medical imaging engineers

Abstract: Unsupervised 4D medical image interpolation reconstructs intermediate anatomical states from temporally sparse observations without intermediate supervision. Distinct motion fields may attain comparable endpoint agreement while producing different intermediate anatomy, giving rise to motion ambiguity. This ambiguity is difficult to constrain when many independently adjustable motion variables must be estimated from the observed endpoints. We develop a framework that learns a motion manifold to restrict candidate motion fields while retaining sample-specific variation. Cross-Sample Spectral Basis Learning extracts recurring motion structure from endpoint-derived dense estimates and encodes it in a shared spectral basis. Sample-Conditioned Cayley Basis Reorientation uses predicted motion coordinates to rotate the effective motion directions for each endpoint pair without increasing the number of independent coordinates. Their composition defines a nonlinear family of complete velocity fields across endpoint pairs, accommodating anatomical and motion-state differences within a restricted representation. Integrating each predicted field supports bidirectional reconstruction at arbitrary intermediate times. Theoretical analysis establishes sufficient conditions under which endpoint observations distinguish nearby motions within the learned family. Experiments on ACDC and 4D-Lung demonstrate state-of-the-art performance among the evaluated methods trained without intermediate volumes and competitive results against methods using intermediate supervision.

Abstract: Computing optimal transport maps between medical images plays a fundamental role in morphological analysis. However, existing methods are either difficult to scale to large 3D medical images or rely on regularized formulations that provide only approximate transport maps. To improve the accuracy of downstream medical image analysis, we propose a novel approach for estimating optimal transport maps by parameterizing the convex potential function. By construction, the resulting transport map is guaranteed to be curl-free, consistent with Brenier's theorem. We evaluate the proposed method on both 2D and 3D medical imaging datasets. Experimental results demonstrate that our approach achieves lower transport estimation errors and produces higher-quality image reconstructions than existing methods.

Abstract: Machine learning (ML) models used in clinical workflows often perform systematically differently across patient groups, raising concerns about equity and patient safety. Traditional subgroup analyses can expose such disparities only when rich metadata (e.g., patient demographics) is available and captures the sources of performance variation, conditions rarely met in practice. Algorithmic subgroup discovery methods offer a solution by identifying coherent groups from learned feature representations, but because true underlying stratifications are unknown, these methods are hard to evaluate. As a result, subgroup discovery has not been systematically applied or assessed for performance monitoring. Our main objective is to evaluate algorithmic subgroup discovery for performance monitoring, assessing the discovered subgroups' performance gaps and semantic coherence. Investigating cardiomegaly classification in a dataset of 223,228 chest X-rays, we showed that the discovered subgroups exhibited larger performance gaps (accuracies of 0.61-0.90) than traditional metadata-based analysis (0.80-0.94) and were frequently interpretable using patient, acquisition, and model metadata. As a proof of concept, we also showed that annotations from learned subgroups can be used to mitigate the biases they expose. We conclude that subgroup discovery is a practical and effective tool to enhance the performance validation and monitoring of ML systems in healthcare.

Abstract: Medical image classifiers typically return predictions without a native contract for independently reconstructing their spatial decision computation. Evidence Field is a trainable spatial-program architecture that jointly produces class scores, selected covering programs and signed evidence. Its encoder combines absolute and image-relative response fields with associative spatial moments and learned characteristic sums. A typed classifier scores individual regions and parent-conditioned multiplicative groups; a covering recursion selects scale, partition and composition. We establish exact one-fold coverage, optimality within the registered grammar, a bound relating smooth training to hard inference, signed-score conservation and class-centred offset invariance. Direct contractions and their adjoint specify arithmetic and storage scaling on two- and three-dimensional grids. Native output records bind inputs, parameters, supports, types and contextual dependencies to individual and ensemble predictions. In a separately reported histopathology application, patient-separated training and evaluation across held-out centres provide empirical evidence for the architecture. Trained mechanism and corrected-loss comparisons distinguish predictive effects from implementation correctness; independent readers reconstruct descriptors, routes, scores and probability mixtures. The principal contribution is a coupled representation, decision and evidence architecture whose selected computation can be reproduced independently.

Abstract: Image representation affects both the forward model and quantitative feature recovery in model-based iterative CT reconstruction. For isotropically bandlimited signals, the hexagonal lattice is the most sampling-efficient lattice in two dimensions, with greater directional isotropy and a larger alias-free bandwidth than the Cartesian grid at equal density. We develop constant and linear hexagonal projectors for two-dimensional fan-beam CT using box spline calculus. Both bases form a partition of unity on common coefficient centers; the linear tent also reproduces affine functions. We derive analytic ray footprints and effective detector-blur expressions and implement efficient GPU forward and backprojection. On simulated FORBILD data, the linear model improves on Cartesian and hexagonal pixels, with its best noisy-data accuracy at the coarser resolution. Real-world 2DeteCT comparisons use high-dose, high-resolution Cartesian reconstructions as pseudo ground truth and show competitive image and feature agreement. These results establish a practical hexagonal representation for quantitative CT.

Abstract: The joint reconstruction of the initial pressure and spatially varying sound speed in photoacoustic tomography from boundary measurements is considered. A regularized data-driven framework is proposed in which the unknown fields are represented in finite-dimensional wavelet spaces and fixed nonlinear features generated by an untrained convolutional neural network (CNN) are used to reconstruct the initial-pressure coefficients through Tikhonov-regularized least squares. A learned coefficient-space prior is subsequently used to infer the squared sound-speed coefficients. Numerical experiments demonstrate accurate reconstruction on held-out data and strong generalization to previously unseen phantom geometries. The frozen reconstruction map also remains stable under measurement noise not represented during training, with only minor changes in reconstruction accuracy for noise levels up to $10\%$. In comparison with the supervised trained-CNN approach considered in this work, the untrained representation yields substantially smaller reconstruction errors while requiring approximately one-sixth of the computational time. These results demonstrate that fixed random convolutional features combined with regularized coefficient-space learning provide an efficient and robust approach to joint reconstruction in photoacoustic tomography.

Abstract: Anatomical labels help 3D Gaussian splatting preserve vessels in cinematic renderings of CT, but the representation is still found by optimising each patient's scene, where densification decides where Gaussians go, while real-time displays cap their number. We address one part of this process: deciding where a fixed budget of B Gaussians should be placed. We propose a reusable, labelaware allocation front end that maps a patient's CT, labels and transfer function to a density over 2mm cells and draws exactly B positions from it without per-patient optimisation; the other Gaussian attributes are still fitted per patient. The front end is learned once from per-patient optimised scenes and implemented as a population-trained neural prior and an interpretable seven-parameter visibility-aware closed form (VACF). With identical attribute fitting on 20 held-out patients at 10K-100K Gaussians, both raise vessel-masked PSNR over uniform allocation by 4.5-7.1dB and over pruning a dense voxel-aligned model by 1.6-3.3dB. The neural prior does not differ significantly from per-patient optimised allocation at any budget, and VACF is within 0.6dB of it on vessels; on 19 external patients the neural prior again matches it on vessels and VACF is within 0.7dB. As an initialisation for position optimisation, VACF allocation beats per-patient densification on vessels at 10K Gaussians and, at 25K, reaches a higher vessel PSNR after 118s of optimisation than densification after 248s. Under altered rendering presets, VACF transfers to new colours and lighting but not to a label-free transfer function, whereas the neural prior shows the opposite pattern.

Abstract: Adapting a single vision-language model to medical image parsing requires training choices that reflect the demands of each task. We study task-specific adaptation with Qwen3.5-9B for FLARE 2026 Task 3, covering six task families and seven imaging modalities. Our system couples a shared, frozen 4-bit backbone with LoRA adapters selected from the input question. We customize adapter ranks and prompts, rebalance rare classification targets, and supplement regression training with dermatology classification examples. On the fixed internal holdout, the task-specific adapters achieve a dataset-macro balanced accuracy of 0.7791 for classification, a dataset-macro micro-F1 of 0.6286 for multi-label classification, a counting mean absolute error (MAE) of 11.73, a dataset-macro detection F1 of 0.8914, a dataset-macro regression MAE of 9.78, and a report-generation CRIMSON score of 0.8204. On the organizer's 1,703-example hidden-validation set, the submitted system achieves 0.8496 classification balanced accuracy, 0.5338 sample-averaged multi-label F1, and 14.5950 regression MAE. The final 30.1 GB container averages 3.1 seconds per case, including model loading, and produces identical outputs across repeated verification runs. The benefits vary across tasks, supporting the use of task-specific adapter configurations and image budgets within a shared medical vision-language model. Code is available at https://github.com/TahaSabir0/FLARE26-Hexapus.

Abstract: Background: Estimating subvoxel tissue fractions from magnetic resonance fingerprinting (MRF) is challenging. Conventional dictionary matching and segmentation pipelines can propagate errors from intermediate parametric maps into tissue fraction estimates. Purpose: We introduce DeepPV-MRF, a deep learning framework that directly estimates voxel-wise tissue fractions from raw MRF signals. Methods: A cascaded spatial-temporal network was trained on subject-derived Bloch simulations with radial k-space undersampling. The network combines temporal encoding and spatial U-Net refinement to estimate cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) fractions without intermediate T1/T2 maps. We compared DeepPV-MRF with partial-volume dictionary matching (PV-DM) and pseudoinverse estimation (PV-Pinv) using simulated and in vivo data. Results: DeepPV-MRF outperformed both methods across acquisition settings. In single-shot simulations, CSF/WM/GM mean absolute errors were 0.0418/0.0744/0.0757, versus 0.1281/0.2443/0.2958 for PV-DM and 0.2021/0.2793/0.2630 for PV-Pinv. Corresponding structural similarity values were 0.960/0.916/0.922. In vivo results showed sharper anatomical boundaries and smoother tissue transitions, while cross-shot analysis indicated improved consistency across volunteers. Conclusions: DeepPV-MRF enables accurate and efficient direct tissue fraction estimation from MRF signals, particularly with limited shots. Further validation is needed before clinical deployment.

Abstract: We present a real-time, hybrid framework for occlusion handling and depth-aware tracking in minimally invasive surgeries (MIS). Occlusions caused by surgical instruments often obscure the region of interest (ROI), affecting surgical precision. To address this, our approach integrates enhanced You Only Look Once (YOLO) based detection, Particle Filtering (PF), and monocular depth estimation using Multiple Depth Estimation Accuracy with Single Network (MiDaS). Occlusion is detected using a distance-based threshold between instruments and ROI. Experimental results demonstrate robust instrument detection with a confidence score of 0.85, effective occlusion event handling, and accurate depth prediction with an MAE of 0.34 cm and RMSE of 0.53 cm. Independent phantom-based validation against stereo depth measurements yielded an MAE of 0.65 cm and RMSE of 0.66 cm. The framework further achieved an occlusion detection accuracy of 81.95\% while maintaining real-time performance at 38.7 FPS. Preliminary surgeon feedback indicates that the proposed visualization framework is clinically relevant and holds promise for future intraoperative image-guided navigation and decision support in MIS.

Abstract: Dual-student learning enriches predictive diversity in SSMIS by introducing a strongly augmented view alongside a weakly augmented view. Insufficient strong augmentation may homogenize the students, whereas excessive augmentation can corrupt anatomical evidence and destabilize collaboration. This challenge echoes feedback-regulated human instruction, where learners receive differentiated tasks and the task difficulty is continually adjusted according to their evolving responses. Inspired by these, we propose Human-Inspired Asymmetric Collaboration (HAC), a closed-loop dual-student framework that maintains weak--strong learning through adaptive difficulty calibration and geometry preservation. Specifically, Reinforcement-guided Difficulty Calibration (RDC) formulates strong-augmentation control as a window-level reinforcement learning process, using augmentation history, realized perturbations, and training responses to dynamically adjust the augmentation magnitude, operation number, and magnitude range. Meanwhile, the Gramian Geometry Preservation Constraint (G2PC) preserves the early-stage three-branch geometry through global volume and pairwise area constraints, preventing shared supervision from homogenizing the two students. Comprehensive evaluations across LA, Pancreas, and BraTS-2019 validate both the segmentation effectiveness and capability-aware difficulty calibration of HAC.

Abstract: Contrastive vision-language (VL) pretraining in computational pathology has generally relied on curated image-caption datasets sourced from social media, educational videos, and research publications. These corpora are sparse relative to the diversity of tissue morphology and difficult to scale further, as pathologists do not routinely produce descriptive captions in clinical practice. We propose to instead leverage slide-level pathology reports which can be generated during routine diagnostic workflows in a scalable manner. A key challenge in this weakly-supervised setting is that pathology reports describe macroscopic, diagnostic findings while patch-level visual features describe microscopic findings. We introduce Locked Image Multiple Instance PreTraining (LIMIT), which addresses this gap by freezing a pretrained vision encoder and fine-tuning only the text encoder: report embeddings serve as cross-attention queries over bags of patch features, producing report-conditioned slide representations optimized via InfoNCE. Using LIMIT, we establish CONCH-Z, which aligns the text encoder of CONCH v1.5 to 335k clinical reports. Evaluated across 22 tasks spanning patch-level classification, tumor detection, and slide-level subtyping, CONCH-Z establishes state-of-the-art zero-shot performance over VL encoders trained on curated caption datasets, while simultaneously closing the gap with slide-level foundation models trained with substantially more parameters and compute. The code and model is available at https://github.com/mahmoodlab/LIMIT.

Abstract: Functional brain connectome represents neural connectivity as a matrix of pairwise interactions between brain regions. Generation of functional connectomes is not only a question of validity; rather, having satisfied the constraints on the correlation matrix, the next step is to recover the class-conditional geometry buried under coarse labels. We propose MAGNET, a Manifold-Aware Graph Diffusion Network which uses a normalized-Cholesky representation of the manifold of correlation matrices that guarantees validity. MAGNET lifts noisy latent states into ROI-level region tokens and performs denoising with a relational inductive bias over brain atlas regions. To deal with structural problems induced by coarse labels, MAGNET employs class-anchored conditioning, amortized structural bridge, and relevance-preserving corruption. Across ABIDE, ADNI, and OASIS-3, MAGNET consistently achieves favorable results compared to previous manifold-aware approaches, demonstrating improvements of 7-21% in class-conditional fidelity ($α,β$-F1) across three cohorts and better sampling efficiency. Moreover, while training only with strict binary labels, MAGNET is capable of maintaining clinical heterogeneity through fine substructure of the connectomes in a zero-shot setting, improving subclass covariance alignment ($λ$-MSE) by over 30%. These results suggest that geometric validity is a necessary but insufficient condition for clinical utility in connectome synthesis. Moreover, efforts in making the diffusion denoising class-conditional manifold aware finds utility beyond the highly curved brain connectome generation as this is a critical problem in various general settings. The code repository can be found at https://github.com/protyayofficial/MAGNET.

Abstract: While contrastive learning is widely used to learn deterministic representations, it does not inherently provide estimates of uncertainty. Post-hoc uncertainty estimation methods, such as the Linearized Laplace approximation (LLA), offer a way to quantify uncertainty without retraining the encoder. However, we show that directly using the LLA induced distribution over the contrastive embedding does not yield reliable pointwise uncertainty estimates for downstream tasks: embedding variance alone does not reflect whether decisions such as nearest-neighbor retrieval or cluster assignment are stable. To address this limitation, we develop a post-hoc framework based on LLA that propagates encoder uncertainty through the downstream task. We characterize the curvature of contrastive objectives and introduce positive-semidefinite repairs where needed to obtain valid local Gaussian approximations without retraining the encoder. We test the proposed approach in metagenomic binning and image classification tasks. For metagenomic binning, posterior coassignment probabilities support consensus partitions and the selection of reliable cores, leading to improvements over existing baselines. Additional image classification experiments show calibration improvements on standard benchmarks and real histopathology datasets.

Abstract: Generative MRI reconstruction maps an initial source distribution to the target image distribution along a learned recovery trajectory. Common generative methods, such as diffusion and flow, typically learn fine-grained local dynamics whose integration defines this global mapping, hence requiring many network evaluations at inference. Existing few-step sampling approaches can lower computational burden by approximating large transformations from local dynamics, albeit at the expense of reconstruction fidelity. FLEX-MRI instead partitions recovery into a small number of finite intervals between retained states defined by progressive changes in k-space support, and directly learns the reconstruction change across each interval. Because such finite transitions can admit multiple plausible outcomes, FLEX-MRI combines support-relaxed finite-transition learning with stochastic exploration. During training, randomized k-space sampling masks define finite-transition targets with varying support, while the prediction loss remains unrestricted by each individual mask. At inference, FLEX-MRI perturbs a random subset of currently estimated k-space coefficients, allowing the learned predictor to stochastically explore alternative transition paths. Each predicted state is then reconciled with the acquired measurements through data consistency. We theoretically show that this stochastic exploration induces nonzero transition-level variation through the learned recovery map and data consistency without requiring an auxiliary generative sampler. Experiments on multi-coil MRI datasets show that FLEX-MRI outperforms competing methods while maintaining computational efficiency comparable to few-step baselines.

Abstract: Frozen features of brain MRI foundation models lose accuracy on new datasets, a failure usually blamed on the features encoding where each scan came from. We show that the failure lies elsewhere. Across 17 public datasets and eight frozen representations, every representation recognizes the MRI sequence within each dataset, yet most fail on an unseen one. The cause is neither dataset encoding nor a shift of each dataset: the content itself is encoded along different directions in each dataset. This explains which datasets fail, for the sequence and for sex, and why removing the dataset signal with INLP, LEACE, CORAL or adversarial training never improves sequence transfer. Only the broadly pretrained 3DINO and SAM-Med3D encode the sequence consistently enough to transfer; the brain-specific BrainIAC and BrainFM do no better than an untrained network. Code is available at https://github.com/BrainFM/brainfm-profiler/tree/main/representation_utility.

Abstract: Multi-teacher distillation allows transferring knowledge from multiple "teacher" networks to a single "student" network. This method is promising in fields such as digital pathology, where many powerful foundation models were proposed recently. However, as we show in this paper, the standard multi-teacher distillation approach reacts poorly to an increase in the number of teachers used to train a student encoder. We demonstrate that learning teacher-specific representations is a key to scaling in MTD. Importantly, different design choices, such as learnable teacher tokens, a tailored attention scheme, additional mixture-of-experts layers and a contrastive loss, are proposed to better learn such teacher-specific representations. We show that our method better scales with respect to the number of considered teachers, allowing us to train compact student encoders, up to 10x more efficient than larger teacher foundation models, while matching their performance and even outperforming them on a large set of tile-level and slide-level tasks. We conduct a thorough empirical validation, evaluating more than 10 foundation models on 39 tasks spanning tile and slide levels. As a result, we release a new collection of strong and efficient foundation models, named OMNI, trained from the knowledge of 10 state-of-the-art foundation models. We finally conduct an analysis of the learned teacher-specific representations, highlighting their complementarity and explaining why they can be easily aggregated at downstream time.

Abstract: NeRF and Gaussian splatting methods have been successfully applied on X-ray scenes where the views are too sparse for 3D reconstruction via classical methods. Ultra-sparse scenes with 10 or fewer views such as those with high-rate or low-dose acquisition still, however, present a significant challenge. To address this problem we present a new framework, Optimised X-ray Neural Radiance Fields (OX-NeRF), that combines cross-scene feature learning with scene-specific optimisation to reconstruct sets of related scenes. OX-NeRF employs a convolutional neural network (CNN) to identify cross-scene features while maintaining scene-specific multi-resolution hash grids of spatial features. The paired representations are fused and passed to a multilayer perceptron (MLP); the CNN, hash grids and MLP are then jointly optimised end-to-end. Benchmarking on parallel-beam and cone-beam X-ray datasets shows OX-NeRF provides significantly higher reconstruction accuracy on ultra-sparse scenes compared to existing radiance field methods.

Abstract: Trajectory optimisation for cone-beam computed tomography (CT) determines which information sparse-view scans acquire. Fixed candidate pools prevent off-grid refinement and require new object-specific precomputation for each acquisition manifold. We make every source pose an individual continuous variable and move all poses jointly by gradient ascent on the scanner's kinematic manifold. The objective combines soft-Tuy plane coverage, continuous View Covariance Loss, and an analytic attenuation-aware ray-bundle penalty. The same optimiser handles circular, limited C-arm, two-axis, and freesphere parametrisations. On a Defrise flange, continuous selection recovers laminar defects invisible to a circular orbit, matches discrete swap search on the free sphere at the sparser budget, and leads at the denser one, with the same objective evaluated in every arm. A moderate elevation band already recovers most of the free-sphere gain at the defects, so the same optimiser transfers to bounded scanner envelopes. Photon noise preserves the ordering on the flange and compresses it on a dense fuel nozzle. Sparseprescan planning benefits from matching prescan and planned acquisition manifolds. Selection takes seconds rather than minutes without an object-specific reconstruction basis. Prescan-planned poses were executed on a robot CT bench and reconstructed in a common frame, demonstrating feasibility but no consistent metric gain over uniform band sampling. Continuous pose optimisation incorporates attenuation and scanner constraints directly into sparse-view acquisition design.

Abstract: Volumetric material decomposition in multi-energy computed tomography requires a representation that organizes multiple three-dimensional material fields in a common spatial domain while retaining differences in composition and local structure. We observe that spatial primitives can be shared across materials without tying their coefficients, but their local capacity must respond to material-specific reconstruction needs. We introduce Gaussian material fields, which represent multiple material distributions with shared anisotropic 3D Gaussian primitives and independent nonnegative material coefficients. The shared geometry defines a continuous spatial basis, while the coefficients determine each primitive's contribution to the individual material fields. To reconstruct this representation from multi-energy projections, a differentiable spectral forward model combines Gaussian material path integrals with a calibrated basis matrix, enabling joint optimization of spatial geometry and material composition. Material-aware adaptive density control retains material-specific refinement evidence before aggregation and adjusts local representation capacity to accommodate both spatially extensive components and sparse details. Experiments use synthesized multi-energy projections generated from pseudo-reference material maps constructed by conventional methods from publicly available CT data. Across 15 cases, our approach improves average PSNR by 4.03 dB and SSIM by 4.96% over the strongest baseline, while reducing NRMSE by 33.45%. Material-wise comparisons and component ablations support improved recovery of localized structures, while runtime and memory measurements show favorable computational scaling. These results establish Gaussian material fields as an explicit, adaptive representation for volumetric multi-material reconstruction.

Abstract: Reconstructing 3D Computed Tomography (CT) images from a few X-ray projections is a highly ill-posed inverse problem due to the loss of volumetric information. We propose PhyDiCT, a training-free framework that integrates a differentiable Physics-based forward model, grounded in the Beer-Lambert law, with a text-conditioned Diffusion as a strong prior to reconstruct 3D lung CT images. We refer to our approach as training-free since the prior model is used without fine-tuning, and our goal is to steer the denoising procedure to generate samples consistent with X-ray observations. We guide the diffusion generation using Split Gibbs sampling to jointly optimize for projection fidelity (reward) and consistency with prior knowledge. Also, we introduce a test-time refinement step that enhances image realism and anatomical coherence. We extensively evaluate our method on publicly available 3D CT datasets using both perceptual and semantic metrics, demonstrating that it surpasses existing plug-and-play diffusion and fully trained reconstruction approaches. Our findings highlight that combining a strong generative prior with the underlying physics of image formation substantially improves reconstruction quality, e.g., 7.5\% improvement on SSIM compared to full training methods. Code will be released at https://github.com/batmanlab/PhyDiCT.

Abstract: Background: Biomedical AI can generate plausible explanations without reliably verifying whether each statement is supported by patient-specific evidence. We developed a neuro-semantic verification framework that converts radiomic measurements into addressable evidence records and machine-checkable claims. Methods: UPenn-GBM radiomics were aligned with de novo CaPTk extraction from standardized MRI and expert-validated segmentations in an independent multicenter cohort. The shared space comprised 1,728 features from T1, T1GD, T2, and FLAIR MRI across three tumor regions. Reference-defined semantic states were derived from 611 UPenn cases. We evaluated cross-cohort transportability, model-linked provenance, deterministic verification, controlled predictive degradation, and an LLM claim-extraction pilot; MGMT prediction served only as a transport stress test. Results: Median semantic-state agreement was 0.786 (weighted kappa 0.709), ranging from 0.918 for morphologic to 0.252 for intensity features. The external evidence ledger contained 1,655 model-linked records for 331 patients. The verifier achieved 100% exact-set accuracy in a 6,620-claim corruption benchmark. In a 24-case pilot, GPT-5.6 Sol reproduced 72/72 prespecified atomic claims, and the frozen verifier recovered 24/24 expected conditions. During controlled degradation, ROC AUC declined from 0.899 to 0.500 while verification accuracy remained 1.000. External MGMT discrimination was weak (ROC AUC 0.543). Conclusions: Verifiability can be engineered and evaluated independently of predictive performance. LLMs may structure explanations, while final evidence-consistency checking remains deterministic.

Abstract: Electroencephalography (EEG) offers millisecond temporal resolution, but inferring underlying neural sources is a severely ill-posed spatial inverse problem. While deep learning has advanced spatial reconstruction, current architectures face a critical dilemma: frame-by-frame models discard vital temporal context, whereas full 4D spatiotemporal networks introduce an architectural trade-off between reconstruction accuracy and inference cost. We propose a novel two-stream framework that explicitly decouples global temporal representation learning from per-time-point spatial refinement. A Transformer-based Temporal Condition Encoder processes the entire EEG sequence via factorized spatiotemporal attention, retaining sensor-resolved features. A fixed inverse then maps these features into source-indexed conditioning for a per-timestep Source-Space Transformer or volumetric convolutional refiner. Extensive evaluations on realistic synthetic data demonstrate that this temporal prior dramatically improves spatial localization, outperforming classical and spatiotemporal baselines, particularly in high-noise and multi-source regimes. Training across diverse leadfields and explicit operator mismatches improves transfer to unseen head geometries and brings template-based reconstruction closer to subject-specific inversion. Furthermore, we apply the model trained only on synthetic EEG data to real-world EEG. A logistic regressor fit on source power differences in eyes-open, eyes-closed conditions successfully decodes age groups.

Abstract: Extracting patient-specific vascular trees from volumetric medical images is fundamental to computational angiography and non-invasive hemodynamic assessment. Conventional voxel segmentation models often sever delicate bifurcations, while heuristic Euclidean Minimum Spanning Trees introduce non-anatomical shortcuts. Moreover, linear Poiseuille flow neglects quadratic kinetic dissipation across arterial narrowings, underestimating ischemia. We formulate an end-to-end framework decoupling continuous geometric arborescence generation from non-linear hemodynamics. First, an autonomous 3D Ostium Landmark Localization Head with dual-sinus query channels and spherical-gated refinement eliminates centerline seeding dependency, achieving cohort mean localization error of 7.63 mm (7.43 mm LCA, 7.83 mm RCA; 71.4% <= 8.0 mm) from raw contrast context. Second, a Spatially-Grounded Deformable Step Flow Architecture queries continuous 3D feature pyramids via trilinear sampling, sequentially generating trajectories with anchor boundary enforcement (X(0) = P_start). Third, a Top-Down Recursive Arborescence State Machine detects bifurcation peaks via Tree-NMS and parameterizes predecessor parent pointers (p_k < k), guaranteeing single connected acyclic tree topology (beta_0 = 1, beta_1 = 0) with differentiable step termination. Fourth, an iterative Picard non-linear Kirchhoff solver with Young-Tsai / Gould quadratic dissipation enforces machine-precision mass conservation (residual 5.82e-11 mL/s). Across 14 development patients under standardized in-silico stenosis stress testing (Q_0 = 4.0 mL/s), linear Poiseuille flow misclassifies 75% diameter lesions as non-ischemic (FFR > 0.80) in 14/14 cases, whereas our non-linear solver captures functional ischemia (FFR = 0.5864, lesion disparity 32.89 mmHg, p = 6.10e-5) with 3.66x collateral shunting. Test set firewall isolation was maintained.

Abstract: In weakly supervised Whole Slide Image (WSI) classification, feature extractors typically compress each image tile into a single global embedding. Consequently, slide-level aggregators are restricted to this coarse tile scale, concealing fine-grained sub-tile evidence from the attention mechanism. We introduce DI-MIL, a framework that decouples encoding context from instance granularity through decomposed instances. By clustering dense spatial tokens from a frozen foundation model within each tile, DI-MIL converts a single tile into multiple independently weighted instance embeddings. As a training-free post-encoding module, DI-MIL integrates seamlessly into existing pipelines without requiring re-encoding or downstream architectural modifications. We evaluate DI-MIL on cytopathology, a challenging testbed where sparse diagnostic signals are easily diluted within standard tiles. Across four datasets, three frozen foundation models, and two attention-based aggregators, DI-MIL demonstrates consistent efficacy, improving 67 of 72 metric-level comparisons, with the largest mean gains reaching 3.64 points under cytopathology-specific backbones. In a broader comparison against seven representative MIL baselines, DI-MIL paired with ACMIL achieves highest mean performance in 33 of 36 backbone-dataset-metric comparisons. Ablations show that direct smaller tiling inflates the extracted tile count by up to 43.3$\times$ with non-monotonic performance, whereas DI-MIL incurs zero additional image-extraction overhead while achieving the strongest overall results. These results establish instance construction as an orthogonal design dimension in MIL, supporting DI-MIL as a cost-efficient solution under sparse diagnostic evidence.

Abstract: Accurate thyroid ultrasound segmentation is often challenged by low contrast, speckle noise, and unclear boundaries. Although recent methods have improved segmentation accuracy, many rely on resource-intensive architectures or lack explicit integration of multiscale features with global biomedical visual guidance. In this paper, we introduce ThyCLIPNet, a lightweight semantic-guided hybrid encoder-decoder framework that integrates BiomedCLIP-derived biomedical semantic guidance into a lightweight multi-scale CNN segmentation pipeline. The encoder integrates MobileNetV2 with efficient channel attention, while atrous spatial pyramid pooling and a custom convolutional block attention module enrich bottleneck features. The decoder combines hierarchical skip connections and lightweight attention refinement with a BiomedCLIP-guided gated fusion pathway that projects vision-only global biomedical embeddings into decoder feature space and selectively integrates them through semantic-local fusion and spatial gating. To the best of our knowledge, ThyCLIPNet is among the first lightweight thyroid ultrasound segmentation frameworks to use BiomedCLIP's vision encoder alone for image-only global semantic guidance without text prompting. Experiments on TG3K, TN3K, DDTI, and PKTN achieve dice similarity coefficients of 96.22%, 87.58%, 84.73%, and 80.70%; intersection over union scores of 92.72%, 77.91%, 73.51%, and 67.64%; and 95th-percentile hausdorff distances of 3.75, 16.38, 18.23, and 10.86, respectively. ThyCLIPNet uses 8.55M parameters and 22.99G FLOPs. Overall, the results support integrating global biomedical semantic guidance with lightweight multi-scale CNN representations for robust and computationally efficient thyroid ultrasound segmentation. Source code: https://github.com/Tasnim-Jahan/ThyCLIPNet. [Abstract shortened for arXiv. See PDF for full abstract.]

Abstract: Guided diffusion samplers are increasingly used to reconstruct physical fields from sparse observations, but standard diagnostics do not say how much of the reconstruction was actually determined by the data. We introduce effective data resolution for black-box generative posteriors: a comparison between the resolution warranted by the inverse problem, $\mathrm{dof}_{\mathrm{ref}}$, and the resolution realised by the sampler, $\mathrm{dof}_{\mathrm{samp}}$. A perturbation estimator measures $\mathrm{dof}_{\mathrm{samp}}$ and the spatial map $R(x,x)$ from sampler queries alone. We validate the estimator against exact references and use it to study guided diffusion. The resulting measurements show that guidance weight can strongly alter apparent information transfer, that mean, spread and resolution are not jointly corrected by one weight even with an exact prior and score, and that resolution fidelity does not follow reliably from the apparent principledness of a guidance rule.

Abstract: We propose a data-driven framework for estimating the Bayesian Cramér-Rao bound (CRB) in high-dimensional imaging systems with complex, analytically intractable priors. Direct CRB computation is challenging in this setting due to the need to model the prior score and to form and invert the Bayesian Fisher information matrix in very high dimensions. To address these issues, we first reformulate the inverse problem in the latent space of a pre-trained variational autoencoder, thereby dramatically reducing the dimensionality of the bound estimation problem while preserving the spatial structure of the images. The Bayesian CRB is formed in this latent space and mapped back to the native parameter space using a change-of-variables formula. Second, to learn the latent prior score, we introduce a new sliced score matching objective defined in a Bochner space endowed with an $H^1(Ω)$ Sobolev norm in space. This "Bochner-space sliced score matching" objective is consistent with standard sliced score matching, but penalizes errors in the spatial gradients of the score, suppressing high-frequency artifacts that otherwise contaminate the resulting CRB estimates. We validate the approach on a stylized quantitative photoacoustic computed tomography (qPACT) breast imaging problem with over one million unknown parameters, using a foundation-model autoencoder derived from Stable Diffusion. The proposed method yields stable, artifact-free Bayesian CRB estimates that reflect the highly non-Gaussian structure of the learned prior and reveal the substantial impact of the prior on the relative performance of competing qPACT design schemes.

Abstract: In this work we formulate ultrasound multistatic recovery from arbitrary transmit sequences as a Bayesian inference problem. To that end, we train a deep generative prior on multistatic data sets to tackle the rank-deficient regime in which classical linear REFoCUS decoders fail. This appproach, which we term Deep Bayesian REFoCUS, outperforms the linear baselines for all regimes of rank-deficiency and noise levels, and regresses to linear decoding when inversion is exact. The model also expresses uncertainty in the null space of the acquisitions, whereas the linear REFoCUS decoders only provide point estimates. Finally, we analyze the impact of distribution shift between simulation and in-vivo acquisitions, showing remarkable generalization ability without any fine-tuning or adaptation.

Abstract: Sampling from the posterior is the central task of computational Bayesian inverse problems. The standard workhorse in Bayesian inference - Markov chain Monte Carlo (MCMC) - is sequential, yields correlated samples, and must be rerun for each observation. Conditional flow matching offers an amortized alternative: a transport map, trained once on joint samples of parameter and data, that yields independent approximate posterior samples for any observation at negligible online cost, without new likelihood evaluations. We give a careful, MCMC-literate assessment of flow matching for PDE-based inverse problems with function-valued parameters. Exploiting the flow's tractable density, we derive computable accuracy estimates of the underlying approximate posterior in total-variation distance and Kullback-Leibler divergence and, moreover, propose a hybrid sampler that is asymptotically exact by Metropolization. We validate the accuracy estimates and demonstrate the amortization in several numerical examples, including electrical impedance tomography and a likelihood-free Lotka-Volterra model.

Abstract: Fine-grained vision-language alignment in chest radiography enables zero-shot classification, grounding, and segmentation without task-specific annotations. However, this alignment is fundamentally hindered by two intertwined sources of ambiguity: projection-induced visual mismatch and patient-agnostic semantic overlap. First, at the local feature level, frontal and lateral radiographs exhibit distinct appearances for the same clinical finding, rendering a shared patch-text similarity geometry inherently suboptimal. Compounding this visual ambiguity is a semantic mismatch during global contrastive optimization, where instance-level objectives penalize cross-patient pairs as strict negatives even when they share identical positive clinical concepts. To address this dual ambiguity, we propose PLRS-IC, a unified dual-calibration framework for chest X-ray representation learning. At the local alignment stage, Projection-Conditioned Low-Rank Residual Similarity (PLRS) dynamically adapts patch-text matching to projection-specific manifolds using a bounded, parameter-efficient low-rank residual. At the global optimization stage, Information-Content-Calibrated Soft False-Negative Suppression (IC-SFNS) leverages a corpus-derived information-theoretic prior to soften the penalty of semantically overlapping negatives without altering original contrastive assignments. Extensive experiments across nine public zero-shot benchmark settings demonstrate that our framework yields consistent improvements in classification, grounding, and segmentation, validating the necessity of dual-calibration in medical vision-language pre-training.

Abstract: The vocal tract is the region of the human body responsible for filtering one's voice to create speech. In this paper, we present a differentiable and GPU accelerated acoustic simulator for the vocal tract. The differentiable simulator synthesizes speech by propagating sound along an acoustic tube model of the vocal tract, and via its gradients, can solve the inverse problem: reconstructing the shape of the vocal tract solely from the sound it produces. Although the inverse mapping between geometry and sound is notoriously non-convex, we discover that gradient descent succeeds with three technical contributions: (1) we design a frequency domain formulation of the vocal tract's fluid dynamics that is 70x more GPU parallelizable than finite differences in time, (2) we integrate a differentiable model for turbulence to synthesize consonants, and (3) similar to prior work in implicit neural representations (INRs) and neural fields, we find that parameterizing the geometry with a neural network accelerates convergence and escapes local minima that trap discrete representations. Because the simulator is differentiable, it is readily integrated with other deep learning pipelines to enable novel linguistics and medical imaging applications. (1) We demonstrate self-supervised autoencoding of vocal tract shapes across 11 languages, and (2) we couple our simulator with a generative model of MRI (magnetic resonance imaging) images to reconstruct one's moving vocal tract from only their speech without paired data.

Abstract: Cross-resolution knowledge distillation aims to improve low-magnification whole- slide analysis by transferring high-magnification representations, yet the conditions for useful transfer remain unclear. We develop a decomposition-based analysis of teacher access, representation loss, and model excess, motivating three questions: whether (a) teacher targets help the task, (b) low-magnification students can predict them, and (c) slide models benefit from those predictions. We investigate them through controlled experiments across ten pathology cohorts spanning classifi- cation, grading, and survival prediction. In the main comparison, providing teacher regional means alongside native low-magnification features improves downstream performance in all ten cohorts. Direct prediction achieves lower reconstruction error than residual prediction, yet the predicted features underrepresent variation in the teacher targets. Moreover, better reconstruction does not consistently improve downstream scores, and retaining native features changes performance even when the predicted teacher features are held fixed. Together, these findings expose a gap between reconstructing teacher representations and realizing their downstream value. They challenge the sufficiency of reconstruction error as a measure of cross-resolution transfer and provide a diagnostic framework for examining where that transfer breaks down. Future distillation designs must account for both what students can predict and how slide models use those predictions.

Abstract: Recovering hidden transport mechanisms from sparse spatiotemporal observations is a fundamental inverse problem in scientific machine learning. In brain tracer imaging, dynamic contrast-enhanced MRI (DCE-MRI) provides time-resolved measurements of tracer concentration, while the underlying velocity and source mechanisms governing tracer propagation remain unobserved. We formulate this problem as physics-informed latent-state inference, in which the transport field itself is the primary object of inference rather than an auxiliary variable used only to reconstruct observed densities. We propose Physics-Informed Neural Optimal Mass Transport (PI-NOMT), a framework that represents density, velocity, and source as continuous neural fields and combines a continuous neural density teacher, recursive differentiable advection--diffusion--source rollout, unbalanced optimal-transport regularization, and governing-equation supervision. Physical laws act as structural priors that constrain the space of admissible transport mechanisms, while observed tracer dynamics provide evidence for estimating the latent transport state. We evaluate PI-NOMT on a synthetic benchmark with known ground-truth transport and on DCE-MRI sequences from nine control rats. On the synthetic benchmark, PI-NOMT accurately recovers the prescribed velocity field, including its magnitude, direction, and integrated trajectories, rather than merely reconstructing endpoint densities. Across the nine rat datasets, the framework yields sub-percent local endpoint error, consistent physical speed scales, and low post-training PDE and incompressibility residuals. These results support physics-informed latent-state inference as a general framework for recovering hidden transport mechanisms from observed dynamic scalar fields.

Abstract: Three-dimensional dense convolutional networks are the strongest performers on volumetric medical image segmentation, but their parameter counts scale poorly: moving a dense k x k convolution to k x k x k multiplies its weights by k. We observe that depthwise separable factorization does not share this penalty. Because the cubic kernel term applies only to the depthwise stage while the pointwise projection, which dominates the parameter count, is unchanged, the same architecture grows by 5 % from 2D to 3D where a dense convolutional U-Net grows by 200 %. We exploit this asymmetry to build a 3D U-Net with 536,990 parameters, 24x fewer than an identical dense 3D U-Net. On MSD Task03 Liver (the Medical Segmentation Decathlon liver task, derived from LiTS), evaluated per case under five-fold cross-validation over all 131 public volumes, the model reaches a tumor Dice of 0.577 (95% CI [0.518, 0.633]) and a liver Dice of 0.947 (95% CI [0.941, 0.952]). Its liver Dice exceeds previously reported performance. Its tumor Dice exceeds their low-resolution configuration (0.4701) by 0.107 and their 2D configuration (0.5394), at approximately one twenty-fourth of the parameters and roughly half the in-plane resolution. Trained under identical conditions on a common held-out split, it exceeds a dense 3D U-Net on liver by +0.031 Dice (paired p = 0.006) and on tumor by +0.041 (95 % CI [+0.005, +0.081], paired p = 0.056), suggesting the factorization also acts as a regularizer in the small-data regime characteristic of medical imaging. We further show, on both LiTS and a 2D endoscopy benchmark, that a large fraction of the network's learnable spatial filters can be replaced by fixed shifts at no cost in accuracy, but that replacing all of them is measurably worse, the placement of spatial capacity matters more than its total amount.

Abstract: Recursive self-improvement (RSI) offers a promising path for overcoming the limited visual capability of current medical imaging agents. Yet applying RSI to volumetric imaging remains difficult: failures can arise from acquisition, perception, training recipe, or downstream inference, while self-generated feedback and logged trajectories provide little guidance on which component should change. We introduce ReVision3D, an RSI system that leverages 3D volumes with spatially grounded annotations to determine where visual evidence is lost and recursively improve the corresponding visual capability. A frozen language-model designer proposes revisions to acquisition, perception, training, or inference, while the verifier and system-level objective remain fixed. Our key insight is that an annotated volume forms an exact replay world for view rendering and spatial verification: unvisited views can be rendered on demand, and localized predictions can be checked directly against reference masks. This grounded feedback directs targeted revision, while only changes that improve beyond measured seed noise are retained. Each accepted change triggers renewed attribution, allowing the dominant bottleneck to shift across rounds. On abdominal CT, attribution identifies perception as the dominant remaining limitation. Revising that level enables ReVision3D to achieve 79% liver recall and 83% kidney recall at under 0.4 false positives per patient, outperforming the evaluated frozen multimodal foundation models, with the largest gains on small lesions.

Abstract: Biomedical image segmentation is central to medical image analysis, but practical deployment often faces limited annotations, memory constraints, and cross-site distribution shifts. Implicit Neural Representations (INRs) have recently emerged as a lightweight alternative for semantic segmentation, achieving competitive performance with substantially fewer parameters than conventional architectures. However, the mechanisms, scaling behavior, and domain generalization abilities of INR-based segmentation remain insufficiently understood. In this work, we study these questions in the context of cross-domain brain MRI segmentation. We analyze INR-based segmentation across low-parameter regimes, comparing it with conventional pipelines in both in-domain and out-of-domain settings. Surprisingly, we find that INR-based models do not simply improve with increasing parameter budget. Their advantage is most pronounced under low-parameter and limited-augmentation settings, while U-Net-based models benefit more from larger capacity and standard augmentation. We also investigate how INRs encode semantic information in their hidden features and show that complementary segmentation-relevant structure is distributed across multiple INR layers. Building on this insight, we introduce HierINRSeg, a hierarchical INR-based architecture that aggregates multi-layer representations for improved robustness and generalization. Extensive experiments show that HierINRSeg consistently outperforms MetaSeg, a strong recent INR-based segmentation baseline, with an average improvement of 5.6 percentage points in Dice for the in-domain test set and 8.2 percentage points out-of-domain. Overall, our analysis identifies the conditions under which INR-based segmentation is most effective, providing concrete guidance for model selection and future research.

Abstract: Ultrasound is one of the most widely used medical imaging modalities, and recent large vision-language models(VLMs) have shown increasing capabilities in ultrasound image understanding. However, these models fail to provide pixel-level visual evidence aligned with their semantic predictions, and their fine-grained grounding capability in ultrasound remains largely unclear. We introduce UltraG-Bench, a large-scale multi-task benchmark for evaluating pixel-level evidence grounding in ultrasound. UltraG-Bench is built by annotating 40 public ultrasound segmentation datasets spanning 13 anatomical categories, and comprises three progressive tasks: instruction-guided segmentation, evidence-grounded VQA, and evidence-grounded report generation, with 331125, 666779, and 138832 annotations, respectively. Comprehensive evaluation of 14 state-of-the-art models reveals a substantial gap between semantic understanding and fine-grained pixel-level localization. We further propose UltraG-Agent, which combines the semantic reasoning capabilities of a VLM with the ultrasound-specific segmentation capability of UltraSAM3. Experiments show that UltraG-Agent substantially improves both semantic prediction and pixel-level visual grounding. Our dataset and code are available at https://github.com/zhuqh19/UltraG-Bench.

Abstract: CryoEM map interpretation requires features that are spatially localized, consistent across samples, and informative across spatial scales. Most deep learning methods for map annotation extract features from fixed voxel grids. However, implicit neural representations (INRs) are able to model volumetric data as scale-agnostic, coordinate-conditioned functions. INRs are therefore attractive for cryoEM, but fitting a separate INR for each map is too expensive for large-scale feature extraction and produces representations that are not aligned across samples. We introduce Atelier, a self-supervised framework that amortizes INR fitting for reconstructed cryoEM maps. Pretrained on 5,439 Electron Microscopy Data Bank maps, Atelier is a transformer-based hypernetwork that generates high-fidelity reconstructions across a wide range of protein structures, including large multi-subunit assemblies. Beyond reconstruction, the INR generated by the pretrained transformer exposes a continuous, local feature field through its intermediate activations at any spatial query point, a property that voxel grid and patch-tokenizer architectures do not naturally provide. Used as auxiliary channels to a 3D nested U-Net annotation head trained from scratch, these coordinate-conditioned features improve performance on eight voxel-level property prediction tasks over a volume-only baseline. Our results demonstrate that amortized implicit neural representations are an effective primitive for geometry-aware analysis of cryoEM data.

Abstract: Patient-specific 4D myocardial reconstruction from cine MRI supports quantitative functional assessment, regional motion analysis, and simulation-based modeling. However, routinely acquired short-axis (SAX) cine MRI is sparsely sampled along the through-plane direction, making dense and anatomically consistent surface reconstruction challenging. In this study, we propose an anatomy-aligned surface learning framework that parameterizes the epicardial and endocardial surfaces on a shared circumferential-longitudinal UV domain. This formulation converts irregular 3D reconstruction into structured coordinate-field completion with explicit correspondence across subjects and cardiac phases. Sparse SAX contours are encoded as UV observation fields, coverage-aware sampling improves robustness to incomplete slice coverage, and topology- and distortion-aware learning preserves circumferential continuity and local surface quality. Experiments on three public cine MRI datasets showed that the proposed method consistently outperformed representative mesh-based and implicit reconstruction approaches, achieving overall Chamfer distances of $2.887$~mm on ACDC, $2.641$~mm on M\&Ms, and $2.810$~mm on M\&Ms-2. The reconstructed sequences also preserved ventricular function, with end-diastolic volume and ejection fraction errors of $3.3$~mL and $1.1 \%$, respectively. These results demonstrate that anatomy-aligned UV learning provides an accurate, efficient, and correspondence-aware representation for sparse cine MRI reconstruction and myocardial modeling. The source code will be available at https://github.com/yuan-xiaohan/SAX2MyoSurf.

Abstract: We introduce NeuralSRNF, a novel framework for the statistical shape analysis and generation of genus-zero 3D and 4D objects that undergo nonrigid deformations. Traditional methods rely on complex and computationally expensive nonlinear elastic metrics that measure bending and stretching. Recent advances in elastic shape analysis achieve computational efficiency by mapping input 3D shapes to the space of Square Root Normal Fields (SRNFs) where the L2 metric approximates the partial elastic metric, significantly facilitating the process of computing geodesics and summary statistics. SRNFs, however, are not invertible, and the numerical algorithms used to map SRNFs back to the original space of surfaces remain computationally very expensive and often lead to approximate results. This paper addresses this fundamental SRNF inversion problem using a novel neural representation, termed NeuralSRNF. Unlike the commonly used numerical SRNF, NeuralSRNF is (1) continuous, and thus resolution-agnostic, enabling full functional shape analysis, (2) more accurate, and (3) computationally more efficient as it can compute inverse SRNF maps along a geodesic path in less than 3 s compared to over 10 min for the numerical SRNF. We demonstrate, using various datasets, the utility and efficiency of the proposed NeuralSRNF in multiple elastic 3D and 4D shape analysis tasks such as geodesic computation, deformation transfer, statistical summaries computation, and 3D shape generation. We show that it outperforms competing methods on most evaluated datasets and metrics by a wide margin in both accuracy and computational efficiency. The source code and additional results are available at https://awaisnizamani16.github.io/awais/NeuralSRNF/.

Abstract: We address adaptive computation in 3D medical image segmentation: instead of designing another backbone, we ask how much spectral mixing each network stage needs and let optimization answer. We derive FHEAT, a two-parameter operator family, from the discrete cosine transform (DCT) solution of a fractional heat equation. A fractional order alpha and a diffusion strength D govern the operator, and at D=0 it is exactly the identity. Reparametrized by the semigroup time tau = D*alpha, same-resolution instances compose exactly, so any distribution of diffusion across same-resolution stages amounts to a single Sobolev-type regularizer of learned strength. This identity limit lets the optimizer of each layer, not the designer, decide whether global mixing is needed and how sharp it should be. We instantiate FHEAT in a lightweight U-shaped architecture (Light-UNETR) paired with a Kolmogorov-Arnold mixer (KAN3D) with adaptive rational activations, yielding FHEAT-Seg. At 5% to 20% label rates on three public benchmarks, training produces gradient-driven spectral sparsification: seven of the eight stage-level operators drive D to zero, and the survivor saturates at the sharpest low-pass (alpha ~ 0.9) in the decoder layer feeding the semi-supervised attention map. The retired layers become exact identity shortcuts at inference, cutting FLOPs from 4.29G to 0.90G (a 79% drop) at 0.975M parameters. Under a standard semi-supervised protocol, FHEAT-Seg reaches Dice scores of 90.47% (left atrium), 78.79% (Pancreas-CT), and 81.90% (BraTS 2019), ahead of five semi-supervised methods and the Light-UNETR baseline. The large variant also surpasses Light-UNETR-L under full supervision (Dice 93.09%, 85.11%, and 87.19%) with 2.851M parameters and 55.75G FLOPs. These results suggest that the allocation of spectral computation is a learnable property of optimization dynamics, not a manual design commitment.

Abstract: In this paper, we proposed GAD-MambaUNet, a lightweight medical image segmentation network that combines efficient local modeling, direction--group state-space interaction, and training-time foundation-model supervision. To improve contextual modeling in compact segmentation networks, we introduced Direction-Group Graph Selective Scan (DG-GSS), which treated scan-direction and channel-group responses as graph nodes and enabled structured information exchange before multi-directional fusion. We further incorporated DINOv3-GAD supervision, where a frozen DINOv3 teacher provided semantic guidance during training, and Gradient-Adaptive Distillation dynamically regulated the distillation strength. GAD-MambaUNet achieves a favorable accuracy--efficiency balance compared with representative lightweight and general segmentation methods. Ablation studies further verify the effectiveness of DG-GSS and training-time DINOv3-GAD supervision. In future work, we will explore more flexible teacher--student alignment strategies and extend the proposed framework to more diverse medical segmentation scenarios, such as multi-class and multi-modal segmentation tasks.

Abstract: Ultra low-field MRI expands global access to neuroimaging but produces scans with low signal-to-noise ratio, reduced contrast, and thick slices. While regression-based super-resolution can recover anatomical detail for segmentation, it returns a single deterministic estimate that gives no indication of regions where the low-field input leaves anatomy underdetermined. Generative diffusion models offer an alternative by sampling the posterior distribution of plausible high-field images, quantifying this anatomical ambiguity. However, applying them to 3D whole-brain MRI is restricted by memory bottlenecks, slow sampling, and scanner domain shifts. We propose a 3D residual wavelet diffusion model that combines three ideas to overcome these hurdles. A lossless wavelet reparameterisation shrinks the spatial grid to fit a whole brain on a single GPU, residual shifting accelerates sampling by starting from the low-field input, and domain randomisation promotes scanner generalisation without paired training data. As the high-field reference is not a voxel-aligned ground truth, we evaluate downstream volumetric agreement. On a healthy cohort (n=19) imaged at 0.064T and 3T, our method matches a leading general-purpose regression approach in volumetric accuracy while additionally generating per-voxel uncertainty maps highlighting underdetermined regions. Furthermore, on a pilot dataset (n=11) of participants with cognitive impairment, disease-relevant atrophy is preserved rather than normalised towards a healthy prior. Our framework brings whole-brain posterior sampling to low-field super-resolution without sacrificing volumetric accuracy.

Abstract: We introduce Ananke, a representation-learning framework that scaffolds latent representations onto a structured product-torus prior, and its flagship visual backbone realization, Contractive Torus Attractor Networks (CTAN). By factorizing high-dimensional latent spaces into an orthogonal direct sum of two-dimensional phase planes ($\bigoplus_{k=1}^K \R^2$), Ananke coordinates feature updates via a decoupled dual-phase continuous flow: skew-symmetric Hamiltonian transport moves features tangentially along energy level sets to preserve semantic phase invariants, while signed gradient dissipation contracts transverse perturbations normally toward target invariant manifolds. For circular potential families with frozen parameters, logarithmic radial feedback yields the Exact Log-Symplectic Flow (ELSF), an analytical closed-form mapping with exact exponential decay of log-radius error that evaluates in a single forward pass without numerical integration. We establish local input-to-state bounds for level-set deviations and log-radius errors, and characterize the normal hyperbolicity and persistence of the ideal product torus under bounded perturbations. We further formulate the architecture through Lie--Trotter operator splitting, unifying spatial depthwise diffusion with local manifold contraction, and analyze both exact trigonometric flows and hardware-friendly symplectic dual-shear variants. Across natural image benchmarks (CIFAR-100) and clinically challenging endoscopy datasets (Kvasir-v2), CTAN demonstrates exceptional parameter efficiency: an ultra-compact hierarchical model with merely 0.27M parameters achieves 90.52\% accuracy on Kvasir-v2, outperforming 25M+ baselines (ResNet-50, DenseNet-161) by nearly two orders of magnitude in capacity, while scaled variants attain 80.32\% top-1 accuracy on CIFAR-100.

Abstract: Automated brain tumor segmentation supports diagnosis, treatment planning, and monitoring of disease progression, but building models that generalize across heterogeneous tumors and limited annotated data remains difficult. We present VGG16-MCA UNet, a hybrid architecture pairing an ImageNet-pretrained VGG16 encoder with a decoder in which a Multi-Channel Attention (MCA) module recalibrates features after each skip-connection fusion, trained with the Focal Tversky loss to counter severe foreground-background imbalance. We evaluate the model as a 2D, FLAIR-only, whole-tumor segmenter on tumor-positive slices from two public datasets: the BraTS 2020 benchmark and the LGG MRI Segmentation dataset. Using 5-fold cross-validation and a single network formed by averaging the weights of the five fold models, the method attains an aggregate pixel-level Dice (F1) of 95.10% on our held-out BraTS 2020 split and 88.32% on LGG. These scores are computed over all test pixels pooled into a single confusion matrix rather than averaged per case, and are therefore not directly comparable to the per-case mean Dice used in the BraTS challenge protocol. All partitions were drawn over individual slices rather than over patients, so every patient contributes slices to both training and test; the figures above therefore measure interpolation within known patients and should be read as an upper bound rather than as generalization to new ones. The model segments a 256x256 slice in 66.32 ms on a single 6 GB NVIDIA RTX 2060, approximately 8 ms more than an equivalent VGG16-UNet without MCA. We release the split records and report the protocol in full, with the aim of providing a precisely specified and reproducible 2D FLAIR baseline.

Abstract: Lossy compression of scientific simulation data increasingly relies on learned, latent-space architectures such as Residual Vector Quantization (RVQ), which iteratively quantize a base representation and its residuals to progressively reduce reconstruction error. While effective, RVQ performs this residual modeling entirely in latent space, leaving the pixel-space error structure of the reconstruction largely unaddressed. In this work, we propose a post-processing pipeline that augments an RVQ-based compressor with a U-Net trained to predict and correct pixel-space residuals between the original volume and its RVQ reconstruction. We show that these residuals are spatially structured rather than driven by local intensity or gradient features, motivating the need for a deep spatial model rather than simple statistical correction. The U-Net-corrected reconstruction is then passed through a Guaranteed Autoencoder (GAE) stage, which projects the remaining residual onto a per-block PCA basis to enforce a user-specified block-wise error bound. To the best of our knowledge, this is the first pipeline to combine latent-space RVQ, explicit pixel-space residual correction via a deep spatial post-processing network, and GAE-based error-bound guarantees within a single framework for scientific data compression. We evaluate our approach on S3D, JHTDB and E3SM datasets, demonstrating consistent improvements in NRMSE, compression ratio] over RVQ-only and standard residual-correction baselines, while maintaining strict error guarantees required for scientific data fidelity.

Abstract: Gradient-guided diffusion samplers provide flexible priors for inverse problems and conditional generation, but strong guidance can move the sampling trajectory into regions where the learned score is poorly supported. Existing tangent-projection strategies limit first-order departure from an iso-density surface, yet discard potentially useful normal motion and overlook the second-order departure induced by tangent motion on a curved surface. We introduce curvature-adaptive tubular correction (CAT), a training-free plugin that regulates both effects within a shared, noise-dependent geometric budget. CAT decomposes the guidance gradient into normal and tangent components, charges normal displacement at first order and tangent displacement according to directional curvature, and obtains their jointly optimal magnitudes from a one-dimensional dual equation. Armijo backtracking calibrates the resulting finite step against the actual guidance objective, while matrix-free directional derivatives avoid constructing the full score Jacobian. We establish local guarantees for the tubular approximation, uniqueness of the correction, and sufficient objective decrease. Across seven inverse problems on FFHQ and ImageNet, CAT improves the evaluated pixel- and latent-space host samplers, with particularly consistent gains in perceptual metrics. It also improves black hole reconstruction on InverseBench and yields the lowest FID among the compared methods at every tested classifier-free guidance scale, while maintaining stable saturation and contrast. These results support curvature-aware tubular control as a reusable mechanism for stabilizing diffusion guidance.

Abstract: Clinical B-mode images are widely available as potential data sources for quantitative ultrasound (QUS) analysis for tissue characterization. However, standard clinical ultrasound devices apply unknown log-compression to RF envelope data before display and storage. Previous work has demonstrated estimation of the underlying RF envelope statistics in the presence of an unknown compression law. Using Fisher information analysis, we show that finite-offset log compression causes severe information loss when estimating the Rayleigh scale $σ$, which controls diffuse speckle. For a single image window, unknown compression raises the minimum achievable variance for unbiased estimation of $σ$ by a compression-independent factor of approximately $\FisherMinInflation$. When $M$ equal-sized windows share the same unknown compression settings, the excess variance decays as $1/M$; even in the most favorable regime, reducing the variance inflation factor below $1.1$ requires $\FisherBestCaseWindows$ windows. Our analysis treats the contrast parameter $a$ as unknown and the boundary offset $b$ as known; estimating $b$ experimentally shows even larger variance. We validate this theory using synthetic estimation experiments and demonstrate RF-scale recovery on real RF-envelope windows from the OASBUD dataset. Together, these results clarify the limitations of using routine B-mode images for QUS.

Abstract: Reducing radiation exposure in Positron Emission Tomography (PET) is important for patient safety; however, ultra-low-dose imaging suffers from severe noise, which may affect diagnostic interpretation without appropriate image enhancement. While current 3D deep generative models, particularly diffusion models, have shown strong reconstruction fidelity, their practical use can be limited by long inference times. In contrast, faster 2D-based alternatives may have difficulty maintaining volumetric consistency, an important consideration for whole-body PET imaging analysis. To bridge this gap, we propose a one-pass conditional 3D rectified flow (3D Flow) framework for whole-body PET image denoising that incorporates a novel optimized non-uniform sampling strategy. The model is trained with a one-pass linear-interpolant velocity-matching objective. This approach reconstructs a full 3D volume in approximately 30 seconds in our implementation, compared with multi-hour inference for the evaluated 3D DDPM baseline. Evaluations including zero-shot transfer to an independent clinical dataset show that our model achieves favorable global image quality and lesion conspicuity compared with the evaluated 3D DDPM and DDIM baselines, including on challenging short-acquisition data. Furthermore, the proposed method shows promising zero-shot transfer performance across the evaluated datasets and unseen dose levels (down to 1/100 of the standard dose), with artifact-focused visual comparisons supporting the need for further lesion-level validation. By balancing reconstruction fidelity and computational efficiency, this work presents a candidate approach for ultra-low-dose whole-body PET image denoising.

Abstract: Convolutional neural networks (CNNs) are typically evaluated using held-out classification accuracy, an approach that presupposes predictions are based primarily on the intended object of interest rather than incidental surrounding context. We test this assumption in CNN-based agricultural image classification by comparing model performance on original images with performance on background-dominated patches extracted from the same images across eight publicly available agricultural benchmark datasets and four widely used CNN architectures. Background-dominated patches were classified above dataset-specific random chance for six of the eight datasets, and substantially above chance for four of them, indicating that contextual information contributes to model predictions for the majority of datasets evaluated. For these four datasets, we further evaluated whether this behavior reflected genuine class-discriminative information or was primarily attributable to class imbalance using macro-averaged precision, recall, and F1 together with class-balanced test subsets. The results show that contextual reliance does not admit a single explanation: class imbalance accounts for a substantial portion of the observed signal for some datasets and architectures, whereas above-chance contextual classification persists after balancing for others. Together with previous evidence from curated object recognition and cancer pathology imaging, these findings support the growing view that contextual bias is a recurring characteristic of CNN-based image classification rather than a phenomenon confined to a single application domain. More broadly, this work provides a systematic framework for quantifying contextual bias across heterogeneous image datasets by combining dataset-specific random-chance baselines, contextual bias categorization, macro-averaged evaluation, and class-balanced robustness analysis.

Abstract: Complex-valued signals, such as Magnetic Resonance Imaging (MRI) and audio spectrograms, are almost always modelled as flat two-channel Euclidean data. For nonzero values the amplitude-phase chart $z \mapsto (|z|, z/|z|)$ identifies the signal domain with the cylinder $(0, \infty) \times S^1$, on which we deliberately replace the inherited metric $dA^2 + A^2 dθ^2$ by the decoupled product metric $dA^2 + dθ^2$. In this empirical study we measure what that substitution costs and what it buys. By computing exact analytical bridges, we demonstrate that Cartesian paths induce a heavy-tailed distribution of angular velocity (power law index $\approx 1.0$), with nearly half of the probability paths exceeding an angular speed of $π$ under independent coupling, a rate no cylindrical path ever exceeds. To resolve this, we analyze Cylindrical Flow Matching (CyFM), which strictly bounds the regression target, and couple noise and data by exact minibatch Optimal Transport computed jointly over whole fields in the cylindrical metric. Although the transport-cost reduction of this coupling collapses with field dimension (from 86% for scalar pairs to 3% for $64\times64$ fields), its benefit to few-step generation does not: it lowers the few-step error of the cylindrical model by 3-60% at every evaluated resolution. With this coupling, CyFM has a lower error than the best Cartesian baseline at every step count up to $k = 8$ and every evaluated resolution, with all five seeds separated and without distillation, and at convergence we detect no significant difference between the two geometries. Finally, we expose the "Factorized Coupling Trap," showing that dimension-wise or patch-wise transport factorizations silently destroy the joint distribution of the data. All experiments are on synthetic complex fields.

Abstract: Radiomic texture features are commonly extracted from anisotropic CT and MRI acquisitions, where identical voxel offsets may represent different physical distances. We implemented and validated a voxel-spacing-aware extension of PyRadiomics that incorporates spacing information without generating interpolated gray levels. The framework operates across the Python frontend, C wrapper, and computational backend. GLCM uses anisotropy-relative feature-level angular aggregation, NGTDM uses anisotropy-relative weighted neighborhood averaging, and GLRLM, GLDM, and GLSZM are computed on a finite-volume zero-order-hold representation derived from the native anisotropic grid. Synthetic 3D phantoms were used for software validation. The modified implementation reproduced standard PyRadiomics exactly when spacing-aware mode was disabled and remained equivalent under isotropic spacing across 75 texture features. Under anisotropic spacing, the method selectively modified texture families and was numerically distinct from nearest-neighbor, linear, and B-spline resampling. Computational profiling showed moderate runtime and memory increases, while sensitivity analyses quantified finite-volume rounding effects and confirmed that spacing-aware differences persisted across binWidth settings. The framework provides a backward-compatible technical basis for future evaluation of spacing-aware radiomics in heterogeneous medical imaging datasets.

Abstract: Given a grid-sampled 1-Lipschitz function $f:\mathbb{R}^3 \rightarrow \mathbb{R}$ (such as a signed distance function) sampled on a regular grid, we determine the sharp infimum $σ_\star$ such that for every $σ> σ_\star$ the true zero-level set $f^{-1}(0)$ is contained in the marching cubes mesh for $f = σ$. For grids with spacing $h$, the sharp infimum is $σ_\star = \frac{\sqrt{3}}{2} h$. This result is proven \emph{despite} the planar marching cube faces potentially lying on either side of the level set of the trilinearly interpolated approximation of $f$ (which shares the same infimum). The proof instead constructs a convex lift of the corner samples and shows that the high-side portion of each marching-cubes cell lies in the projection of its $σ$-superlevel portion, which cannot contain a point of $f^{-1}(0)$.

Abstract: Dementia is a major and growing global health burden, with Alzheimer's disease (AD) accounting for most cases. Timely and accurate diagnosis is central to managing this burden and increasingly depends on integrating complementary clinical and imaging information. Multimodal deep learning can combine these modalities for AD diagnosis, but how its explanations behave across modalities, fusion strategies, and cohorts remains unclear. We developed an explainable multimodal framework pairing a 3D CNN encoder for T1-weighted MRI with a feedforward network for harmonized clinical and demographic data, comparing varied model setups on three-way and pairwise diagnostic tasks using 6,479 internal records from the ADNI and 1,703 independent records from the OASIS-3. On ADNI, the tabular-only model achieved the highest three-class AUC-ROC of 0.879 and best discriminated cognitively normal (CN) versus mild cognitive impairment (MCI; 0.903), while cross-attention performed best for MCI versus AD (0.861); CN versus AD was highly discriminative overall. On OASIS-3, the vision-only model performed best (three-class AUC-ROC 0.910); CN versus MCI remained difficult, and no fusion strategy consistently outperformed single modalities across tasks and cohorts. SHAP and Integrated Gradients identified the MMSE as the dominant tabular feature in both cohorts, with global feature rankings agreeing strongly in ADNI ($ρ=0.94$) and OASIS-3 ($ρ=0.96$); CAM-based explanations, however, changed with model configuration and cohort. These findings show that multimodal performance and explanations are task, modality, fusion, and cohort-dependent: a dominant cognitive signal persisted across cohorts, but feature contributions and CAM explanations did not, underscoring the need to evaluate explainability under cohort shift rather than as a stable, intrinsic property.

Abstract: We present a framework for tracking topological features directly within continuous implicit models. Such models, including implicit neural representations (INRs) and multivariate functional approximations (MFAs), are increasingly adopted to represent scientific data without the resolution constraints of discrete grids. They offer compact, smooth, and differentiable representations of complex fields, enabling new opportunities for high-performance data storage, reconstruction, and analysis. Given a continuous implicit model, our method tracks the evolution of critical points by querying the model and its derivatives, thereby eliminating the need to resample onto a grid. This approach enables faithful feature tracking while avoiding discretization-induced artifacts such as aliasing. We demonstrate the generality of our framework across a range of implicit representations, including analytic functions, MFAs, and INRs, and show that it produces smooth, coherent critical point trajectories. By enabling feature tracking directly on continuous representations, our method supports a new class of feature-driven visualization workflows centered on implicit models.

Abstract: While accelerators for AI have seen great commercial success, it is challenging to replicate that success for other specialized domains due to a number of factors. We make the case that barriers for new accelerators can be lowered by starting with a baseline AI accelerator, and adding minimal logic to support new operators demanded by new specialized domains. This leads to a versatile chip that can be manufactured at high volume and deployed for a range of popular applications. We refer to this as the AI+X approach. This paper explores its potential for the emerging domain of Computational Pathology, which involves analysis of large whole-slide tissue images with a multi-stage pipeline. The pipeline requires support for a number of different kernels and operators - early stages perform segmentation and feature extraction, followed by graph creation with k nearest neighbor (kNN) algorithms, and finally inference with an iterative graph convolutional network (GCN) that alternates between Aggregation and Combination. We show that these stages execute inefficiently on a range of baseline CPU, GPU, AI, and GCN accelerators. That inefficiency is addressed with a combination of software re-structuring and small modifications to a baseline systolic AI accelerator. Many of the above kernels can be mapped to a systolic accelerator by offering a flexible datapath between processing elements and register access mechanisms. We add support for feature aggregation, load balanced execution, Euclidean distance calculation, binning, and counter aggregation. This additional flexibility and logic grows the area of a baseline AI chiplet by 1.1x, but by avoiding the memory wall and offering high parallelism, the proposed accelerator BEACON yields over an order of magnitude higher throughput for Computational Pathology than baseline CPU and GPU platforms.

Abstract: Multi-modal medical image segmentation leverages complementary diagnostic information, yet fusion can underperform single-modality baselines when spatially aligned inputs differ in quality. Here, "corruption" primarily denotes resolution-induced degradation rather than misalignment or complete modality absence, while synthetic noise is evaluated only as an auxiliary setting. We identify a critical optimization-inference inconsistency: degraded modalities can receive weak training updates yet substantially affect predictions, indicating active interference with fusion. We attribute this failure to resampling-induced feature corruption and optimization bias, where noisy features propagate through skip connections and encourage unreliable modality selection. We therefore propose CoReFuse-Med, a Corruption-aware Rebalanced Fusion framework that suppresses corruption during feature transmission and rebalances modality contributions during high-level fusion. Experiments on EPVS, BraTS, and WMH, including multiple Z-axis slice-retention ratios and an auxiliary noise test, demonstrate improved accuracy and robustness under modality-quality discrepancies. Our code is available at https://github.com/lrever/CoReFuse.

Abstract: Model pruning is widely used to compress deep neural networks, reducing memory and computational requirements with minimal impact on aggregate performance. However, its effect on model behavior remains poorly understood, particularly for long-tailed medical datasets where rare but clinically important conditions are underrepresented. Furthermore, it remains unclear whether pruned models preserve reliable explanations of their predictions. To address this gap, we present a systematic study of long-tail forgetting and explanation reliability under model pruning. Across two long-tailed medical imaging datasets, two CNN architectures, four pruning methods, and sparsity levels up to 95\%, we evaluate predictive performance, explanation stability, and explanation faithfulness. Our results show that predictive performance exhibits a strong frequency-dependent trend, with lower-frequency classes generally experiencing earlier and larger degradation than higher-frequency classes. In contrast, explanation stability and faithfulness are influenced primarily by the pruning strategy, with gradient-informed methods preserving explanation reliability more effectively under aggressive compression. Qualitative and mechanistic analyses further indicate that explanation degradation is primarily associated with the collapse of class-discriminative gradients rather than the disappearance of feature activations. These findings suggest that model compression should be evaluated beyond aggregate performance. Incorporating class-aware and explanation-aware evaluation reveals failure modes that would otherwise remain hidden, while moderate sparsity levels provide a practical balance between compression, predictive performance, and explanation reliability.

Abstract: Most automated brain parcellation tools are developed and validated on T1-weighted (T1w) MRI. Yet, some clinical workflows for which parcellation is relevant only use contrast-enhanced T1w (T1ce) MRI, on which T1w-trained models are less accurate. We present a unified network that parcellates both pre- and post-contrast agent T1w MRI reliably, trained on a combination of the two with conditioning that spatially modulates its response differently for each. Feature-wise Linear Modulation (FiLM) is a known approach for input-based modulation in networks. It applies a per-channel scale and shift uniformly across the input. However, the appearance change between pre- and post-contrast varies locally across the brain, making FiLM suboptimal for our use case. In this work, we introduce Spatial FiLM (SpFiLM), a conditioning layer whose modulation varies spatially, assembling a voxel-wise scale and shift from image-derived spatial patterns. Using a cohort of 134 patients with paired T1w and T1ce MRI parcellated into 106 classes, the addition of SpFiLM layers in a UNet increased the mean Dice on the test set of 25 patients from 80.2% to 84.1%, a 4.9% relative improvement. Adding SpFiLM layers led to the best performance on both pre- and post-contrast MRI, even when controlling for network parameter counts.