a weighted average of all 2D slices. These weights directly quantify the contribution of each slice to the contribution and thus make the model prediction inspectable. We show on all 3D MedMNIST datasets as benchmark and two real-world datasets consisting of several hundred high-resolution CT or MRI scans that our approach performs on par with existing methods. Furthermore, we compare the in-built interpretability of our approach to HiResCam, a state-of-the-art retrospective interpretability approach.

The automatic generation of radiology reports has the potential to assist radiologists in the time-consuming task of report writing. Existing methods generate the full report from image-level features, failing to explicitly focus on anatomical regions in the image. We propose a simple yet effective region-guided report generation model that detects anatomical regions and then describes individual, salient regions to form the final report. While previous methods generate reports without the possibility of human intervention and with limited explainability, our method opens up novel clinical use cases through additional interactive capabilities and introduces a high degree of transparency and explainability. Comprehensive experiments demonstrate our method's effectiveness in report generation, outperforming previous state-of-the-art models, and highlight its interactive capabilities. The code and checkpoints are available at https://github.com/ttanida/rgrg ., Comment: Accepted at CVPR 2023

Detection of pathologies is a fundamental task in medical imaging and the evaluation of algorithms that can perform this task automatically is crucial. However, current object detection metrics for natural images do not reflect the specific clinical requirements in pathology detection sufficiently. To tackle this problem, we propose Robust Detection Outcome (RoDeO); a novel metric for evaluating algorithms for pathology detection in medical images, especially in chest X-rays. RoDeO evaluates different errors directly and individually, and reflects clinical needs better than current metrics. Extensive evaluation on the ChestX-ray8 dataset shows the superiority of our metrics compared to existing ones. We released the code at https://github.com/FeliMe/RoDeO and published RoDeO as pip package (rodeometric)., Comment: Accepted at MIDL 2023

Collecting personally identifiable information (PII) on data subjects has become big business. Data brokers and data processors are part of a multi-billion-dollar industry that profits from collecting, buying, and selling consumer data. Yet there is little transparency in the data collection industry which makes it difficult to understand what types of data are being collected, used, and sold, and thus the risk to individual data subjects. In this study, we examine a large textual dataset of privacy policies from 1997-2019 in order to investigate the data collection activities of data brokers and data processors. We also develop an original lexicon of PII-related terms representing PII data types curated from legislative texts. This mesoscale analysis looks at privacy policies overtime on the word, topic, and network levels to understand the stability, complexity, and sensitivity of privacy policies over time. We find that (1) privacy legislation correlates with changes in stability and turbulence of PII data types in privacy policies; (2) the complexity of privacy policies decreases over time and becomes more regularized; (3) sensitivity rises over time and shows spikes that are correlated with events when new privacy legislation is introduced.

The failure of heterogeneous materials with microstructures is a complex process of damage nucleation, growth and localisation. This process spans multiple length scales and is challenging to simulate numerically due to its high computational cost. One option is to use domain decomposed multi-scale methods with dynamical refinement. If needed, these methods refine coarse regions into a fine-scale representation to explicitly model the damage in the microstructure. However, damage evolution is commonly restricted to fine-scale regions only. Thus, they are unable to capture the full complexity and breath of the degradation process in the material. In this contribution, a generic procedure that allows to account for damage in all representations is proposed. The approach combines a specially designed orthotropic damage law, with a scheme to generate pre-damaged fine-scale microstructures. Results indicate that the damage approximation for the coarse representation works well. Furthermore, the generated fine-scale damage patterns are overall consistent with explicitly simulated damage patterns. Minor discrepancies occur in the generation but subsequently vanish when explicit damage evolution continuous; for instance under increased load. The presented approach provides a methodological basis for adaptive multi-scale simulation schemes with consistent damage evolution.

Image-text contrastive learning has proven effective for pretraining medical image models. When targeting localized downstream tasks like semantic segmentation or object detection, additional local contrastive losses that align image regions with sentences have shown promising results. We study how local contrastive losses are related to global (per-sample) contrastive losses and which effects they have on localized medical downstream tasks. Based on a theoretical comparison, we propose to remove some components of local losses and replace others by a novel distribution prior which enforces uniformity of representations within each sample. We empirically study this approach on chest X-ray tasks and find it to be very effective, outperforming methods without local losses on 12 of 18 tasks., Comment: NeurIPS 2022 Workshop: Self-Supervised Learning - Theory and Practice (Reason for updated version: correction of a typo in Eq. (2) and (3))

Contrastive learning has proven effective for pre-training image models on unlabeled data with promising results for tasks such as medical image classification. Using paired text (like radiological reports) during pre-training improves the results even further. Still, most existing methods target image classification downstream tasks and may not be optimal for localized tasks like semantic segmentation or object detection. We therefore propose Localized representation learning from Vision and Text (LoVT), to our best knowledge, the first text-supervised pre-training method that targets localized medical imaging tasks. Our method combines instance-level image-report contrastive learning with local contrastive learning on image region and report sentence representations. We evaluate LoVT and commonly used pre-training methods on an evaluation framework of 18 localized tasks on chest X-rays from five public datasets. LoVT performs best on 10 of the 18 studied tasks making it the preferred method of choice for localized tasks., Comment: Accepted at ECCV 2022

Convolutional networks are successful, but they have recently been outperformed by new neural networks that are equivariant under rotations and translations. These new networks work better because they do not struggle with learning each possible orientation of each image feature separately. So far, they have been proposed for 2D and 3D data. Here we generalize them to 6D diffusion MRI data, ensuring joint equivariance under 3D roto-translations in image space and the matching 3D rotations in $q$-space, as dictated by the image formation. Such equivariant deep learning is appropriate for diffusion MRI, because microstructural and macrostructural features such as neural fibers can appear at many different orientations, and because even non-rotation-equivariant deep learning has so far been the best method for many diffusion MRI tasks. We validate our equivariant method on multiple-sclerosis lesion segmentation. Our proposed neural networks yield better results and require fewer scans for training compared to non-rotation-equivariant deep learning. They also inherit all the advantages of deep learning over classical diffusion MRI methods. Our implementation is available at https://github.com/philip-mueller/equivariant-deep-dmri and can be used off the shelf without understanding the mathematical background., Comment: 24 pages, 8 figures