arXiv subjects

Ulas Bagci

Publications and source records attributed to Ulas Bagci.

At least 55 records · Page 3Linked to original sources

arXiv2026

What They Saw, Not Just Where They Looked: Semantic Scanpath Similarity via VLMs and NLP metric

Scanpath similarity metrics are central to eye-movement research, yet existing methods predominantly evaluate spatial and temporal alignment while neglecting semantic equivalence between attended image regions. We present a semantic scanpath similarity framework that integrates vision-language models (VLMs) into eye-tracking analysis. Each fixation is encoded under controlled visual context (patch-based and marker-based strategies) and transformed into concise textual descriptions, which are aggregated into scanpath-level representations. Semantic similarity is then computed using embedding-based and lexical NLP metrics and compared against established spatial measures, including MultiMatch and DTW. Experiments on free-viewing eye-tracking data demonstrate that semantic similarity captures partially independent variance from geometric alignment, revealing cases of high content agreement despite spatial divergence. We further analyze the impact of contextual encoding on description fidelity and metric stability. Our findings suggest that multimodal foundation models enable interpretable, content-aware extensions of classical scanpath analysis, providing a complementary dimension for gaze research within the ETRA community.

cs.CV↗

arXiv2026

PRS-Med: Position Reasoning Segmentation in Medical Imaging

Prompt-based medical image segmentation has rapidly emerged, yet existing methods rely on explicit prompts like bounding boxes and struggle to reason about the spatial relationships essential for clinical diagnosis. While general-domain models attempt complex coordinate regression, these approaches often lack the structured reliability required for medical applications. In this work, we introduce PRS-Med, a unified framework that adopts an elegant, clinical-first approach to position reasoning segmentation. By utilizing a medical vision-language model integrated with a segmentation decoder, PRS-Med mimics the structured "search patterns" used by radiologists to identify pathologies within specific anatomical zones. To support this robust reasoning, we present the Medical Position Reasoning Segmentation (PosMed) dataset, comprising 116,000 expert-validated, spatially grounded question-answer pairs across six imaging modalities. Unlike previous brittle attempts at spatial reasoning, PosMed leverages a scalable, deterministic pipeline validated by board-certified radiologists to ensure clinical accuracy. Extensive experiments demonstrate that our zone-based reasoning not only improves segmentation accuracy (mean Dice improvements up to +31.2\%) but also provides a high-confidence interpretability layer that outperforms state-of-the-art complex reasoning models. By prioritizing functional reliability over unnecessary technical complexity, PRS-Med offers a practical and scalable baseline for the next generation of intelligent medical assistants.

cs.CV↗

arXiv2026

REN: Anatomically-Informed Mixture-of-Experts for Interstitial Lung Disease Diagnosis

Mixture-of-Experts (MoE) architectures achieve scalable learning by routing inputs to specialized subnetworks through conditional computation. However, conventional MoE designs assume homogeneous expert capability and domain-agnostic routing-assumptions that are fundamentally misaligned with medical imaging, where anatomical structure and regional disease heterogeneity govern pathological patterns. We introduce Regional Expert Networks (REN), the first anatomically-informed MoE framework for medical image classification. REN encodes anatomical priors by training seven specialized experts, each dedicated to a distinct lung lobe or bilateral lung combination, enabling precise modeling of region-specific pathological variation. Multi-modal gating mechanisms dynamically integrate radiomics biomarkers with deep learning (DL) features extracted by convolutional (CNN), Transformer (ViT), and state-space (Mamba) architectures to weight expert contributions at inference. Applied to interstitial lung disease (ILD) classification on a 597-patient, 1,898-scan longitudinal cohort, REN achieves consistently superior performance: the radiomics-guided ensemble attains an average AUC of 0.8646 +- 0.0467, a +12.5 % improvement over the SwinUNETR single-model baseline (AUC 0.7685, p=0.031). Lower-lobe experts reach AUCs of 0.88-0.90, outperforming DL baselines (CNN: 0.76-0.79) and mirroring known patterns of basal ILD progression. Evaluated under rigorous patient-level cross-validation, REN demonstrates strong generalizability and clinical interpretability, establishing a scalable, anatomically-guided framework potentially extensible to other structured medical imaging tasks. Code is available on our GitHub https://github.com/NUBagciLab/MoE-REN.

cs.CV↗

arXiv2026

Robust White Blood Cell Classification with Stain-Normalized Decoupled Learning and Ensembling

White blood cell (WBC) classification is fundamental for hematology applications such as infection assessment, leukemia screening, and treatment monitoring. However, real-world WBC datasets present substantial appearance variations caused by staining and scanning conditions, as well as severe class imbalance in which common cell types dominate while rare but clinically important categories are underrepresented. To address these challenges, we propose a stain-normalized, decoupled training framework that first learns transferable representations using instance-balanced sampling, and then rebalances the classifier with class-aware sampling and a hybrid loss combining effective-number weighting and focal modulation. In inference stage, we further enhance robustness by ensembling various trained backbones with test-time augmentation. Our approach achieved the top rank on the leaderboard of the WBCBench 2026: Robust White Blood Cell Classification Challenge at ISBI 2026.

cs.CV↗

arXiv2026

Handling Supervision Scarcity in Chest X-ray Classification: Long-Tailed and Zero-Shot Learning

Chest X-Ray (CXR) classification in clinical practice is often limited by imperfect supervision, arising from (i) extreme long-tailed multi-label disease distributions and (ii) missing annotations for rare or previously unseen findings. The CXR-LT 2026 challenge addresses these issues on a PadChest-based benchmark with a 36-class label space split into 30 in-distribution classes for training and 6 out-of-distribution (OOD) classes for zero-shot evaluation. We present task-specific solutions tailored to the distinct supervision regimes. For Task 1 (long-tailed multi-label classification), we adopt an imbalance-aware multi-label learning strategy to improve recognition of tail classes while maintaining stable performance on frequent findings. For Task 2 (zero-shot OOD recognition), we propose a prediction approach that produces scores for unseen disease categories without using any supervised labels or examples from the OOD classes during training. Evaluated with macro-averaged mean Average Precision (mAP), our method achieves strong performance on both tasks, ranking first on the public leaderboard of the development phase. Code and pre-trained models are available at https://github.com/hieuphamha19/CXR_LT.

cs.CV↗

arXiv2026

Scribble-Supervised Medical Image Segmentation with Dynamic Teacher Switching and Hierarchical Consistency

Scribble-supervised methods have emerged to mitigate the prohibitive annotation burden in medical image segmentation. However, the inherent sparsity of these annotations introduces significant ambiguity, which results in noisy pseudo-label propagation and hinders the learning of robust anatomical boundaries. To address this challenge, we propose SDT-Net, a novel dual-teacher, single-student framework designed to maximize supervision quality from these weak signals. Our method features a Dynamic Teacher Switching (DTS) module to adaptively select the most reliable teacher. This selected teacher then guides the student via two synergistic mechanisms: high-confidence pseudo-labels, refined by a Pick Reliable Pixels (PRP) mechanism, and multi-level feature alignment, enforced by a Hierarchical Consistency (HiCo) module. Extensive experiments on the ACDC and MSCMRseg datasets demonstrate that SDT-Net achieves state-of-the-art performance, producing more accurate and anatomically plausible segmentation.

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arXiv2026

Domain-invariant Mixed-domain Semi-supervised Medical Image Segmentation with Clustered Maximum Mean Discrepancy Alignment

Deep learning has shown remarkable progress in medical image semantic segmentation, yet its success heavily depends on large-scale expert annotations and consistent data distributions. In practice, annotations are scarce, and images are collected from multiple scanners or centers, leading to mixed-domain settings with unknown domain labels and severe domain gaps. Existing semi-supervised or domain adaptation approaches typically assume either a single domain shift or access to explicit domain indices, which rarely hold in real-world deployment. In this paper, we propose a domain-invariant mixed-domain semi-supervised segmentation framework that jointly enhances data diversity and mitigates domain bias. A Copy-Paste Mechanism (CPM) augments the training set by transferring informative regions across domains, while a Cluster Maximum Mean Discrepancy (CMMD) block clusters unlabeled features and aligns them with labeled anchors via an MMD objective, encouraging domain-invariant representations. Integrated within a teacher-student framework, our method achieves robust and precise segmentation even with very few labeled examples and multiple unknown domain discrepancies. Experiments on Fundus and M&Ms benchmarks demonstrate that our approach consistently surpasses semi-supervised and domain adaptation methods, establishing a potential solution for mixed-domain semi-supervised medical image segmentation.

cs.CV↗

arXiv2026

VHU-Net: Variational Hadamard U-Net for Body MRI Bias Field Correction

Bias field artifacts in magnetic resonance imaging (MRI) scans introduce spatially smooth intensity inhomogeneities that degrade image quality and hinder downstream analysis. To address this challenge, we propose a novel variational Hadamard U-Net (VHU-Net) for effective body MRI bias field correction. The encoder comprises multiple convolutional Hadamard transform blocks (ConvHTBlocks), each integrating convolutional layers with a Hadamard transform (HT) layer. Specifically, the HT layer performs channel-wise frequency decomposition to isolate low-frequency components, while a subsequent scaling layer and semi-soft thresholding mechanism suppress redundant high-frequency noise. To compensate for the HT layer's inability to model inter-channel dependencies, the decoder incorporates an inverse HT-reconstructed transformer block, enabling global, frequency-aware attention for the recovery of spatially consistent bias fields. The stacked decoder ConvHTBlocks further enhance the capacity to reconstruct the underlying ground-truth bias field. Building on the principles of variational inference, we formulate a new evidence lower bound (ELBO) as the training objective, promoting sparsity in the latent space while ensuring accurate bias field estimation. Comprehensive experiments on body MRI datasets demonstrate the superiority of VHU-Net over existing state-of-the-art methods in terms of intensity uniformity. Moreover, the corrected images yield substantial downstream improvements in segmentation accuracy. Our framework offers computational efficiency, interpretability, and robust performance across multi-center datasets, making it suitable for clinical deployment.

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arXiv2026

CTest-Metric: A Unified Framework to Assess Clinical Validity of Metrics for CT Report Generation

In the generative AI era, where even critical medical tasks are increasingly automated, radiology report generation (RRG) continues to rely on suboptimal metrics for quality assessment. Developing domain-specific metrics has therefore been an active area of research, yet it remains challenging due to the lack of a unified, well-defined framework to assess their robustness and applicability in clinical contexts. To address this, we present CTest-Metric, a first unified metric assessment framework with three modules determining the clinical feasibility of metrics for CT RRG. The modules test: (i) Writing Style Generalizability (WSG) via LLM-based rephrasing; (ii) Synthetic Error Injection (SEI) at graded severities; and (iii) Metrics-vs-Expert correlation (MvE) using clinician ratings on 175 "disagreement" cases. Eight widely used metrics (BLEU, ROUGE, METEOR, BERTScore-F1, F1-RadGraph, RaTEScore, GREEN Score, CRG) are studied across seven LLMs built on a CT-CLIP encoder. Using our novel framework, we found that lexical NLG metrics are highly sensitive to stylistic variations; GREEN Score aligns best with expert judgments (Spearman~0.70), while CRG shows negative correlation; and BERTScore-F1 is least sensitive to factual error injection. We will release the framework, code, and allowable portion of the anonymized evaluation data (rephrased/error-injected CT reports), to facilitate reproducible benchmarking and future metric development.

cs.CL↗

arXiv2026

Ensemble Models for Predicting Treatment Response in Pediatric Low-Grade Glioma Managed with Chemotherapy

In this paper, we introduce a novel pipeline for predicting chemotherapy response in pediatric brain tumors that are not amenable to complete surgical resection, using pre-treatment magnetic resonance imaging combined with clinical information. Our method integrates a state-of-the-art pediatric brain tumor segmentation framework with radiomic feature extraction and clinical data through an ensemble of a Swin UNETR encoder and XGBoost classifier. The segmentation model delineates four tumor subregions enhancing tumor, non-enhancing tumor, cystic component and edema which are used to extract imaging biomarkers and generate predictive features. The Swin UNETR network classifies the response to treatment directly from these segmented MRI scans, while XGBoost predicts response using radiomics and clinical variables including legal sex, ethnicity, race, age at event (in days), molecular subtype, tumor locations, initial surgery status, metastatic status, metastasis location, chemotherapy type, protocol name and chemotherapy agents. The ensemble output provides a non-invasive estimate of chemotherapy response in this historically challenging population characterized by lower progression-free survival. Among compared approaches, our Swin-Ensemble achieved the best performance (precision for non effective cases=0.68, recall for non effective cases=0.85, precision for chemotherapy effective cases=0.64 and overall accuracy=0.69), outperforming Mamba-FeatureFuse, Swin UNETR encoder, and Swin-FeatureFuse models. Our findings suggest that this ensemble framework represents a promising step toward personalized therapy response prediction for pediatric low-grade glioma patients in need of chemotherapy treatment who are not suitable for complete surgical resection, a population with significantly lower progression free survival and for whom chemotherapy remains the primary treatment option.

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arXiv2025

ProDM: Synthetic Reality-driven Property-aware Progressive Diffusion Model for Coronary Calcium Motion Correction in Non-gated Chest CT

Coronary artery calcium (CAC) scoring from chest CT is a well-established tool to stratify and refine clinical cardiovascular disease risk estimation. CAC quantification relies on the accurate delineation of calcified lesions, but is oftentimes affected by artifacts introduced by cardiac and respiratory motion. ECG-gated cardiac CTs substantially reduce motion artifacts, but their use in population screening and routine imaging remains limited due to gating requirements and lack of insurance coverage. Although identification of incidental CAC from non-gated chest CT is increasingly considered for it offers an accessible and widely available alternative, this modality is limited by more severe motion artifacts. We present ProDM (Property-aware Progressive Correction Diffusion Model), a generative diffusion framework that restores motion-free calcified lesions from non-gated CTs. ProDM introduces three key components: (1) a CAC motion simulation data engine that synthesizes realistic non-gated acquisitions with diverse motion trajectories directly from cardiac-gated CTs, enabling supervised training without paired data; (2) a property-aware learning strategy incorporating calcium-specific priors through a differentiable calcium consistency loss to preserve lesion integrity; and (3) a progressive correction scheme that reduces artifacts gradually across diffusion steps to enhance stability and calcium fidelity. Experiments on real patient datasets show that ProDM significantly improves CAC scoring accuracy, spatial lesion fidelity, and risk stratification performance compared with several baselines. A reader study on real non-gated scans further confirms that ProDM suppresses motion artifacts and improves clinical usability. These findings highlight the potential of progressive, property-aware frameworks for reliable CAC quantification from routine chest CT imaging.

cs.CV↗

arXiv2025

DuetMatch: Harmonizing Semi-Supervised Brain MRI Segmentation via Decoupled Branch Optimization

The limited availability of annotated data in medical imaging makes semi-supervised learning increasingly appealing for its ability to learn from imperfect supervision. Recently, teacher-student frameworks have gained popularity for their training benefits and robust performance. However, jointly optimizing the entire network can hinder convergence and stability, especially in challenging scenarios. To address this for medical image segmentation, we propose DuetMatch, a novel dual-branch semi-supervised framework with asynchronous optimization, where each branch optimizes either the encoder or decoder while keeping the other frozen. To improve consistency under noisy conditions, we introduce Decoupled Dropout Perturbation, enforcing regularization across branches. We also design Pair-wise CutMix Cross-Guidance to enhance model diversity by exchanging pseudo-labels through augmented input pairs. To mitigate confirmation bias from noisy pseudo-labels, we propose Consistency Matching, refining labels using stable predictions from frozen teacher models. Extensive experiments on benchmark brain MRI segmentation datasets, including ISLES2022 and BraTS, show that DuetMatch consistently outperforms state-of-the-art methods, demonstrating its effectiveness and robustness across diverse semi-supervised segmentation scenarios.

cs.CV↗

arXiv2025

Upstream Probabilistic Meta-Imputation for Multimodal Pediatric Pancreatitis Classification

Pediatric pancreatitis is a progressive and debilitating inflammatory condition, including acute pancreatitis and chronic pancreatitis, that presents significant clinical diagnostic challenges. Machine learning-based methods also face diagnostic challenges due to limited sample availability and multimodal imaging complexity. To address these challenges, this paper introduces Upstream Probabilistic Meta-Imputation (UPMI), a light-weight augmentation strategy that operates upstream of a meta-learner in a low-dimensional meta-feature space rather than in image space. Modality-specific logistic regressions (T1W and T2W MRI radiomics) produce probability outputs that are transformed into a 7-dimensional meta-feature vector. Class-conditional Gaussian mixture models (GMMs) are then fit within each cross-validation fold to sample synthetic meta-features that, combined with real meta-features, train a Random Forest (RF) meta-classifier. On 67 pediatric subjects with paired T1W/T2W MRIs, UPMI achieves a mean AUC of 0.908 $\pm$ 0.072, a $\sim$5% relative gain over a real-only baseline (AUC 0.864 $\pm$ 0.061).

cs.CV↗

arXiv2025

GMAT: Grounded Multi-Agent Clinical Description Generation for Text Encoder in Vision-Language MIL for Whole Slide Image Classification

Multiple Instance Learning (MIL) is the leading approach for whole slide image (WSI) classification, enabling efficient analysis of gigapixel pathology slides. Recent work has introduced vision-language models (VLMs) into MIL pipelines to incorporate medical knowledge through text-based class descriptions rather than simple class names. However, when these methods rely on large language models (LLMs) to generate clinical descriptions or use fixed-length prompts to represent complex pathology concepts, the limited token capacity of VLMs often constrains the expressiveness and richness of the encoded class information. Additionally, descriptions generated solely by LLMs may lack domain grounding and fine-grained medical specificity, leading to suboptimal alignment with visual features. To address these challenges, we propose a vision-language MIL framework with two key contributions: (1) A grounded multi-agent description generation system that leverages curated pathology textbooks and agent specialization (e.g., morphology, spatial context) to produce accurate and diverse clinical descriptions; (2) A text encoding strategy using a list of descriptions rather than a single prompt, capturing fine-grained and complementary clinical signals for better alignment with visual features. Integrated into a VLM-MIL pipeline, our approach shows improved performance over single-prompt class baselines and achieves results comparable to state-of-the-art models, as demonstrated on renal and lung cancer datasets.

cs.CV↗

arXiv2025

MammoClean: Toward Reproducible and Bias-Aware AI in Mammography through Dataset Harmonization

The development of clinically reliable artificial intelligence (AI) systems for mammography is hindered by profound heterogeneity in data quality, metadata standards, and population distributions across public datasets. This heterogeneity introduces dataset-specific biases that severely compromise the generalizability of the model, a fundamental barrier to clinical deployment. We present MammoClean, a public framework for standardization and bias quantification in mammography datasets. MammoClean standardizes case selection, image processing (including laterality and intensity correction), and unifies metadata into a consistent multi-view structure. We provide a comprehensive review of breast anatomy, imaging characteristics, and public mammography datasets to systematically identify key sources of bias. Applying MammoClean to three heterogeneous datasets (CBIS-DDSM, TOMPEI-CMMD, VinDr-Mammo), we quantify substantial distributional shifts in breast density and abnormality prevalence. Critically, we demonstrate the direct impact of data corruption: AI models trained on corrupted datasets exhibit significant performance degradation compared to their curated counterparts. By using MammoClean to identify and mitigate bias sources, researchers can construct unified multi-dataset training corpora that enable development of robust models with superior cross-domain generalization. MammoClean provides an essential, reproducible pipeline for bias-aware AI development in mammography, facilitating fairer comparisons and advancing the creation of safe, effective systems that perform equitably across diverse patient populations and clinical settings. The open-source code is publicly available from: https://github.com/Minds-R-Lab/MammoClean.

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arXiv2025

Aligning What You Separate: Denoised Patch Mixing for Source-Free Domain Adaptation in Medical Image Segmentation

Source-Free Domain Adaptation (SFDA) is emerging as a compelling solution for medical image segmentation under privacy constraints, yet current approaches often ignore sample difficulty and struggle with noisy supervision under domain shift. We present a new SFDA framework that leverages Hard Sample Selection and Denoised Patch Mixing to progressively align target distributions. First, unlabeled images are partitioned into reliable and unreliable subsets through entropy-similarity analysis, allowing adaptation to start from easy samples and gradually incorporate harder ones. Next, pseudo-labels are refined via Monte Carlo-based denoising masks, which suppress unreliable pixels and stabilize training. Finally, intra- and inter-domain objectives mix patches between subsets, transferring reliable semantics while mitigating noise. Experiments on benchmark datasets show consistent gains over prior SFDA and UDA methods, delivering more accurate boundary delineation and achieving state-of-the-art Dice and ASSD scores. Our study highlights the importance of progressive adaptation and denoised supervision for robust segmentation under domain shift.

cs.CV↗

arXiv2025

UP2D: Uncertainty-aware Progressive Pseudo-label Denoising for Source-Free Domain Adaptive Medical Image Segmentation

Medical image segmentation models face severe performance drops under domain shifts, especially when data sharing constraints prevent access to source images. We present a novel Uncertainty-aware Progressive Pseudo-label Denoising (UP2D) framework for source-free domain adaptation (SFDA), designed to mitigate noisy pseudo-labels and class imbalance during adaptation. UP2D integrates three key components: (i) a Refined Prototype Filtering module that suppresses uninformative regions and constructs reliable class prototypes to denoise pseudo-labels, (ii) an Uncertainty-Guided EMA (UG-EMA) strategy that selectively updates the teacher model based on spatially weighted boundary uncertainty, and (iii) a quantile-based entropy minimization scheme that focuses learning on ambiguous regions while avoiding overconfidence on easy pixels. This single-stage student-teacher framework progressively improves pseudo-label quality and reduces confirmation bias. Extensive experiments on three challenging retinal fundus benchmarks demonstrate that UP2D achieves state-of-the-art performance across both standard and open-domain settings, outperforming prior UDA and SFDA approaches while maintaining superior boundary precision.

eess.IV↗

arXiv2025

Morphology-Aware KOA Classification: Integrating Graph Priors with Vision Models

Knee osteoarthritis (KOA) diagnosis from radiographs remains challenging due to the subtle morphological details that standard deep learning models struggle to capture effectively. We propose a novel multimodal framework that combines anatomical structure with radiographic features by integrating a morphological graph representation - derived from Segment Anything Model (SAM) segmentations - with a vision encoder. Our approach enforces alignment between geometry-informed graph embeddings and radiographic features through mutual information maximization, significantly improving KOA classification accuracy. By constructing graphs from anatomical features, we introduce explicit morphological priors that mirror clinical assessment criteria, enriching the feature space and enhancing the model's inductive bias. Experiments on the Osteoarthritis Initiative dataset demonstrate that our approach surpasses single-modality baselines by up to 10\% in accuracy (reaching nearly 80\%), while outperforming existing state-of-the-art methods by 8\% in accuracy and 11\% in F1 score. These results underscore the critical importance of incorporating anatomical structure into radiographic analysis for accurate KOA severity grading.

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