Redefining Instance Matching: A Unified Framework for Part-Aware Matching in Panoptic Segmentation Evaluation

The Panoptic Quality (PQ) metric is the standard for jointly evaluating instance and semantic segmentation. However, its original definition relies on a One-to-One matching between predicted and ground truth segments, which is only straightforward when the IoU threshold exceeds 0.5. Below 0.5, multiple matching strategies emerge in a poorly explored problem space. We systematically elucidate this space by recasting segment matching as a constrained bipartite assignment problem. Independently bounding the prediction- and ground-truth-side degrees yields four matching strategies: One-to-One, Many-to-One, One-to-Many, and Many-to-Many. We show that the first three are well-defined within the PQ framework, while Many-to-Many falls outside it. These strategies become relevant when instances are fragmented, adjacent objects are difficult to delineate, or annotations are noisy. Central to our framework is a vertex-based accounting of TP, FN, and FP, anchored to ground truth and predicted segments rather than to matching edges. We further show that the framework extends naturally to part-aware panoptic segmentation, and we explore part-aware evaluation on biomedical data. Across configurable case studies we report how different combinations of thresholds and matching strategies behave in practice. We release a unified open-source package built on Panoptica. It exposes Voronoi-based region-wise analysis, part-aware evaluation, and Area Under Threshold Curve computations as configurable options.

Generating Reports or Repeating Templates? Measuring and Mitigating Template Collapse in 3D CT Report Generation

Modern 3D medical vision-language models (VLMs) can generate fluent radiology-style text while exhibit critically low pathology detection and output diversity, collapsing to generic templates that under-report rare yet critical findings. We identify this failure mode as Template Collapse. This failure stems from the unique constraints of 3D medical imaging, e.g., limited data, severe label imbalance, and weak signals from volumetric encoders. Under these constraints, text-generation objectives encourage shortcut learning and fluent but weakly grounded reports. We systematically diagnose the Template Collapse through clinical fidelity, output diversity, normal-template bias, and rare-finding survival. To mitigate it, we propose CLarGen, a decoupled framework that separates what to say (clinical detection) from how to say it (language synthesis). CLarGen uses (i) a Latent Query Transformer for multi-label pathology detection, (ii) pathology-guided retrieval for clinically matched exemplars, and (iii) a medical language model to synthesize the final report from detected findings and retrieved context. Across state-of-the-art 3D CT report generation baselines, CLarGen mitigates Template Collapse and substantially improves clinical accuracy (macro-F1 0.487 vs. 0.189; CRG 0.472 vs. 0.368) while maintaining fluent reporting. Our results suggest that explicit, measurable clinical grounding is essential for template-collapse-resistant 3D CT report generation. Code will be released upon acceptance.

DDX-TRACE: A Benchmark for Medical Diagnostic Trajectories in VLMs

Medical diagnosis is not a single prediction from a fully specified vignette. It is a sequential workup: clinicians decide what evidence to obtain, revise a differential diagnosis, and stop when the diagnosis is sufficiently supported. Most medical AI benchmarks instead reveal the relevant context upfront and score only the final answer, making unsupported correct guesses, premature closure, inefficient workups, and poor uncertainty updating invisible. We introduce DDX-TRACE, a physician-adjudicated benchmark for multimodal neuroradiology that evaluates diagnostic trajectories under hidden evidence over 211 challenging cases. Each case begins with limited clinical history; models request imaging studies in free form, receive matched image bundles when available, update a probabilistic differential diagnosis after each turn, and stop with a localized final diagnosis. Evaluating state-of-the-art VLMs, we find that final diagnosis scores can substantially misrepresent workup quality: models may guess plausible diagnoses without essential evidence, request useful studies but misinterpret raw images, or acquire evidence inefficiently while updating uncertainty poorly. Controlled evidence variants isolate bottlenecks in planning, visual evidence extraction, and downstream differential reasoning. DDX-TRACE shifts medical AI evaluation from final answers to evidence-supported diagnostic trajectories.

Calibrated Confidence Expression for Radiology Report Generation

Safe deployment of Large Vision-Language Models (LVLMs) in radiology report generation requires not only accurate predictions but also clinically interpretable indicators of when outputs should be thoroughly reviewed, enabling selective radiologist verification and reducing the risk of hallucinated findings influencing clinical decisions. One intuitive approach to this is verbalized confidence, where the model explicitly states its certainty. However, current state-of-the-art language models are often overconfident, and research on calibration in multimodal settings such as radiology report generation is limited. To address this gap, we introduce ConRad (Confidence Calibration for Radiology Reports), a reinforcement learning framework for fine-tuning medical LVLMs to produce calibrated verbalized confidence estimates alongside radiology reports. We study two settings: a single report-level confidence score and a sentence-level variant assigning a confidence to each claim. Both are trained using the GRPO algorithm with reward functions based on the logarithmic scoring rule, which incentivizes truthful self-assessment by penalizing miscalibration and guarantees optimal calibration under reward maximization. Experimentally, ConRad substantially improves calibration and outperforms competing methods. In a clinical evaluation we show that ConRad's report level scores are well aligned with clinicians' judgment. By highlighting full reports or low-confidence statements for targeted review, ConRad can support safer clinical integration of AI-assistance for report generation.

MedOpenClaw: Auditable Medical Imaging Agents Reasoning over Uncurated Full Studies

Currently, evaluating vision-language models (VLMs) in medical imaging tasks oversimplifies clinical reality by relying on pre-selected 2D images that demand significant manual labor to curate. This setup misses the core challenge of realworld diagnostics: a true clinical agent must actively navigate full 3D volumes across multiple sequences or modalities to gather evidence and ultimately support a final decision. To address this, we propose MEDOPENCLAW, an auditable runtime designed to let VLMs operate dynamically within standard medical tools or viewers (e.g., 3D Slicer). On top of this runtime, we introduce MEDFLOWBENCH, a full-study medical imaging benchmark covering multi-sequence brain MRI and lung CT/PET. It systematically evaluates medical agentic capabilities across viewer-only, tool-use, and open-method tracks. Initial results reveal a critical insight: while state-of-the-art LLMs/VLMs (e.g., Gemini 3.1 Pro and GPT-5.4) can successfully navigate the viewer to solve basic study-level tasks, their performance paradoxically degrades when given access to professional support tools due to a lack of precise spatial grounding. By bridging the gap between static-image perception and interactive clinical workflows, MEDOPENCLAW and MEDFLOWBENCH establish a reproducible foundation for developing auditable, full-study medical imaging agents.

VesselTok: Tokenizing Vessel-like 3D Biomedical Graph Representations for Reconstruction and Generation

Spatial graphs provide a lightweight and elegant representation of curvilinear anatomical structures such as blood vessels, lung airways, and neuronal networks. Accurately modeling these graphs is crucial in clinical and (bio-)medical research. However, the high spatial resolution of large networks drastically increases their complexity, resulting in significant computational challenges. In this work, we aim to tackle these challenges by proposing VesselTok, a framework that approaches spatially dense graphs from a parametric shape perspective to learn latent representations (tokens). VesselTok leverages centerline points with a pseudo radius to effectively encode tubular geometry. Specifically, we learn a novel latent representation conditioned on centerline points to encode neural implicit representations of vessel-like, tubular structures. We demonstrate VesselTok's performance across diverse anatomies, including lung airways, lung vessels, and brain vessels, highlighting its ability to robustly encode complex topologies. To prove the effectiveness of VesselTok's learnt latent representations, we show that they (i) generalize to unseen anatomies, (ii) support generative modeling of plausible anatomical graphs, and (iii) transfer effectively to downstream inverse problems, such as link prediction.

TumorFlow: Physics-Guided Longitudinal MRI Synthesis of Glioblastoma Growth

Glioblastoma exhibits diverse, infiltrative, and patient-specific growth patterns that are only partially visible on routine MRI, making it difficult to reliably assess true tumor extent and personalize treatment planning and follow-up. We present a biophysically-conditioned generative framework that synthesizes biologically realistic 3D brain MRI volumes from estimated, spatially continuous tumor-concentration fields. Our approach combines a generative model with tumor-infiltration maps that can be propagated through time using a biophysical growth model, enabling fine-grained control over tumor shape and growth while preserving patient anatomy. This enables us to synthesize consistent tumor growth trajectories directly in the space of real patients, providing interpretable, controllable estimation of tumor infiltration and progression beyond what is explicitly observed in imaging. We evaluate the framework on longitudinal glioblastoma cases and demonstrate that it can generate temporally coherent sequences with realistic changes in tumor appearance and surrounding tissue response. These results suggest that integrating mechanistic tumor growth priors with modern generative modeling can provide a practical tool for patient-specific progression visualization and for generating controlled synthetic data to support downstream neuro-oncology workflows. In longitudinal extrapolation, we achieve a consistent 75% Dice overlap with the biophysical model while maintaining a constant PSNR of 25 in the surrounding tissue. Our code is available at: https://github.com/valentin-biller/lgm.git

VariViT: A Vision Transformer for Variable Image Sizes

Vision Transformers (ViTs) have emerged as the state-of-the-art architecture in representation learning, leveraging self-attention mechanisms to excel in various tasks. ViTs split images into fixed-size patches, constraining them to a predefined size and necessitating pre-processing steps like resizing, padding, or cropping. This poses challenges in medical imaging, particularly with irregularly shaped structures like tumors. A fixed bounding box crop size produces input images with highly variable foreground-to-background ratios. Resizing medical images can degrade information and introduce artefacts, impacting diagnosis. Hence, tailoring variable-sized crops to regions of interest can enhance feature representation capabilities. Moreover, large images are computationally expensive, and smaller sizes risk information loss, presenting a computation-accuracy tradeoff. We propose VariViT, an improved ViT model crafted to handle variable image sizes while maintaining a consistent patch size. VariViT employs a novel positional embedding resizing scheme for a variable number of patches. We also implement a new batching strategy within VariViT to reduce computational complexity, resulting in faster training and inference times. In our evaluations on two 3D brain MRI datasets, VariViT surpasses vanilla ViTs and ResNet in glioma genotype prediction and brain tumor classification. It achieves F1-scores of 75.5% and 76.3%, respectively, learning more discriminative features. Our proposed batching strategy reduces computation time by up to 30% compared to conventional architectures. These findings underscore the efficacy of VariViT in image representation learning. Our code can be found here: https://github.com/Aswathi-Varma/varivit

Optimizing Rank for High-Fidelity Implicit Neural Representations

Implicit Neural Representations (INRs) based on vanilla Multi-Layer Perceptrons (MLPs) are widely believed to be incapable of representing high-frequency content. This has directed research efforts towards architectural interventions, such as coordinate embeddings or specialized activation functions, to represent high-frequency signals. In this paper, we challenge the notion that the low-frequency bias of vanilla MLPs is an intrinsic, architectural limitation to learn high-frequency content, but instead a symptom of stable rank degradation during training. We empirically demonstrate that regulating the network's rank during training substantially improves the fidelity of the learned signal, rendering even simple MLP architectures expressive. Extensive experiments show that using optimizers like Muon, with high-rank, near-orthogonal updates, consistently enhances INR architectures even beyond simple ReLU MLPs. These substantial improvements hold across a diverse range of domains, including natural and medical images, and novel view synthesis, with up to 9 dB PSNR improvements over the previous state-of-the-art. Our project page, which includes code and experimental results, is available at: (https://muon-inrs.github.io).

Learning to reason about rare diseases through retrieval-augmented agents

Rare diseases represent the long tail of medical imaging, where AI models often fail due to the scarcity of representative training data. In clinical workflows, radiologists frequently consult case reports and literature when confronted with unfamiliar findings. Following this line of reasoning, we introduce RADAR, Retrieval Augmented Diagnostic Reasoning Agents, an agentic system for rare disease detection in brain MRI. Our approach uses AI agents with access to external medical knowledge by embedding both case reports and literature using sentence transformers and indexing them with FAISS to enable efficient similarity search. The agent retrieves clinically relevant evidence to guide diagnostic decision making on unseen diseases, without the need of additional training. Designed as a model-agnostic reasoning module, RADAR can be seamlessly integrated with diverse large language models, consistently improving their rare pathology recognition and interpretability. On the NOVA dataset comprising 280 distinct rare diseases, RADAR achieves up to a 10.2% performance gain, with the strongest improvements observed for open source models such as DeepSeek. Beyond accuracy, the retrieved examples provide interpretable, literature grounded explanations, highlighting retrieval-augmented reasoning as a powerful paradigm for low-prevalence conditions in medical imaging.