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Bernhard Kainz

Publications and source records attributed to Bernhard Kainz.

At least 19 recordsLinked to original sources
arXiv2026

Self-Supervised Cardiac Phase Detection via Single-Parameter Latent Orbits

Accurate identification of end-diastole (ED) and end-systole (ES) in echocardiography underpins the quantification of ventricular function, yet manual selection of these key frames is subjective and introduces clinically significant inter-operator variability. Recent self-supervised methods either prescribe strict periodic trajectories or learn an unconstrained low-dimensional motion subspace from reconstruction or registration objectives. The former offers interpretability but imposes restrictive assumptions on temporal progression, whereas the latter leaves cardiac phase implicit and ED/ES must be recovered through post-hoc geometric processing of the learned trajectory. We translate the physiological observation that cardiac phase is a one-dimensional signal into a prior by constraining the latent motion component to a single-parameter latent orbit, i.e., a global linear trajectory in latent space indexed by a bounded scalar phase variable. Mapping this variable through a sinusoidal nonlinearity yields an oscillatory motion signal with consistent temporal ordering, enabling direct identification of ED and ES from the learned phase signal. This inductive bias allows the model to capture an interpretable representation of the cardiac cycle, while maintaining flexibility to capture irregular heartbeats. Trained on EchoNet-Dynamic without annotations, our minimal single-parameter cardiac phase model learns an effective latent orbit, significantly improves upon the previous state of the art in ED localisation and matches it in ES localisation while using a more constrained representation and fewer training epochs. This demonstrates that a principled physiological inductive bias can match or exceed the performance of more complex representations. Code is available at: https://github.com/BonniciJ/OrbitalEcho/

cs.CV↗
arXiv2026

Frozen DINO Localizes Image Edits Without a Localizer

Localized image edits can change a photograph's meaning while leaving most of it authentic, so forensic analysis must identify where an edit occurred. We show that patch-level perturbation responses from frozen DINO encoders are themselves localization maps. Training-free Localization of AI-image Edits from patch-token Drift (TRAIL) applies one global Haar perturbation and maps cosine drift between corresponding patch tokens. On 80 source-disjoint CocoGlide test images, TRAIL reaches .903 patch AUROC versus .912 for the mask-supervised Detective SAM; fixed-threshold Dice is .619 versus .709, while an oracle threshold raises TRAIL to .790. Transferred unchanged to Poisson image interpolation, TRAIL reaches .855 AUROC versus .864, showing that the cue persists without a generator. Across sixteen DINO encoders, the best block lies at normalized depth .80-.94. Global context matters: AUROC falls from .903 globally to .857 for local-in-canvas perturbations and .735 for independently encoded crops. Frozen DINO patch tokens therefore contain a strong late-layer localization signal whose visibility depends on the perturbation and preserved context. Code: https://github.com/VishalJ99/trail-image-edit-localization.

cs.CV↗
arXiv2026

Entangled by Design: Spurious Intra-Variable Signal Routing in Tabular In-Context Learners

Consider a model trained at a single hospital to predict patient recovery, where the measured feature $X$ bundles the patient's true health signal ($C$) with a systematic artefact from that hospital's equipment ($S$). Within that hospital, the artefact correlates with outcomes through unmeasured confounders such as patient demographics; an in-context learner rationally routes predictions through $S$, not $C$, and fails silently when deployed at a new hospital with different equipment. We formalise this as \emph{spurious routing in composite representations}: when a feature $X = [C;\,\alpha S;\,\eta]$ encodes a causal signal $C$ and a spurious signal $S$ in distinct subspaces, the ICL cannot determine which drives predictions. We prove that under ridge ICL, a linear in-context learner, this routing is unavoidable regardless of context size; TabPFN, a state-of-the-art pretrained tabular ICL model, shows qualitatively consistent behaviour empirically. We derive a closed-form characterisation, $\mathrm{CSR} \propto \rho_S/\rho_C$, confirmed at $r = 0.997$ for linear ICL and $r = 0.979$ for TabPFN. Contrary to intuition, larger context sharpens commitment to the dominant in-context signal, amplifying spurious routing by up to $1.74\times$; in the high-spurious corner, more expressive models show greater vulnerability empirically ($+2.22$ CSR gap at high entanglement). We introduce two lightweight mitigations: environment-stratified context construction and S-swap augmentation, that require only weak environment labels and no knowledge of the causal partition. S-swap reduces spurious routing by $74\%$ for linear ICL and $98.8\%$ for TabPFN, with TabPFN's causal sensitivity increasing $8.4\times$ simultaneously: the model does not become agnostic, it reroutes through the causal signal.

cs.AI↗
arXiv2026

From Training to Deployment: Post-Hoc Causal Feature Identification via Sensitivity Ratios

Given a model that is already trained, which features does it rely on causally versus spuriously? Existing methods require access to the training procedure and cannot answer this post-hoc. We introduce the \textbf{Normalised Sensitivity Ratio~(NSR)}, a post-hoc, model-agnostic diagnostic for this question under a structured-shift regime: environments differ primarily in the mean of spurious features while the causal mechanism and causal marginals remain stable, as in multi-site clinical data or multi-batch genomics. Within this regime, causal features induce constant model sensitivity across environments while spurious features track shift. NSR formalises this as the squared coefficient of variation of per-environment sensitivity. Under a linear structural causal model (SCM) with $K\ge3$ non-degenerate environments, NSR achieves exact identification (Theorem~1). We fully characterise failure: weak shifts ($O(\varepsilon^4)$ collapse), degenerate geometry, and proxy attenuation ($O((1-\alpha)^4)$), giving practitioners quantitative criteria for assessing whether the regime holds. Finite-sample rates are $O_p(n^{-1})$ under the null and $O_p(n^{-1/2})$ under the alternative. Experiments confirm all theoretical predictions on synthetic data (area under the ROC curve [AUROC] $= 1.000$ under conditions satisfying the regime), show consistent rankings across five model families (Kendall $\tau\ge0.529$), and recover six of eight causal features on bike-sharing data (Precision@7 $= 0.75$) without modifying any trained model.

cs.AI↗
arXiv2026

CPAgents: Agentic Composite Phenotype Generation for Cardiac Disease Association

Identifying robust associations between cardiac imaging phenotypes and clinical diseases is fundamental to population-scale cardiovascular research and reliable risk stratification. However, current phenome-wide association studies rely on pre-defined, single-variable phenotypes or expert-crafted features, which limits their ability to capture clinically meaningful non-linear effects and cross-phenotype interactions. To address this, we propose CPAgents, an iterative phenotype-Composition framework for cardiovascular Phenome-wide association study (PheWAS) that automatically constructs and validates interpretable composite phenotypes (e.g., polynomial, ratio, and interaction forms) from base imaging features. Specifically, our system coordinates three agents: (i) an Analyst that identifies statistical pathologies and nominates candidate transformations; (ii) a Proposer that generates constrained, medically and statistically motivated expressions under numerical safety rules; and (iii) a Verifier that evaluates candidates using multi-stage criteria and produces transparent evidence trails for accepted phenotypes. Evaluated on a population-scale cardiac imaging cohort, the discovered composite phenotypes markedly improve disease discrimination: across 72 classifier-disease-metric combinations, our variants achieve the top rank in 56 cases versus 18 for baselines, with gains observed across all nine clinical disease categories. Our framework yields compact, clinically interpretable phenotype formulas with transparent evidence trails, enabling scalable discovery of stronger phenotype-disease associations beyond expert-driven feature selection.

cs.LG↗
arXiv2026

Distribution-Aware Diffusion-LLM for Robust Ultra-Long-Term Time Series Forecasting

Time series forecasting is a fundamental machine learning task. Recent work has explored Large Language Models (LLMs) for this purpose due to their strong generalization, pattern recognition, and zero-shot or few-shot capabilities. Despite their suitability for long-context learning, LLMs face challenges in multimodal settings: they lack calibrated probabilistic modeling for non-text data and struggle to align heterogeneous representations. To address these issues, we propose a new framework Diffusion-LLM that integrates a conditional diffusion model into an LLM-based forecasting pipeline. This joint design enables learning the conditional distribution of future data while improving semantic alignment in a shared latent space. We evaluate Diffusion-LLM on six long-term forecasting benchmarks, including ETT, Weather, and ECL. Our method consistently outperforms existing LLM-based baseline, achieving notable gains in ultra-long-term and few-shot forecasting and demonstrating the value of distribution-aware regularization for enhancing robustness and generalization in time series LLMs.

cs.LG↗
arXiv2026

Vision-Language Models as Zero-Annotation Oracles in Histopathology

Foreground segmentation is the critical first step of every computational pathology pipeline, yet existing methods rely on hand-tuned heuristics or supervised models that overfit to narrow stain and scanner distributions, failing silently on specialised stains such as Jones silver or Elastica van Gieson. We propose a coarse-to-fine approach that recasts foreground segmentation as a visual perception task and leverages general-purpose vision-language models (VLMs) as zero-annotation oracles. Our key insight is that tissue-versus-background discrimination is a natural-image recognition problem, not a histopathological one, so VLMs trained on internet-scale corpora generalise where domain-specific models cannot. We introduce Leica-75, a benchmark of 75 renal transplant whole-slide images spanning three stain families. On Leica-75, our method achieves the highest segmentation quality on out-of-distribution stains (Dice 0.858 +/- 0.027 on Jones, 0.853 +/- 0.041 on EVG) with 7x lower cross-stain variance than the best supervised baseline, while remaining competitive on in-distribution H&E. Few-shot prompting with automatically curated exemplars (Auto-context) rescues hard cases on Stress-32 (n=32), a curated stress-test subset (Dice 0.470 to 0.819 for the 2B model). VLM-based annotation review matches human expert consensus (kappa=0.989 for blur detection; mean precision/recall grading accuracy 0.708 vs. human 0.646 for segmentation mask review). The resulting pseudo-labels are used to distil lightweight student models that are as performant as the teacher model while running for a fraction of the cost. Our framework provides a principled, scalable solution to a persistent infrastructure bottleneck in digital pathology.

cs.CV↗
arXiv2026

Stain-Aware Wavelet Regularization for Instant Adversarial Purification in Histopathology

Deep learning has become prevalent in computational pathology pipelines that support tasks such as cancer screening and digital pathology analysis. However, the susceptibility of neural networks to adversarial perturbations raises safety concerns for reliable deployment in clinical practice. In histopathological images, this challenge is exacerbated by the difficulty of distinguishing high-frequency adversarial noise from subtle and diagnostically relevant tissue structures. To address this issue, we propose Stain-Aware Wavelet Regularization (SAWR), an adversarial purification framework that leverages multi-level wavelet-domain regularization based on Haar transform to hierarchically disentangle adversarial perturbations from diagnostic structural information. This spectral constraint is further extended to individual histological channels, enabling stain-specific frequency regulation consistent with the biological properties of Hematoxylin and Eosin. Extensive experiments demonstrate that SAWR improves adversarial robustness by up to 10.69\% over the baseline approach, while maintaining texture and spectral fidelity under adversarial perturbations.

cs.CV↗
arXiv2026

Multi-Camera AR Guidance System for Surgical Instrument Handling and Assembly: Investigating Workload and Efficiency

The handling and assembly of instruments during surgery imposes high cognitive demands on scrub nurses, particularly when instruments are unfamiliar. We present a supporting guidance system for surgical instrumentation that combines multi-camera 6D pose estimation with augmented reality in-situ visualization on a head-mounted display without the requirement for additional markers. Pose estimation and consecutive camera calibration are achieved through known objects. The 6D pose estimation network is trained purely on synthetic data, aiming for better generalizability and real-world applicability. The AR guidance displays tooltip localization cues and step-wise assembly animations. Via gaze-based selection and a foot pedal, users can switch between assembly steps in intraoperative use. In a technical evaluation, our approach outperforms state-of-art 6D pose estimation. A user study with 29 scrub nurses was conducted in a surgical simulation of knee arthroplasty, comparing the system against a paper manual. AR guidance significantly reduced the perceived workload compared. Objectively, AR guidance reduced task completion time by 21.3\% (4.76 minutes). Specifically, scrub nurses less experienced with the instrument set benefited when using the system. Error frequencies were comparable between conditions. Qualitative feedback highlighted improved process clarity, reduced information overload, and perceived independence. To summarize, our marker-free multi-camera AR guidance approach for surgical instruments can, subjectively and objectively, improve intraoperative instrumentation performance, particularly for untrained scrub nurses.

cs.CV↗
arXiv2026

Wasserstein Equilibrium Decoding for Reliable Medical Visual Question Answering

Small vision-language models (2-8B) are well-suited for clinical deployment due to privacy constraints, limited connectivity, and low-latency requirements favouring on-device or on-premise inference. However, their limited capacity exacerbates the generation of plausible but incorrect outputs. We extend game-theoretic decoding, previously restricted to text-only, closed-ended NLP tasks, to vision-language models for open-ended Medical VQA. We introduce a semantically aware Wasserstein stopping criterion that replaces lexical order matching, enabling convergence based on semantic consensus among near-synonymous candidate answers and avoiding unnecessary iterations caused by clinically equivalent ranking swaps. On VQA-RAD and PathVQA, we obtain consistent, statistically significant improvements over greedy and discriminative baselines. On VQA-RAD, we improve Qwen3-VL-2B by +3.5 percentage points (p < 0.01), surpassing the greedy 4B model, with similar trends at larger scales. On PathVQA, Gemma-3-4B with BDG matches MedGemma-4B under greedy decoding despite no domain-specific fine-tuning. At accuracy parity with classic BDG, the Wasserstein criterion reduces average convergence iterations by approximately 20%, improving inference efficiency while preserving the game-theoretic equilibrium behaviour. Code is available at https://github.com/luca-hagen/ Wasserstein-BDG-medical-VQA.

cs.CV↗
arXiv2026

Geometry-Aware Uncertainty Coresets for Robust Visual In-Context Learning in Histopathology

Vision-language models (VLMs) can couple visual perception with open-ended clinical reasoning, making them attractive for computational histopathology. However, fine-tuning billions of parameters on scarce, expert-annotated pathology data is prohibitive, while in-context learning (ICL), which conditions the VLM on demonstrative image-text pairs without parameter updates, suffers from high sensitivity to which examples are selected and how the query is phrased, producing unreliable diagnostics. Existing selection strategies rely on query-dependent nearest-neighbour retrieval that ignores global data structure, require costly parameter updates, or disregard the joint vision-text embedding geometry of VLMs. We propose GAUC, a training-free coreset selection method operating directly in the pre-trained multimodal embedding space. GAUC jointly optimises three objectives: (1) a Maximum Mean Discrepancy term enforcing distributional fidelity between coreset and full dataset, (2) an Effective Mutual Information Difference regulariser bounding performance degradation under prompt paraphrases by exploiting the VLM's joint vision-text alignment, and (3) a predictive-uncertainty (entropy) penalty suppressing ambivalent, hallucination-prone outputs. On CRC-100K and MHIST across multiple open-source VLM architectures, GAUC \emph{matches} the accuracy of the strongest ICL selection and dataset-distillation baselines while substantially improving calibration, prompt robustness, and hallucination rates, all without a single gradient update.

cs.CV↗
arXiv2026

The Learnability Gap in Medical Latent Diffusion

Generative data augmentation with latent diffusion models is a promising strategy for addressing class imbalance in medical imaging, yet current approaches focus on perceptual fidelity and domain-specific autoencoder fine-tuning while neglecting a more fundamental bottleneck. We identify and formalize the learnability gap: large-scale pretrained autoencoders faithfully encode discriminative features for medical classification, as evidenced by near-lossless performance in reconstruction space, yet their latent representations are structured in ways that are difficult for classifiers to learn from. Across five autoencoder families and four medical benchmarks spanning chest radiography, dermatoscopy, computed tomography, and echocardiography, we show that this gap persists regardless of architecture, initialization strategy, or hyperparameter tuning, and that medical-domain fine-tuning of the autoencoder does not close it. To probe and partially narrow the gap, we develop noise-conditioned latent classifiers with FiLM layers and image-space distillation that offer 64x throughput and 120x memory gains over image-space models while serving as diagnostic tools for latent space quality. Our analysis provides a new framework for evaluating autoencoder latent spaces and identifies their structure, rather than their fidelity or domain specificity, as the primary obstacle to closing the performance gap between real and synthetic medical training data.

cs.CV↗
arXiv2026

Flow Matching with Optimized Subclass Priors for Medical Image Augmentation

Rare diseases dominate the diagnostic challenge in medical imaging yet are severely underrepresented in clinical datasets, causing classifiers to fail on exactly the conditions where reliable detection matters most. Generative augmentation can supply the missing tail-class coverage, but coarse disease labels aggregate diverse subtypes and acquisition settings into multi-modal conditionals that bias generators toward dominant submodes, while a shared Gaussian source forces rare subpopulations through disproportionately long transport paths. We propose an offline strategy that introduces informative priors at two levels: first, we partition each coarse label into coherent submodes via Gaussian mixture modeling in the generative model's latent space; second, we learn subclass-conditioned source distributions that re-center and re-scale the starting distribution per submode, shortening trajectories and reducing within-subclass dispersion. To prevent degenerate solutions we impose explicit geometric control, moderately concentrating normalized displacement directions around learnable prototypes while capping path-length outliers. On long-tailed chest X-ray (MIMIC-LT, NIH-LT) and CT slice (CT-RATE) benchmarks the proposed method consistently improves tail-class generation fidelity and diversity (FID, IRS) and is a promising augmentation strategy that reliably improves downstream balanced accuracy and macro-F1 over a non-augmented baseline across modalities.

eess.IV↗
arXiv2026

Wasserstein-Aligned Localisation for VLM-Based Distributional OOD Detection in Medical Imaging

Zero-shot anomaly localisation via vision-language models (VLMs) offers a compelling approach for rare pathology detection, yet its performance is fundamentally limited by the absence of healthy anatomical context. We reformulate zero-shot localisation as a comparative inference problem in which anomalies are identified through structured comparison against reference distributions of normal anatomy. We introduce WALDO, a training-free framework grounded in optimal transport theory that enables comparative reasoning through: (i) entropy-weighted Sliced Wasserstein distances for anatomically-aware reference selection from DINOv2 patch distributions, (ii) Goldilocks zone sampling exploiting the non-monotonic relationship between reference similarity and localisation accuracy, and (iii) self-consistency aggregation via weighted non-maximum suppression. We theoretically analyse the Goldilocks effect through distributional divergence, and show that references with moderate similarity minimize a bias-variance trade-off in comparative visual reasoning. On the NOVA brain MRI benchmark, WALDO with Qwen2.5-VL-72B achieves $43.5_{\pm1.6}\%$ mAP@30 (95\% CI: [40.4, 46.7]), representing a 19\% relative improvement over zero-shot baselines. Cross-model evaluation shows consistent gains: GPT-4o achieves $32.0_{\pm6.5}\%$ and Qwen3-VL-32B achieves $32.0_{\pm6.6}\%$ mAP@30. Paired McNemar tests confirm statistical significance ($p<0.01$). Source code is available at https://github.com/bkainz/WALDO_MICCAI26_demo .

cs.CV↗
arXiv2026

Learning from Noisy Prompts: Saliency-Guided Prompt Distillation for Robust Segmentation with SAM

Segmentation is central to clinical diagnosis and monitoring, yet the reliability of modern foundation models in medical imaging still depends on the availability of precise prompts. The Segment Anything Model (SAM) offers powerful zero-shot capabilities, although it collapses under the weak, generic, and noisy prompts that dominate real clinical workflows. In practice, annotations such as centerline points are coarse and ambiguous, often drifting across neighboring anatomy and misguiding SAM toward inconsistent or incomplete masks. We introduce SPD, a Saliency-Guided Prompt Distillation framework that converts these unreliable cues into robust guidance. SPD first learns data-driven anatomical priors through a lightweight saliency head to obtain confident localization maps. These priors then drive Contextual Prompt Distillation, which validates and enriches noisy prompts using cues from anatomically adjacent slices, producing a consensus prompt set that matches the behavior of expert reasoning. A Pairwise Slice Consistency objective further enforces local anatomical coherence during segmentation. Experiments on four challenging MRI and CT benchmarks demonstrate that SPD consistently outperforms existing SAM adaptations and supervised baselines, delivering large gains in both region-based and boundary-based metrics. SPD provides a practical and principled path toward reliable foundation model deployment in clinical environments where only imperfect prompts are available.

cs.CV↗
arXiv2026

SigVLP: Sigmoid Volume-Language Pre-Training for Self-Supervised CT-Volume Adaptive Representation Learning

Large-scale, volumetric medical imaging datasets typically aggregate scans from different vendors and devices, resulting in highly variable resolution, slice thicknesses, and numbers of slices per study. Consequently, training representation models usually requires cropping or interpolating along the z-axis to obtain fixed-size blocks, which inevitably causes information loss. We propose a new training approach to overcome this limitation. Instead of absolute position embeddings, we interpret volumes as sequences of 3D chunks and adopt Rotary Position Embeddings, allowing us to treat the z-axis as an unconstrained temporal dimensions. Building on this idea, we introduce a new vision-language model: SigVLP. In SigVLP, we implement Rotary Position Embedding as the positional encoding method, which is applied directly within the attention operation, generating input-conditioned sine and cosine weights on the fly. This design ensures consistent alignment between query and key projections and adapts to any input sizes. To allow for variable input size during training, we sample Computed Tomography volumes in chunks and pair them with localized organ-wise textual observations. Compared to using entire reports for conditioning, chunkwise alignment provides finer-grained supervision, enabling the model to establish stronger correlations between the text and volume representations, thereby improving the precision of text-to-volume alignment. Our models are trained with the Muon optimizer and evaluated on a diverse set of downstream tasks, including zero-shot abnormality and organ classification, segmentation, and retrieval tasks.

cs.CV↗
arXiv2026

Generalist Foundation Models from a Multimodal Dataset for 3D Computed Tomography

Advancements in medical imaging AI, particularly in 3D imaging, have been limited due to the scarcity of comprehensive datasets. We introduce CT-RATE, a public dataset that pairs 3D medical images with corresponding textual reports. CT-RATE comprises 25,692 non-contrast 3D chest CT scans from 21,304 unique patients. Each scan is accompanied by its corresponding radiology report. Leveraging CT-RATE, we develop CT-CLIP, a CT-focused contrastive language-image pretraining framework designed for broad applications without the need for task-specific training. We demonstrate how CT-CLIP can be used in multi-abnormality detection and case retrieval, and outperforms state-of-the-art fully supervised models across all key metrics. By combining CT-CLIP's vision encoder with a pretrained large language model, we create CT-CHAT, a vision-language foundational chat model for 3D chest CT volumes. Finetuned on over 2.7 million question-answer pairs derived from the CT-RATE dataset, CT-CHAT underscores the necessity for specialized methods in 3D medical imaging. Collectively, the open-source release of CT-RATE, CT-CLIP, and CT-CHAT not only addresses critical challenges in 3D medical imaging but also lays the groundwork for future innovations in medical AI and improved patient care.

cs.CV↗
arXiv2026

Downscaling Neural Network for Coastal Simulations

Learning the fine-scale details of a coastal ocean simulation from a coarse representation is a challenging task. For real-world applications, high-resolution simulations are necessary to advance understanding of many coastal processes, specifically, to predict flooding resulting from tsunamis and storm surges. We propose a Downscaling Neural Network for Coastal Simulation (DNNCS) for spatiotemporal enhancement to learn the high-resolution numerical solution. Given images of coastal simulations produced on low-resolution computational meshes using low polynomial order discontinuous Galerkin discretizations and a coarse temporal resolution, the proposed DNNCS learns to produce high-resolution free surface elevation and velocity visualizations in both time and space. To model the dynamic changes over time and space, we propose grid-aware spatiotemporal attention to project the temporal features to the spatial domain for non-local feature matching. The coordinate information is also utilized via positional encoding. For the final reconstruction, we use the spatiotemporal bilinear operation to interpolate the missing frames and then expand the feature maps to the frequency domain for residual mapping. Besides data-driven losses, the proposed physics-informed loss guarantees gradient consistency and momentum changes, leading to a 24% reduction in root-mean-square error compared to the model trained with only data-driven losses. To train the proposed model, we propose a coastal simulation dataset and use it for model optimization and evaluation. Our method shows superior downscaling quality and fast computation compared to the state-of-the-art methods.

eess.IV↗