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Medical image classification in radiology faces significant challenges, particularly in generalizing to unseen pathologies. In contrast, CLIP offers a promising solution by leveraging multimodal learning to improve zero-shot classification performance. However, in the medical domain, lesions can be small and might not be well represented in the embedding space. Therefore, in this paper, we explore the potential of visual prompt engineering to enhance the capabilities of Vision Language Models (VLMs) in radiology. Leveraging BiomedCLIP, trained on extensive biomedical image-text pairs, we investigate the impact of embedding visual markers directly within radiological images to guide the model's attention to critical regions. Our evaluation on the JSRT dataset, focusing on lung nodule malignancy classification, demonstrates that incorporating visual prompts $\unicode{x2013}$ such as arrows, circles, and contours $\unicode{x2013}$ significantly improves classification metrics including AUROC, AUPRC, F1 score, and accuracy. Moreover, the study provides attention maps, showcasing enhanced model interpretability and focus on clinically relevant areas. These findings underscore the efficacy of visual prompt engineering as a straightforward yet powerful approach to advance VLM performance in medical image analysis., Comment: Accepted at ECCV 2024 Workshop on Emergent Visual Abilities and Limits of Foundation Models

Semantic segmentation is an essential component of medical image analysis research, with recent deep learning algorithms offering out-of-the-box applicability across diverse datasets. Despite these advancements, segmentation failures remain a significant concern for real-world clinical applications, necessitating reliable detection mechanisms. This paper introduces a comprehensive benchmarking framework aimed at evaluating failure detection methodologies within medical image segmentation. Through our analysis, we identify the strengths and limitations of current failure detection metrics, advocating for the risk-coverage analysis as a holistic evaluation approach. Utilizing a collective dataset comprising five public 3D medical image collections, we assess the efficacy of various failure detection strategies under realistic test-time distribution shifts. Our findings highlight the importance of pixel confidence aggregation and we observe superior performance of the pairwise Dice score (Roy et al., 2019) between ensemble predictions, positioning it as a simple and robust baseline for failure detection in medical image segmentation. To promote ongoing research, we make the benchmarking framework available to the community., Comment: This work has been submitted for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

Content-based image retrieval (CBIR) has the potential to significantly improve diagnostic aid and medical research in radiology. Current CBIR systems face limitations due to their specialization to certain pathologies, limiting their utility. In response, we propose using vision foundation models as powerful and versatile off-the-shelf feature extractors for content-based medical image retrieval. By benchmarking these models on a comprehensive dataset of 1.6 million 2D radiological images spanning four modalities and 161 pathologies, we identify weakly-supervised models as superior, achieving a P@1 of up to 0.594. This performance not only competes with a specialized model but does so without the need for fine-tuning. Our analysis further explores the challenges in retrieving pathological versus anatomical structures, indicating that accurate retrieval of pathological features presents greater difficulty. Despite these challenges, our research underscores the vast potential of foundation models for CBIR in radiology, proposing a shift towards versatile, general-purpose medical image retrieval systems that do not require specific tuning.

The submillimeter and millimeter ((sub-)mm) sky contains a vast wealth of information that is both complementary and inaccessible to other wavelengths. Over half the light we receive is observable at (sub-)mm wavelengths, yet we have mapped only a small portion of the sky at sufficient spatial resolution and sensitivity to detect and resolve distant galaxies or star forming cores within their their large-scale environment. For decades the astronomical community has highlighted the need for a large, high-throughput (sub-)mm ($\lambda\sim0.35-10$ mm) single dish; The Atacama Large Aperture Submillimeter Telescope (AtLAST), with its 50-m aperture and $2^\circ$ maximal field of view, aims to be such a facility. We present here the full design concept for AtLAST, developed through an EU-funded project. Our design approach begins with a long lineage of (sub-)mm telescopes, relies on calculations and simulations to realize the optics, and uses finite element analysis to optimize the mechanical structure and subsystems. The demanding design requirements for AtLAST, set by transformative science goals, combine novel concepts with lessons learned from past experience. The result is an innovative rocking chair design with six instrument bays, two of which are mounted on Nasmyth platforms. AtLAST will be capable of $3^\circ\,\rm s^{-1}$ scanning and $1^\circ\,\rm s^{-2}$ acceleration, and aims to feature a surface accuracy of $\leq 20~\mu$m half wavefront error under static deformations, allowing observations up to $\approx 950$~GHz. Crucially, AtLAST will be a sustainable, visionary facility that will allow upgrades for decades to come. While some aspects require further testing, prototyping, and field demonstrations, we estimate that the design will be construction-ready this decade., Comment: This version addresses the first round A&A referee reports

Despite the remarkable success of deep learning systems over the last decade, a key difference still remains between neural network and human decision-making: As humans, we cannot only form a decision on the spot, but also ponder, revisiting an initial guess from different angles, distilling relevant information, arriving at a better decision. Here, we propose RecycleNet, a latent feature recycling method, instilling the pondering capability for neural networks to refine initial decisions over a number of recycling steps, where outputs are fed back into earlier network layers in an iterative fashion. This approach makes minimal assumptions about the neural network architecture and thus can be implemented in a wide variety of contexts. Using medical image segmentation as the evaluation environment, we show that latent feature recycling enables the network to iteratively refine initial predictions even beyond the iterations seen during training, converging towards an improved decision. We evaluate this across a variety of segmentation benchmarks and show consistent improvements even compared with top-performing segmentation methods. This allows trading increased computation time for improved performance, which can be beneficial, especially for safety-critical applications., Comment: Accepted at 2024 Winter Conference on Applications of Computer Vision (WACV)

The Atacama Large Aperture Submillimeter Telescope (AtLAST) aims to be the premier next generation large diameter (50 meter) single dish observatory capable of observations across the millimeter/submillimeter spectrum, from 30~GHz to 1~THz. AtLAST will be sited in Chile at approximately 5100 meters above sea level, high in the Atacama Desert near Llano de Chajnantor. The novel rocking-chair telescope design allows for a unprecedentedly wide field of view (FoV) of 1-2$^\circ$ diameter, a large receiver cabin housing six major instruments, and high structural stability during fast scanning operations (up to $\sim 3^\circ$ per second in azimuth). Here we describe the current status of, and expected outcomes for, the antenna design study, which will be completed in 2024., Comment: Accepted for the URSI GASS 2023, Sapporo, Japan, 19-26 August 2023. 4 pages, 3 figures

Independently trained machine learning models tend to learn similar features. Given an ensemble of independently trained models, this results in correlated predictions and common failure modes. Previous attempts focusing on decorrelation of output predictions or logits yielded mixed results, particularly due to their reduction in model accuracy caused by conflicting optimization objectives. In this paper, we propose the novel idea of utilizing methods of the representational similarity field to promote dissimilarity during training instead of measuring similarity of trained models. To this end, we promote intermediate representations to be dissimilar at different depths between architectures, with the goal of learning robust ensembles with disjoint failure modes. We show that highly dissimilar intermediate representations result in less correlated output predictions and slightly lower error consistency, resulting in higher ensemble accuracy. With this, we shine first light on the connection between intermediate representations and their impact on the output predictions., Comment: The Second Workshop on Spurious Correlations, Invariance and Stability at ICML 2023

Foundation models have taken over natural language processing and image generation domains due to the flexibility of prompting. With the recent introduction of the Segment Anything Model (SAM), this prompt-driven paradigm has entered image segmentation with a hitherto unexplored abundance of capabilities. The purpose of this paper is to conduct an initial evaluation of the out-of-the-box zero-shot capabilities of SAM for medical image segmentation, by evaluating its performance on an abdominal CT organ segmentation task, via point or bounding box based prompting. We show that SAM generalizes well to CT data, making it a potential catalyst for the advancement of semi-automatic segmentation tools for clinicians. We believe that this foundation model, while not reaching state-of-the-art segmentation performance in our investigations, can serve as a highly potent starting point for further adaptations of such models to the intricacies of the medical domain. Keywords: medical image segmentation, SAM, foundation models, zero-shot learning, Comment: 3 Pages, 1 Figure, Short paper under review for MIDL 2023

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work., Comment: accepted to CVPR 2023

Unsupervised anomaly detection in medical imaging aims to detect and localize arbitrary anomalies without requiring annotated anomalous data during training. Often, this is achieved by learning a data distribution of normal samples and detecting anomalies as regions in the image which deviate from this distribution. Most current state-of-the-art methods use latent variable generative models operating directly on the images. However, generative models have been shown to mostly capture low-level features, s.a. pixel-intensities, instead of rich semantic features, which also applies to their representations. We circumvent this problem by proposing CRADL whose core idea is to model the distribution of normal samples directly in the low-dimensional representation space of an encoder trained with a contrastive pretext-task. By utilizing the representations of contrastive learning, we aim to fix the over-fixation on low-level features and learn more semantic-rich representations. Our experiments on anomaly detection and localization tasks using three distinct evaluation datasets show that 1) contrastive representations are superior to representations of generative latent variable models and 2) the CRADL framework shows competitive or superior performance to state-of-the-art.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Optimal control problems with free terminal time present many challenges including nonsmooth and discontinuous control laws, irregular value functions, many local optima, and the curse of dimensionality. To overcome these issues, we propose an adaptation of the model-based actor-critic paradigm from the field of Reinforcement Learning via an exponential transformation to learn an approximate feedback control and value function pair. We demonstrate the algorithm's effectiveness on prototypical examples featuring each of the main pathological issues present in problems of this type.

Recent research shows that supervised learning can be an effective tool for designing near-optimal feedback controllers for high-dimensional nonlinear dynamic systems. But the behavior of neural network controllers is still not well understood. In particular, some neural networks with high test accuracy can fail to even locally stabilize the dynamic system. To address this challenge we propose several novel neural network architectures, which we show guarantee local asymptotic stability while retaining the approximation capacity to learn the optimal feedback policy semi-globally. The proposed architectures are compared against standard neural network feedback controllers through numerical simulations of two high-dimensional nonlinear optimal control problems: stabilization of an unstable Burgers-type partial differential equation, and altitude and course tracking for an unmanned aerial vehicle. The simulations demonstrate that standard neural networks can fail to stabilize the dynamics even when trained well, while the proposed architectures are always at least locally stabilizing and can achieve near-optimal performance., Comment: arXiv admin note: text overlap with arXiv:2109.07466

Recent research has shown that supervised learning can be an effective tool for designing optimal feedback controllers for high-dimensional nonlinear dynamic systems. But the behavior of these neural network (NN) controllers is still not well understood. In this paper we use numerical simulations to demonstrate that typical test accuracy metrics do not effectively capture the ability of an NN controller to stabilize a system. In particular, some NNs with high test accuracy can fail to stabilize the dynamics. To address this we propose two NN architectures which locally approximate a linear quadratic regulator (LQR). Numerical simulations confirm our intuition that the proposed architectures reliably produce stabilizing feedback controllers without sacrificing optimality. In addition, we introduce a preliminary theoretical result describing some stability properties of such NN-controlled systems.

The ability to estimate how a tumor might evolve in the future could have tremendous clinical benefits, from improved treatment decisions to better dose distribution in radiation therapy. Recent work has approached the glioma growth modeling problem via deep learning and variational inference, thus learning growth dynamics entirely from a real patient data distribution. So far, this approach was constrained to predefined image acquisition intervals and sequences of fixed length, which limits its applicability in more realistic scenarios. We overcome these limitations by extending Neural Processes, a class of conditional generative models for stochastic time series, with a hierarchical multi-scale representation encoding including a spatio-temporal attention mechanism. The result is a learned growth model that can be conditioned on an arbitrary number of observations, and that can produce a distribution of temporally consistent growth trajectories on a continuous time axis. On a dataset of 379 patients, the approach successfully captures both global and finer-grained variations in the images, exhibiting superior performance compared to other learned growth models., Comment: MICCAI 2021

Neural Processes (NPs) are a family of conditional generative models that are able to model a distribution over functions, in a way that allows them to perform predictions at test time conditioned on a number of context points. A recent addition to this family, Convolutional Conditional Neural Processes (ConvCNP), have shown remarkable improvement in performance over prior art, but we find that they sometimes struggle to generalize when applied to time series data. In particular, they are not robust to distribution shifts and fail to extrapolate observed patterns into the future. By incorporating a Gaussian Process into the model, we are able to remedy this and at the same time improve performance within distribution. As an added benefit, the Gaussian Process reintroduces the possibility to sample from the model, a key feature of other members in the NP family., Comment: UAI 2021

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often remains unclear, as the data included in challenges are usually acquired in very controlled settings at few institutions. The seemingly obvious solution of just collecting increasingly more data from more institutions in such challenges does not scale well due to privacy and ownership hurdles. Towards alleviating these concerns, we are proposing the FeTS challenge 2021 to cater towards both the development and the evaluation of models for the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. Specifically, the FeTS 2021 challenge uses clinically acquired, multi-institutional magnetic resonance imaging (MRI) scans from the BraTS 2020 challenge, as well as from various remote independent institutions included in the collaborative network of a real-world federation (https://www.fets.ai/). The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i.e. on data from institutional distributions that were not part of the training datasets.

We report on an initial user study, which explores how players of an augmented mirror game, self-style or self-present themselves when they are allowed to see themselves in the mirror compared to when they do not see themselves. To this end, we customized an open source fruit slicing game into an interactive installation for an architecture museum and conducted with 36 visitors a field study. Based on an analysis of video recordings of participants we identified, for example significant differences in how often participants smile. Ultimately, presenting a self-image to gamers in a social setting resulted in behavior change, which we argue could be utilized carefully from a Somaesthetics perspective as an experience design feature in future games., Comment: 11 pages

In this paper we propose a new computational method for designing optimal regulators for high-dimensional nonlinear systems. The proposed approach leverages physics-informed machine learning to solve high-dimensional Hamilton-Jacobi-Bellman equations arising in optimal feedback control. Concretely, we augment linear quadratic regulators with neural networks to handle nonlinearities. We train the augmented models on data generated without discretizing the state space, enabling application to high-dimensional problems. We use the proposed method to design a candidate optimal regulator for an unstable Burgers' equation, and through this example, demonstrate improved robustness and accuracy compared to existing neural network formulations., Comment: Added IEEE accepted manuscript with copyright notice

Recent research reveals that deep learning is an effective way of solving high dimensional Hamilton-Jacobi-Bellman equations. The resulting feedback control law in the form of a neural network is computationally efficient for real-time applications of optimal control. A critical part of this design method is to generate data for training the neural network and validating its accuracy. In this paper, we provide a survey of existing algorithms that can be used to generate data. All the algorithms surveyed in this paper are causality-free, i.e., the solution at a point is computed without using the value of the function at any other points. At the end of the paper, an illustrative example of optimal feedback design using deep learning is given., Comment: 15 pages, 1 figure

Through training on unlabeled data, anomaly detection has the potential to impact computer-aided diagnosis by outlining suspicious regions. Previous work on deep-learning-based anomaly detection has primarily focused on the reconstruction error. We argue instead, that pixel-wise anomaly ratings derived from a Variational Autoencoder based score approximation yield a theoretically better grounded and more faithful estimate. In our experiments, Variational Autoencoder gradient-based rating outperforms other approaches on unsupervised pixel-wise tumor detection on the BraTS-2017 dataset with a ROC-AUC of 0.94.

Variational Auto-Encoders have often been used for unsupervised pretraining, feature extraction and out-of-distribution and anomaly detection in the medical field. However, VAEs often lack the ability to produce sharp images and learn high-level features. We propose to alleviate these issues by adding a new branch to conditional hierarchical VAEs. This enforces a division between higher-level and lower-level features. Despite the additional computational overhead compared to a normal VAE it results in sharper and better reconstructions and can capture the data distribution similarly well (indicated by a similar or slightly better OoD detection performance).

Uncertainty propagation in nonlinear dynamic systems remains an outstanding problem in scientific computing and control. Numerous approaches have been developed, but are limited in their capability to tackle problems with more than a few uncertain variables or require large amounts of simulation data. In this paper, we propose a data-driven method for approximating joint probability density functions (PDFs) of nonlinear dynamic systems with initial condition and parameter uncertainty. Our approach leverages on the power of deep learning to deal with high-dimensional inputs, but we overcome the need for huge quantities of training data by encoding PDF evolution equations directly into the optimization problem. We demonstrate the potential of the proposed method by applying it to evaluate the robustness of a feedback controller for a six-dimensional rigid body with parameter uncertainty., Comment: This work has been submitted to IFAC for possible publication

Analysis of Earth system dynamics in the Anthropocene requires to explicitly take into account the increasing magnitude of processes operating in human societies, their cultures, economies and technosphere and their growing feedback entanglement with those in the physical, chemical and biological systems of the planet. However, current state-of-the-art Earth System Models do not represent dynamic human societies and their feedback interactions with the biogeophysical Earth system and macroeconomic Integrated Assessment Models typically do so only with limited scope. This paper (i) proposes design principles for constructing World-Earth Models (WEM) for Earth system analysis of the Anthropocene, i.e., models of social (World) - ecological (Earth) co-evolution on up to planetary scales, and (ii) presents the copan:CORE open simulation modeling framework for developing, composing and analyzing such WEMs based on the proposed principles. The framework provides a modular structure to flexibly construct and study WEMs. These can contain biophysical (e.g. carbon cycle dynamics), socio-metabolic/economic (e.g. economic growth) and socio-cultural processes (e.g. voting on climate policies or changing social norms) and their feedback interactions, and are based on elementary entity types, e.g., grid cells and social systems. Thereby, copan:CORE enables the epistemic flexibility needed for contributions towards Earth system analysis of the Anthropocene given the large diversity of competing theories and methodologies used for describing socio-metabolic/economic and socio-cultural processes in the Earth system by various fields and schools of thought. To illustrate the capabilities of the framework, we present an exemplary and highly stylized WEM implemented in copan:CORE that illustrates how endogenizing socio-cultural processes and feedbacks could fundamentally change macroscopic model outcomes.

Unsupervised learning can leverage large-scale data sources without the need for annotations. In this context, deep learning-based autoencoders have shown great potential in detecting anomalies in medical images. However, especially Variational Autoencoders (VAEs)often fail to capture the high-level structure in the data. We address these shortcomings by proposing the context-encoding Variational Autoencoder (ceVAE), which improves both, the sample, as well as pixelwise results. In our experiments on the BraTS-2017 and ISLES-2015 segmentation benchmarks the ceVAE achieves unsupervised AUROCs of 0.95 and 0.89, respectively, thus outperforming other reported deep-learning based approaches., Comment: MIDL 2019 [arXiv:1907.08612]

Computing optimal feedback controls for nonlinear systems generally requires solving Hamilton-Jacobi-Bellman (HJB) equations, which are notoriously difficult when the state dimension is large. Existing strategies for high-dimensional problems often rely on specific, restrictive problem structures, or are valid only locally around some nominal trajectory. In this paper, we propose a data-driven method to approximate semi-global solutions to HJB equations for general high-dimensional nonlinear systems and compute candidate optimal feedback controls in real-time. To accomplish this, we model solutions to HJB equations with neural networks (NNs) trained on data generated without discretizing the state space. Training is made more effective and data-efficient by leveraging the known physics of the problem and using the partially-trained NN to aid in adaptive data generation. We demonstrate the effectiveness of our method by learning solutions to HJB equations corresponding to the attitude control of a six-dimensional nonlinear rigid body, and nonlinear systems of dimension up to 30 arising from the stabilization of a Burgers'-type partial differential equation. The trained NNs are then used for real-time feedback control of these systems., Comment: Added section on validation error computation. Updated convergence test formula and associated results

An assumption-free automatic check of medical images for potentially overseen anomalies would be a valuable assistance for a radiologist. Deep learning and especially Variational Auto-Encoders (VAEs) have shown great potential in the unsupervised learning of data distributions. In principle, this allows for such a check and even the localization of parts in the image that are most suspicious. Currently, however, the reconstruction-based localization by design requires adjusting the model architecture to the specific problem looked at during evaluation. This contradicts the principle of building assumption-free models. We propose complementing the localization part with a term derived from the Kullback-Leibler (KL)-divergence. For validation, we perform a series of experiments on FashionMNIST as well as on a medical task including >1000 healthy and >250 brain tumor patients. Results show that the proposed formalism outperforms the state of the art VAE-based localization of anomalies across many hyperparameter settings and also shows a competitive max performance.

Unsupervised learning can leverage large-scale data sources without the need for annotations. In this context, deep learning-based auto encoders have shown great potential in detecting anomalies in medical images. However, state-of-the-art anomaly scores are still based on the reconstruction error, which lacks in two essential parts: it ignores the model-internal representation employed for reconstruction, and it lacks formal assertions and comparability between samples. We address these shortcomings by proposing the Context-encoding Variational Autoencoder (ceVAE) which combines reconstruction- with density-based anomaly scoring. This improves the sample- as well as pixel-wise results. In our experiments on the BraTS-2017 and ISLES-2015 segmentation benchmarks, the ceVAE achieves unsupervised ROC-AUCs of 0.95 and 0.89, respectively, thus outperforming state-of-the-art methods by a considerable margin.