arXiv subjects

Mostafa Mehdipour Ghazi

Publications and source records attributed to Mostafa Mehdipour Ghazi.

At least 19 recordsLinked to original sources

arXiv2026

CATCH: Counterfactual Anatomical Tissue Inpainting with Conditional Haar Diffusion

BraTS local synthesis replaces masked regions in T1-weighted brain MRI with plausible tumor-free tissue while preserving observed anatomy. We present CATCH, conditional 3D diffusion in an invertible Haar-wavelet domain. Its denoiser receives noisy target coefficients, voided-image coefficients, and a signed mask; tumor-excluded wavelet reconstruction and a hole-focused loss guide training, and hard compositing preserves observed voxels. We compare fixed masks, tumor-component augmentation, and a weighted mixture of tumor-derived, irregular-blob, and ellipsoidal masks. Of 25 development cases, five prespecified cases select each arm's checkpoint and all 25 of their trajectory aggregations; a separate 75-case internal set compares the frozen pipelines and selects a weighted mixture for organizer evaluation. Five-trajectory averaging yielded internal SSIM/PSNR/MSE (mean$\pm$SD) of $0.80\pm0.13$, $19.18\pm1.80$dB, and $0.010\pm0.005$. As the sole officially evaluated pipeline, weighted mixture yielded $0.772\pm0.119$, $20.89\pm3.27$dB, and $0.0098\pm0.0054$ on the 219-case BraTS 2026 validation set. Against compute-matched random augmentation internally, it improved SSIM by 0.019 (95% bootstrap CI: 0.013-0.025), PSNR by 0.95dB, and MSE by 0.003; all three paired comparisons remained significant after Holm correction. Results favor the complete weighted-mixture policy within CATCH; absent official fixed- and random-pipeline scores and a directly comparable external baseline limit broader conclusions.

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arXiv2026

QINA: Quantum-Inspired Nonlinear Adapters for Pretrained Vision Models

Adapting large pretrained vision models under limited data and frozen-backbone constraints remains a central challenge in transfer learning. While lightweight adapters and parameter-efficient fine-tuning methods are widely adopted, most rely on generic multilayer perceptrons or low-rank linear updates, offering limited control over the spectral and geometric structure of feature transformations. We investigate whether structured nonlinear feature lifting can improve representational alignment in frozen regimes. We introduce Quantum-Inspired Nonlinear Adapters (QINA), compact modules that perform learnable trigonometric feature lifting followed by bounded nonlinear aggregation. The design induces structured oscillatory basis functions with an explicit norm-dependent Lipschitz bound, enabling spectral reshaping of pretrained representations without increasing the receptive field or significantly expanding parameter count. Importantly, the method operates entirely within standard deep learning frameworks and does not require quantum hardware. Through systematic experiments across natural and medical imaging datasets, classification and segmentation tasks, multiple adapters and placements, and varying training budgets, we show that performance in frozen regimes is primarily representation-limited. Nonlinear lifting improves adaptation, and the proposed structured trigonometric formulation consistently outperforms identity baselines, fixed Fourier feature mappings, and parameter-matched baseline adapters. Within the evaluated frozen-backbone settings, structured spectral parameterization provides a more effective inductive bias than generic nonlinear adapters. This work highlights the importance of geometry- and spectrum-aware adaptation mechanisms for large pretrained vision models.

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arXiv2026

ActiveAugment: Online Active Learning for Augmentation Selection in Deep Learning

Data augmentation is a cornerstone of deep learning pipelines, yet existing strategies treat it as a static, model-agnostic preprocessing step, either relying on expensive dataset-specific policy search or applying transformations uniformly at random, regardless of what the model has already learned. We introduce ActiveAugment, a unified framework that treats augmentation selection as an online active learning problem. For each training minibatch, ActiveAugment generates a pool of candidate augmented views and scores each candidate using a combination of the model's predictive uncertainty and the feature discrepancy induced by the augmentation. The augmentation under which the current model is most fragile is selected per sample, and the model is then trained with a joint supervised classification and supervised contrastive objective that enforces intra-class invariance to the selected augmentations while maintaining inter-class separation. We evaluate ActiveAugment on eight benchmark datasets spanning natural and medical imaging, using CNN and transformer architectures across three training regimes (training from scratch, full fine-tuning, and linear probing), and comparing eight active selection strategies for augmentation scoring. ActiveAugment outperforms AutoAugment, RandAugment, and TrivialAugment under controlled augmentation shifts across all domains and budgets, with the most pronounced gains at low labelling budgets. On medical imaging datasets, where data is scarce and domain shift relative to natural-image pretrained models is large, ActiveAugment achieves higher test F1 than all baselines, demonstrating strong cross-domain adaptability. Our analysis reveals that the augmentation selection policy evolves meaningfully during training and that strategy choice has a direct impact on generalisation. Code is available at: https://github.com/noahvide/ActiveAugment.

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arXiv2026

Do 3D Medical Foundation Models See Through MRI Artifacts? A Controlled Study of Representation Robustness

Self-supervised 3D medical foundation models are increasingly used as general-purpose feature extractors, yet their sensitivity to MRI artifacts remains poorly understood. We present a controlled evaluation of representation robustness across five pretrained 3D encoders spanning different architectures, objectives, pretraining domains, and dataset scales. Using BraTS-Africa cases with four MRI sequences, we generate seven frequency- and image-domain artifacts at five predefined corruption settings. Robustness is assessed using linear centered kernel alignment (CKA), RankMe, and UMAP, complemented by an independent segmentation-consistency analysis. We find that robustness is strongly model- and artifact-dependent. 3DINO exhibits the most consistently stable representations, while BrainIAC is highly sensitive to several corruptions; NeuroVFM, BrainFM, and Neuro-SimCLR show intermediate but distinct artifact-specific profiles. Across many conditions, CKA decreases substantially while RankMe remains comparatively stable, indicating that artifacts often distort representation geometry without causing dimensional collapse. Segmentation consistency also degrades under corruption, particularly for ghosting and Rician noise, but aligns only partially with representation-level robustness. These findings show that larger-scale or domain-specific pretraining alone does not guarantee artifact invariance and motivate explicit robustness evaluation before deploying 3D foundation models in heterogeneous MRI settings.

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arXiv2026

How Many Labels Are Enough? ALDA: Active Learning Deployment Advisor for Medical Image Classification

Active learning (AL) promises to reduce the cost of medical imaging projects by lowering the number of clinical labels required. However, practical deployment requires committing to a sampling strategy before the full annotation budget is spent, and choosing the wrong strategy can increase rather than decrease costs. We propose Active-Learning Deployment Advisor (ALDA), a deployment-oriented framework for AL method selection under clinical performance constraints. Given a short pilot phase, ALDA fits a parametric learning-curve model to each candidate strategy, estimates whether that strategy is expected to reach a required clinical performance target, and predicts the number of expert annotations needed to do so. In addition to absolute annotation cost, ALDA introduces a deployment window that quantifies the sensitivity of this cost estimate to uncertainty in the clinical threshold. The final recommendation follows a risk-aware rule: among strategies with near-optimal predicted cost, ALDA prefers the strategy with the narrowest deployment window, the most robust to threshold revisions. Experiments on four medical imaging classification domains show that ALDA predicts the deployment-optimal method from a pilot of 15-30% of the intended budget and reduces annotation costs by up to 82% compared with a poor strategy choice. Rather than introducing a new sampling heuristic, ALDA provides a practical decision layer that answers a deployment-critical question: how many labels are enough?

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arXiv2026

A Mechanism-Driven Theory of Phase Transitions in Active Learning

Active learning (AL) performance is known to be budget-dependent, yet regimes are typically defined by heuristic label counts that fail to generalize across datasets or architectures. We characterize AL dynamics by reframing budget regimes as shifts in the dominant generalization mechanism. By reinterpreting PAC-style risk components as dynamic interacting terms, we prove that dominance shifts are structurally unavoidable, creating a moving bottleneck for generalization. We operationalize this using measurable proxies and a segmented regression procedure to identify a tripartite taxonomy: data-driven, transition, and model-driven phases. Our framework explains the long-standing observation that representativeness, coverage, and uncertainty strategies excel at different stages. Experiments across natural and medical imaging show that AL efficiency depends on the alignment between the strategy's inductive bias and the active bottleneck. Moreover, self-supervised representation shift transitions earlier along the labeling trajectory, highlighting the role of representation quality in shaping AL dynamics. Overall, this work provides a unified framework for the next generation of transition-aware AL algorithms.

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arXiv2026

Towards Brain MRI Foundation Models for the Clinic: Findings from the FOMO25 Challenge

Clinical deployment of automated brain MRI analysis faces a fundamental challenge: clinical data is heterogeneous and noisy, and high-quality labels are prohibitively costly to obtain. Self-supervised learning (SSL) can address this by leveraging the vast amounts of unlabeled data produced in clinical workflows to train robust \textit{foundation models} that adapt out-of-domain with minimal supervision. However, the development of foundation models for brain MRI has been limited by small pretraining datasets and in-domain benchmarking focused on high-quality, research-grade data. To address this gap, we organized the FOMO25 challenge as a satellite event at MICCAI 2025. FOMO25 provided participants with a large pretraining dataset, FOMO60K, and evaluated models on data sourced directly from clinical workflows in few-shot and out-of-domain settings. Tasks covered infarct classification, meningioma segmentation, and brain age regression, and considered both models trained on FOMO60K (method track) and any data (open track). Nineteen foundation models from sixteen teams were evaluated using a standardized containerized pipeline. Results show that (a) self-supervised pretraining improves generalization on clinical data under domain shift, with the strongest models trained \textit{out-of-domain} surpassing supervised baselines trained \textit{in-domain}. (b) No single pretraining objective benefits all tasks: MAE favors segmentation, hybrid reconstruction-contrastive objectives favor classification, and (c) strong performance was achieved by small pretrained models, and improvements from scaling model size and training duration did not yield reliable benefits.

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arXiv2026

A large-scale heterogeneous 3D magnetic resonance brain imaging dataset for self-supervised learning

We present FOMO260K, a large-scale, heterogeneous dataset of 260,927 brain Magnetic Resonance Imaging (MRI) scans from 77,589 MRI sessions and 55,378 subjects, aggregated from 910 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing entry barriers for new users. Companion code for self-supervised pretraining and finetuning is provided, along with pretrained models. FOMO260K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

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arXiv2025

Deep Learning-Based Regional White Matter Hyperintensity Mapping as a Robust Biomarker for Alzheimer's Disease

White matter hyperintensities (WMH) are key imaging markers in cognitive aging, Alzheimer's disease (AD), and related dementias. Although automated methods for WMH segmentation have advanced, most provide only global lesion load and overlook their spatial distribution across distinct white matter regions. We propose a deep learning framework for robust WMH segmentation and localization, evaluated across public datasets and an independent Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Our results show that the predicted lesion loads are in line with the reference WMH estimates, confirming the robustness to variations in lesion load, acquisition, and demographics. Beyond accurate segmentation, we quantify WMH load within anatomically defined regions and combine these measures with brain structure volumes to assess diagnostic value. Regional WMH volumes consistently outperform global lesion burden for disease classification, and integration with brain atrophy metrics further improves performance, reaching area under the curve (AUC) values up to 0.97. Several spatially distinct regions, particularly within anterior white matter tracts, are reproducibly associated with diagnostic status, indicating localized vulnerability in AD. These results highlight the added value of regional WMH quantification. Incorporating localized lesion metrics alongside atrophy markers may enhance early diagnosis and stratification in neurodegenerative disorders.

cs.CV↗

arXiv2025

MRI Embeddings Complement Clinical Predictors for Cognitive Decline Modeling in Alzheimer's Disease Cohorts

Accurate modeling of cognitive decline in Alzheimer's disease is essential for early stratification and personalized management. While tabular predictors provide robust markers of global risk, their ability to capture subtle brain changes remains limited. In this study, we evaluate the predictive contributions of tabular and imaging-based representations, with a focus on transformer-derived Magnetic Resonance Imaging (MRI) embeddings. We introduce a trajectory-aware labeling strategy based on Dynamic Time Warping clustering to capture heterogeneous patterns of cognitive change, and train a 3D Vision Transformer (ViT) via unsupervised reconstruction on harmonized and augmented MRI data to obtain anatomy-preserving embeddings without progression labels. The pretrained encoder embeddings are subsequently assessed using both traditional machine learning classifiers and deep learning heads, and compared against tabular representations and convolutional network baselines. Results highlight complementary strengths across modalities. Clinical and volumetric features achieved the highest AUCs of around 0.70 for predicting mild and severe progression, underscoring their utility in capturing global decline trajectories. In contrast, MRI embeddings from the ViT model were most effective in distinguishing cognitively stable individuals with an AUC of 0.71. However, all approaches struggled in the heterogeneous moderate group. These findings indicate that clinical features excel in identifying high-risk extremes, whereas transformer-based MRI embeddings are more sensitive to subtle markers of stability, motivating multimodal fusion strategies for AD progression modeling.

cs.CV↗

arXiv2025

Tooth-Diffusion: Guided 3D CBCT Synthesis with Fine-Grained Tooth Conditioning

Despite the growing importance of dental CBCT scans for diagnosis and treatment planning, generating anatomically realistic scans with fine-grained control remains a challenge in medical image synthesis. In this work, we propose a novel conditional diffusion framework for 3D dental volume generation, guided by tooth-level binary attributes that allow precise control over tooth presence and configuration. Our approach integrates wavelet-based denoising diffusion, FiLM conditioning, and masked loss functions to focus learning on relevant anatomical structures. We evaluate the model across diverse tasks, such as tooth addition, removal, and full dentition synthesis, using both paired and distributional similarity metrics. Results show strong fidelity and generalization with low FID scores, robust inpainting performance, and SSIM values above 0.91 even on unseen scans. By enabling realistic, localized modification of dentition without rescanning, this work opens opportunities for surgical planning, patient communication, and targeted data augmentation in dental AI workflows. The codes are available at: https://github.com/djafar1/tooth-diffusion.

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arXiv2025

To Label or Not to Label: PALM -- A Predictive Model for Evaluating Sample Efficiency in Active Learning Models

Active learning (AL) seeks to reduce annotation costs by selecting the most informative samples for labeling, making it particularly valuable in resource-constrained settings. However, traditional evaluation methods, which focus solely on final accuracy, fail to capture the full dynamics of the learning process. To address this gap, we propose PALM (Performance Analysis of Active Learning Models), a unified and interpretable mathematical model that characterizes AL trajectories through four key parameters: achievable accuracy, coverage efficiency, early-stage performance, and scalability. PALM provides a predictive description of AL behavior from partial observations, enabling the estimation of future performance and facilitating principled comparisons across different strategies. We validate PALM through extensive experiments on CIFAR-10/100 and ImageNet-50/100/200, covering a wide range of AL methods and self-supervised embeddings. Our results demonstrate that PALM generalizes effectively across datasets, budgets, and strategies, accurately predicting full learning curves from limited labeled data. Importantly, PALM reveals crucial insights into learning efficiency, data space coverage, and the scalability of AL methods. By enabling the selection of cost-effective strategies and predicting performance under tight budget constraints, PALM lays the basis for more systematic, reproducible, and data-efficient evaluation of AL in both research and real-world applications. The code is available at: https://github.com/juliamachnio/PALM.

cs.LG↗

arXiv2025

RARE-UNet: Resolution-Aligned Routing Entry for Adaptive Medical Image Segmentation

Accurate segmentation is crucial for clinical applications, but existing models often assume fixed, high-resolution inputs and degrade significantly when faced with lower-resolution data in real-world scenarios. To address this limitation, we propose RARE-UNet, a resolution-aware multi-scale segmentation architecture that dynamically adapts its inference path to the spatial resolution of the input. Central to our design are multi-scale blocks integrated at multiple encoder depths, a resolution-aware routing mechanism, and consistency-driven training that aligns multi-resolution features with full-resolution representations. We evaluate RARE-UNet on two benchmark brain imaging tasks for hippocampus and tumor segmentation. Compared to standard UNet, its multi-resolution augmented variant, and nnUNet, our model achieves the highest average Dice scores of 0.84 and 0.65 across resolution, while maintaining consistent performance and significantly reduced inference time at lower resolutions. These results highlight the effectiveness and scalability of our architecture in achieving resolution-robust segmentation. The codes are available at: https://github.com/simonsejse/RARE-UNet.

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arXiv2025

Towards Scalable and Robust White Matter Lesion Localization via Multimodal Deep Learning

White matter hyperintensities (WMH) are radiological markers of small vessel disease and neurodegeneration, whose accurate segmentation and spatial localization are crucial for diagnosis and monitoring. While multimodal MRI offers complementary contrasts for detecting and contextualizing WM lesions, existing approaches often lack flexibility in handling missing modalities and fail to integrate anatomical localization efficiently. We propose a deep learning framework for WM lesion segmentation and localization that operates directly in native space using single- and multi-modal MRI inputs. Our study evaluates four input configurations: FLAIR-only, T1-only, concatenated FLAIR and T1, and a modality-interchangeable setup. It further introduces a multi-task model for jointly predicting lesion and anatomical region masks to estimate region-wise lesion burden. Experiments conducted on the MICCAI WMH Segmentation Challenge dataset demonstrate that multimodal input significantly improves the segmentation performance, outperforming unimodal models. While the modality-interchangeable setting trades accuracy for robustness, it enables inference in cases with missing modalities. Joint lesion-region segmentation using multi-task learning was less effective than separate models, suggesting representational conflict between tasks. Our findings highlight the utility of multimodal fusion for accurate and robust WMH analysis, and the potential of joint modeling for integrated predictions.

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arXiv2025

Robust Deep Learning for Myocardial Scar Segmentation in Cardiac MRI with Noisy Labels

The accurate segmentation of myocardial scars from cardiac MRI is essential for clinical assessment and treatment planning. In this study, we propose a robust deep-learning pipeline for fully automated myocardial scar detection and segmentation by fine-tuning state-of-the-art models. The method explicitly addresses challenges of label noise from semi-automatic annotations, data heterogeneity, and class imbalance through the use of Kullback-Leibler loss and extensive data augmentation. We evaluate the model's performance on both acute and chronic cases and demonstrate its ability to produce accurate and smooth segmentations despite noisy labels. In particular, our approach outperforms state-of-the-art models like nnU-Net and shows strong generalizability in an out-of-distribution test set, highlighting its robustness across various imaging conditions and clinical tasks. These results establish a reliable foundation for automated myocardial scar quantification and support the broader clinical adoption of deep learning in cardiac imaging.

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arXiv2024

Assessing the Efficacy of Classical and Deep Neuroimaging Biomarkers in Early Alzheimer's Disease Diagnosis

Alzheimer's disease (AD) is the leading cause of dementia, and its early detection is crucial for effective intervention, yet current diagnostic methods often fall short in sensitivity and specificity. This study aims to detect significant indicators of early AD by extracting and integrating various imaging biomarkers, including radiomics, hippocampal texture descriptors, cortical thickness measurements, and deep learning features. We analyze structural magnetic resonance imaging (MRI) scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohorts, utilizing comprehensive image analysis and machine learning techniques. Our results show that combining multiple biomarkers significantly improves detection accuracy. Radiomics and texture features emerged as the most effective predictors for early AD, achieving AUCs of 0.88 and 0.72 for AD and MCI detection, respectively. Although deep learning features proved to be less effective than traditional approaches, incorporating age with other biomarkers notably enhanced MCI detection performance. Additionally, our findings emphasize the continued importance of classical imaging biomarkers in the face of modern deep-learning approaches, providing a robust framework for early AD diagnosis.

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arXiv2024

Yucca: A Deep Learning Framework For Medical Image Analysis

Medical image analysis using deep learning frameworks has advanced healthcare by automating complex tasks, but many existing frameworks lack flexibility, modularity, and user-friendliness. To address these challenges, we introduce Yucca, an open-source AI framework available at https://github.com/Sllambias/yucca, designed specifically for medical imaging applications and built on PyTorch and PyTorch Lightning. Yucca features a three-tiered architecture: Functional, Modules, and Pipeline, providing a comprehensive and customizable solution. Evaluated across diverse tasks such as cerebral microbleeds detection, white matter hyperintensity segmentation, and hippocampus segmentation, Yucca achieves state-of-the-art results, demonstrating its robustness and versatility. Yucca offers a powerful, flexible, and user-friendly platform for medical image analysis, inviting community contributions to advance its capabilities and impact.

cs.CV↗

arXiv2024

Non-Reference Quality Assessment for Medical Imaging: Application to Synthetic Brain MRIs

Generating high-quality synthetic data is crucial for addressing challenges in medical imaging, such as domain adaptation, data scarcity, and privacy concerns. Existing image quality metrics often rely on reference images, are tailored for group comparisons, or are intended for 2D natural images, limiting their efficacy in complex domains like medical imaging. This study introduces a novel deep learning-based non-reference approach to assess brain MRI quality by training a 3D ResNet. The network is designed to estimate quality across six distinct artifacts commonly encountered in MRI scans. Additionally, a diffusion model is trained on diverse datasets to generate synthetic 3D images of high fidelity. The approach leverages several datasets for training and comprehensive quality assessment, benchmarking against state-of-the-art metrics for real and synthetic images. Results demonstrate superior performance in accurately estimating distortions and reflecting image quality from multiple perspectives. Notably, the method operates without reference images, indicating its applicability for evaluating deep generative models. Besides, the quality scores in the [0, 1] range provide an intuitive assessment of image quality across heterogeneous datasets. Evaluation of generated images offers detailed insights into specific artifacts, guiding strategies for improving generative models to produce high-quality synthetic images. This study presents the first comprehensive method for assessing the quality of real and synthetic 3D medical images in MRI contexts without reliance on reference images.

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