arXiv subjects

Ulas Bagci

Publications and source records attributed to Ulas Bagci.

At least 73 records · Page 4Linked to original sources

arXiv2025

VideoAds for Fast-Paced Video Understanding

Advertisement videos serve as a rich and valuable source of purpose-driven information, encompassing high-quality visual, textual, and contextual cues designed to engage viewers. They are often more complex than general videos of similar duration due to their structured narratives and rapid scene transitions, posing significant challenges to multi-modal large language models (MLLMs). In this work, we introduce VideoAds, the first dataset tailored for benchmarking the performance of MLLMs on advertisement videos. VideoAds comprises well-curated advertisement videos with complex temporal structures, accompanied by \textbf{manually} annotated diverse questions across three core tasks: visual finding, video summary, and visual reasoning. We propose a quantitative measure to compare VideoAds against existing benchmarks in terms of video complexity. Through extensive experiments, we find that Qwen2.5-VL-72B, an opensource MLLM, achieves 73.35\% accuracy on VideoAds, outperforming GPT-4o (66.82\%) and Gemini-1.5 Pro (69.66\%); the two proprietary models especially fall behind the opensource model in video summarization and reasoning, but perform the best in visual finding. Notably, human experts easily achieve a remarkable accuracy of 94.27\%. These results underscore the necessity of advancing MLLMs' temporal modeling capabilities and highlight VideoAds as a potentially pivotal benchmark for future research in understanding video that requires high FPS sampling. The dataset and evaluation code will be publicly available at https://videoadsbenchmark.netlify.app.

cs.CV↗

arXiv2025

Pancreas Part Segmentation under Federated Learning Paradigm

We present the first federated learning (FL) approach for pancreas part(head, body and tail) segmentation in MRI, addressing a critical clinical challenge as a significant innovation. Pancreatic diseases exhibit marked regional heterogeneity cancers predominantly occur in the head region while chronic pancreatitis causes tissue loss in the tail, making accurate segmentation of the organ into head, body, and tail regions essential for precise diagnosis and treatment planning. This segmentation task remains exceptionally challenging in MRI due to variable morphology, poor soft-tissue contrast, and anatomical variations across patients. Our novel contribution tackles two fundamental challenges: first, the technical complexity of pancreas part delineation in MRI, and second the data scarcity problem that has hindered prior approaches. We introduce a privacy-preserving FL framework that enables collaborative model training across seven medical institutions without direct data sharing, leveraging a diverse dataset of 711 T1W and 726 T2W MRI scans. Our key innovations include: (1) a systematic evaluation of three state-of-the-art segmentation architectures (U-Net, Attention U-Net,Swin UNETR) paired with two FL algorithms (FedAvg, FedProx), revealing Attention U-Net with FedAvg as optimal for pancreatic heterogeneity, which was never been done before; (2) a novel anatomically-informed loss function prioritizing region-specific texture contrasts in MRI. Comprehensive evaluation demonstrates that our approach achieves clinically viable performance despite training on distributed, heterogeneous datasets.

cs.CV↗

arXiv2025

Imaging-Based Mortality Prediction in Patients with Systemic Sclerosis

Interstitial lung disease (ILD) is a leading cause of morbidity and mortality in systemic sclerosis (SSc). Chest computed tomography (CT) is the primary imaging modality for diagnosing and monitoring lung complications in SSc patients. However, its role in disease progression and mortality prediction has not yet been fully clarified. This study introduces a novel, large-scale longitudinal chest CT analysis framework that utilizes radiomics and deep learning to predict mortality associated with lung complications of SSc. We collected and analyzed 2,125 CT scans from SSc patients enrolled in the Northwestern Scleroderma Registry, conducting mortality analyses at one, three, and five years using advanced imaging analysis techniques. Death labels were assigned based on recorded deaths over the one-, three-, and five-year intervals, confirmed by expert physicians. In our dataset, 181, 326, and 428 of the 2,125 CT scans were from patients who died within one, three, and five years, respectively. Using ResNet-18, DenseNet-121, and Swin Transformer we use pre-trained models, and fine-tuned on 2,125 images of SSc patients. Models achieved an AUC of 0.769, 0.801, 0.709 for predicting mortality within one-, three-, and five-years, respectively. Our findings highlight the potential of both radiomics and deep learning computational methods to improve early detection and risk assessment of SSc-related interstitial lung disease, marking a significant advancement in the literature.

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arXiv2025

Graph-Radiomic Learning (GrRAiL) Descriptor to Characterize Imaging Heterogeneity in Confounding Tumor Pathologies

A significant challenge in solid tumors is reliably distinguishing confounding pathologies from malignant neoplasms on routine imaging. While radiomics methods seek surrogate markers of lesion heterogeneity on CT/MRI, many aggregate features across the region of interest (ROI) and miss complex spatial relationships among varying intensity compositions. We present a new Graph-Radiomic Learning (GrRAiL) descriptor for characterizing intralesional heterogeneity (ILH) on clinical MRI scans. GrRAiL (1) identifies clusters of sub-regions using per-voxel radiomic measurements, then (2) computes graph-theoretic metrics to quantify spatial associations among clusters. The resulting weighted graphs encode higher-order spatial relationships within the ROI, aiming to reliably capture ILH and disambiguate confounding pathologies from malignancy. To assess efficacy and clinical feasibility, GrRAiL was evaluated in n=947 subjects spanning three use cases: differentiating tumor recurrence from radiation effects in glioblastoma (GBM; n=106) and brain metastasis (n=233), and stratifying pancreatic intraductal papillary mucinous neoplasms (IPMNs) into no+low vs high risk (n=608). In a multi-institutional setting, GrRAiL consistently outperformed state-of-the-art baselines - Graph Neural Networks (GNNs), textural radiomics, and intensity-graph analysis. In GBM, cross-validation (CV) and test accuracies for recurrence vs pseudo-progression were 89% and 78% with >10% test-accuracy gains over comparators. In brain metastasis, CV and test accuracies for recurrence vs radiation necrosis were 84% and 74% (>13% improvement). For IPMN risk stratification, CV and test accuracies were 84% and 75%, showing >10% improvement.

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arXiv2025

TAGS: 3D Tumor-Adaptive Guidance for SAM

Foundation models (FMs) such as CLIP and SAM have recently shown great promise in image segmentation tasks, yet their adaptation to 3D medical imaging-particularly for pathology detection and segmentation-remains underexplored. A critical challenge arises from the domain gap between natural images and medical volumes: existing FMs, pre-trained on 2D data, struggle to capture 3D anatomical context, limiting their utility in clinical applications like tumor segmentation. To address this, we propose an adaptation framework called TAGS: Tumor Adaptive Guidance for SAM, which unlocks 2D FMs for 3D medical tasks through multi-prompt fusion. By preserving most of the pre-trained weights, our approach enhances SAM's spatial feature extraction using CLIP's semantic insights and anatomy-specific prompts. Extensive experiments on three open-source tumor segmentation datasets prove that our model surpasses the state-of-the-art medical image segmentation models (+46.88% over nnUNet), interactive segmentation frameworks, and other established medical FMs, including SAM-Med2D, SAM-Med3D, SegVol, Universal, 3D-Adapter, and SAM-B (at least +13% over them). This highlights the robustness and adaptability of our proposed framework across diverse medical segmentation tasks.

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arXiv2025

Learning Disentangled Stain and Structural Representations for Semi-Supervised Histopathology Segmentation

Accurate gland segmentation in histopathology images is essential for cancer diagnosis and prognosis. However, significant variability in Hematoxylin and Eosin (H&E) staining and tissue morphology, combined with limited annotated data, poses major challenges for automated segmentation. To address this, we propose Color-Structure Dual-Student (CSDS), a novel semi-supervised segmentation framework designed to learn disentangled representations of stain appearance and tissue structure. CSDS comprises two specialized student networks: one trained on stain-augmented inputs to model chromatic variation, and the other on structure-augmented inputs to capture morphological cues. A shared teacher network, updated via Exponential Moving Average (EMA), supervises both students through pseudo-labels. To further improve label reliability, we introduce stain-aware and structure-aware uncertainty estimation modules that adaptively modulate the contribution of each student during training. Experiments on the GlaS and CRAG datasets show that CSDS achieves state-of-the-art performance in low-label settings, with Dice score improvements of up to 1.2% on GlaS and 0.7% on CRAG at 5% labeled data, and 0.7% and 1.4% at 10%. Our code and pre-trained models are available at https://github.com/hieuphamha19/CSDS.

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arXiv2025

Describe Anything Model for Visual Question Answering on Text-rich Images

Recent progress has been made in region-aware vision-language modeling, particularly with the emergence of the Describe Anything Model (DAM). DAM is capable of generating detailed descriptions of any specific image areas or objects without the need for additional localized image-text alignment supervision. We hypothesize that such region-level descriptive capability is beneficial for the task of Visual Question Answering (VQA), especially in challenging scenarios involving images with dense text. In such settings, the fine-grained extraction of textual information is crucial to producing correct answers. Motivated by this, we introduce DAM-QA, a framework with a tailored evaluation protocol, developed to investigate and harness the region-aware capabilities from DAM for the text-rich VQA problem that requires reasoning over text-based information within images. DAM-QA incorporates a mechanism that aggregates answers from multiple regional views of image content, enabling more effective identification of evidence that may be tied to text-related elements. Experiments on six VQA benchmarks show that our approach consistently outperforms the baseline DAM, with a notable 7+ point gain on DocVQA. DAM-QA also achieves the best overall performance among region-aware models with fewer parameters, significantly narrowing the gap with strong generalist VLMs. These results highlight the potential of DAM-like models for text-rich and broader VQA tasks when paired with efficient usage and integration strategies. Our code is publicly available at https://github.com/Linvyl/DAM-QA.git.

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arXiv2025

Rethink Domain Generalization in Heterogeneous Sequence MRI Segmentation

Clinical magnetic-resonance (MR) protocols generate many T1 and T2 sequences whose appearance differs more than the acquisition sites that produce them. Existing domain-generalization benchmarks focus almost on cross-center shifts and overlook this dominant source of variability. Pancreas segmentation remains a major challenge in abdominal imaging: the gland is small, irregularly, surrounded by organs and fat, and often suffers from low T1 contrast. State-of-the-art deep networks that already achieve >90% Dice on the liver or kidneys still miss 20-30% of the pancreas. The organ is also systematically under-represented in public cross-domain benchmarks, despite its clinical importance in early cancer detection, surgery, and diabetes research. To close this gap, we present PancreasDG, a large-scale multi-center 3D MRI pancreas segmentation dataset for investigating domain generalization in medical imaging. The dataset comprises 563 MRI scans from six institutions, spanning both venous phase and out-of-phase sequences, enabling study of both cross-center and cross-sequence variations with pixel-accurate pancreas masks created by a double-blind, two-pass protocol. Through comprehensive analysis, we reveal three insights: (i) limited sampling introduces significant variance that may be mistaken for distribution shifts, (ii) cross-center performance correlates with source domain performance for identical sequences, and (iii) cross-sequence shifts require specialized solutions. We also propose a semi-supervised approach that leverages anatomical invariances, significantly outperforming state-of-the-art domain generalization techniques with 61.63% Dice score improvements and 87.00% on two test centers for cross-sequence segmentation. PancreasDG sets a new benchmark for domain generalization in medical imaging. Dataset, code, and models will be available at https://pancreasdg.netlify.app.

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arXiv2025

ViCTr: Vital Consistency Transfer for Pathology Aware Image Synthesis

Synthesizing medical images remains challenging due to limited annotated pathological data, modality domain gaps, and the complexity of representing diffuse pathologies such as liver cirrhosis. Existing methods often struggle to maintain anatomical fidelity while accurately modeling pathological features, frequently relying on priors derived from natural images or inefficient multi-step sampling. In this work, we introduce ViCTr (Vital Consistency Transfer), a novel two-stage framework that combines a rectified flow trajectory with a Tweedie-corrected diffusion process to achieve high-fidelity, pathology-aware image synthesis. First, we pretrain ViCTr on the ATLAS-8k dataset using Elastic Weight Consolidation (EWC) to preserve critical anatomical structures. We then fine-tune the model adversarially with Low-Rank Adaptation (LoRA) modules for precise control over pathology severity. By reformulating Tweedie's formula within a linear trajectory framework, ViCTr supports one-step sampling, reducing inference from 50 steps to just 4, without sacrificing anatomical realism. We evaluate ViCTr on BTCV (CT), AMOS (MRI), and CirrMRI600+ (cirrhosis) datasets. Results demonstrate state-of-the-art performance, achieving a Medical Frechet Inception Distance (MFID) of 17.01 for cirrhosis synthesis 28% lower than existing approaches and improving nnUNet segmentation by +3.8% mDSC when used for data augmentation. Radiologist reviews indicate that ViCTr-generated liver cirrhosis MRIs are clinically indistinguishable from real scans. To our knowledge, ViCTr is the first method to provide fine-grained, pathology-aware MRI synthesis with graded severity control, closing a critical gap in AI-driven medical imaging research.

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arXiv2025

Analysis of the 2024 BraTS Meningioma Radiotherapy Planning Automated Segmentation Challenge

The 2024 Brain Tumor Segmentation Meningioma Radiotherapy (BraTS-MEN-RT) challenge aimed to advance automated segmentation algorithms using the largest known multi-institutional dataset of 750 radiotherapy planning brain MRIs with expert-annotated target labels for patients with intact or postoperative meningioma that underwent either conventional external beam radiotherapy or stereotactic radiosurgery. Each case included a defaced 3D post-contrast T1-weighted radiotherapy planning MRI in its native acquisition space, accompanied by a single-label "target volume" representing the gross tumor volume (GTV) and any at-risk post-operative site. Target volume annotations adhered to established radiotherapy planning protocols, ensuring consistency across cases and institutions, and were approved by expert neuroradiologists and radiation oncologists. Six participating teams developed, containerized, and evaluated automated segmentation models using this comprehensive dataset. Team rankings were assessed using a modified lesion-wise Dice Similarity Coefficient (DSC) and 95% Hausdorff Distance (95HD). The best reported average lesion-wise DSC and 95HD was 0.815 and 26.92 mm, respectively. BraTS-MEN-RT is expected to significantly advance automated radiotherapy planning by enabling precise tumor segmentation and facilitating tailored treatment, ultimately improving patient outcomes. We describe the design and results from the BraTS-MEN-RT challenge.

cs.CV↗

arXiv2025

Uncertainty-Guided Coarse-to-Fine Tumor Segmentation with Anatomy-Aware Post-Processing

Reliable tumor segmentation in thoracic computed tomography (CT) remains challenging due to boundary ambiguity, class imbalance, and anatomical variability. We propose an uncertainty-guided, coarse-to-fine segmentation framework that combines full-volume tumor localization with refined region-of-interest (ROI) segmentation, enhanced by anatomically aware post-processing. The first-stage model generates a coarse prediction, followed by anatomically informed filtering based on lung overlap, proximity to lung surfaces, and component size. The resulting ROIs are segmented by a second-stage model trained with uncertainty-aware loss functions to improve accuracy and boundary calibration in ambiguous regions. Experiments on private and public datasets demonstrate improvements in Dice and Hausdorff scores, with fewer false positives and enhanced spatial interpretability. These results highlight the value of combining uncertainty modeling and anatomical priors in cascaded segmentation pipelines for robust and clinically meaningful tumor delineation. On the Orlando dataset, our framework improved Swin UNETR Dice from 0.4690 to 0.6447. Reduction in spurious components was strongly correlated with segmentation gains, underscoring the value of anatomically informed post-processing.

cs.CV↗

arXiv2025

Pediatric Pancreas Segmentation from MRI Scans with Deep Learning

Objective: Our study aimed to evaluate and validate PanSegNet, a deep learning (DL) algorithm for pediatric pancreas segmentation on MRI in children with acute pancreatitis (AP), chronic pancreatitis (CP), and healthy controls. Methods: With IRB approval, we retrospectively collected 84 MRI scans (1.5T/3T Siemens Aera/Verio) from children aged 2-19 years at Gazi University (2015-2024). The dataset includes healthy children as well as patients diagnosed with AP or CP based on clinical criteria. Pediatric and general radiologists manually segmented the pancreas, then confirmed by a senior pediatric radiologist. PanSegNet-generated segmentations were assessed using Dice Similarity Coefficient (DSC) and 95th percentile Hausdorff distance (HD95). Cohen's kappa measured observer agreement. Results: Pancreas MRI T2W scans were obtained from 42 children with AP/CP (mean age: 11.73 +/- 3.9 years) and 42 healthy children (mean age: 11.19 +/- 4.88 years). PanSegNet achieved DSC scores of 88% (controls), 81% (AP), and 80% (CP), with HD95 values of 3.98 mm (controls), 9.85 mm (AP), and 15.67 mm (CP). Inter-observer kappa was 0.86 (controls), 0.82 (pancreatitis), and intra-observer agreement reached 0.88 and 0.81. Strong agreement was observed between automated and manual volumes (R^2 = 0.85 in controls, 0.77 in diseased), demonstrating clinical reliability. Conclusion: PanSegNet represents the first validated deep learning solution for pancreatic MRI segmentation, achieving expert-level performance across healthy and diseased states. This tool, algorithm, along with our annotated dataset, are freely available on GitHub and OSF, advancing accessible, radiation-free pediatric pancreatic imaging and fostering collaborative research in this underserved domain.

cs.CV↗

arXiv2025

Liver Cirrhosis Stage Estimation from MRI with Deep Learning

We present an end-to-end deep learning framework for automated liver cirrhosis stage estimation from multi-sequence MRI. Cirrhosis is the severe scarring (fibrosis) of the liver and a common endpoint of various chronic liver diseases. Early diagnosis is vital to prevent complications such as decompensation and cancer, which significantly decreases life expectancy. However, diagnosing cirrhosis in its early stages is challenging, and patients often present with life-threatening complications. Our approach integrates multi-scale feature learning with sequence-specific attention mechanisms to capture subtle tissue variations across cirrhosis progression stages. Using CirrMRI600+, a large-scale publicly available dataset of 628 high-resolution MRI scans from 339 patients, we demonstrate state-of-the-art performance in three-stage cirrhosis classification. Our best model achieves 72.8% accuracy on T1W and 63.8% on T2W sequences, significantly outperforming traditional radiomics-based approaches. Through extensive ablation studies, we show that our architecture effectively learns stage-specific imaging biomarkers. We establish new benchmarks for automated cirrhosis staging and provide insights for developing clinically applicable deep learning systems. The source code will be available at https://github.com/JunZengz/CirrhosisStage.

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arXiv2025

Predicting Risk of Pulmonary Fibrosis Formation in PASC Patients

While the acute phase of the COVID-19 pandemic has subsided, its long-term effects persist through Post-Acute Sequelae of COVID-19 (PASC), commonly known as Long COVID. There remains substantial uncertainty regarding both its duration and optimal management strategies. PASC manifests as a diverse array of persistent or newly emerging symptoms--ranging from fatigue, dyspnea, and neurologic impairments (e.g., brain fog), to cardiovascular, pulmonary, and musculoskeletal abnormalities--that extend beyond the acute infection phase. This heterogeneous presentation poses substantial challenges for clinical assessment, diagnosis, and treatment planning. In this paper, we focus on imaging findings that may suggest fibrotic damage in the lungs, a critical manifestation characterized by scarring of lung tissue, which can potentially affect long-term respiratory function in patients with PASC. This study introduces a novel multi-center chest CT analysis framework that combines deep learning and radiomics for fibrosis prediction. Our approach leverages convolutional neural networks (CNNs) and interpretable feature extraction, achieving 82.2% accuracy and 85.5% AUC in classification tasks. We demonstrate the effectiveness of Grad-CAM visualization and radiomics-based feature analysis in providing clinically relevant insights for PASC-related lung fibrosis prediction. Our findings highlight the potential of deep learning-driven computational methods for early detection and risk assessment of PASC-related lung fibrosis--presented for the first time in the literature.

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arXiv2025

Large Scale MRI Collection and Segmentation of Cirrhotic Liver

Liver cirrhosis represents the end stage of chronic liver disease, characterized by extensive fibrosis and nodular regeneration that significantly increases mortality risk. While magnetic resonance imaging (MRI) offers a non-invasive assessment, accurately segmenting cirrhotic livers presents substantial challenges due to morphological alterations and heterogeneous signal characteristics. Deep learning approaches show promise for automating these tasks, but progress has been limited by the absence of large-scale, annotated datasets. Here, we present CirrMRI600+, the first comprehensive dataset comprising 628 high-resolution abdominal MRI scans (310 T1-weighted and 318 T2-weighted sequences, totaling nearly 40,000 annotated slices) with expert-validated segmentation labels for cirrhotic livers. The dataset includes demographic information, clinical parameters, and histopathological validation where available. Additionally, we provide benchmark results from 11 state-of-the-art deep learning experiments to establish performance standards. CirrMRI600+ enables the development and validation of advanced computational methods for cirrhotic liver analysis, potentially accelerating progress toward automated Cirrhosis visual staging and personalized treatment planning.

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arXiv2025

Adaptive Aggregation Weights for Federated Segmentation of Pancreas MRI

Federated learning (FL) enables collaborative model training across institutions without sharing sensitive data, making it an attractive solution for medical imaging tasks. However, traditional FL methods, such as Federated Averaging (FedAvg), face difficulties in generalizing across domains due to variations in imaging protocols and patient demographics across institutions. This challenge is particularly evident in pancreas MRI segmentation, where anatomical variability and imaging artifacts significantly impact performance. In this paper, we conduct a comprehensive evaluation of FL algorithms for pancreas MRI segmentation and introduce a novel approach that incorporates adaptive aggregation weights. By dynamically adjusting the contribution of each client during model aggregation, our method accounts for domain-specific differences and improves generalization across heterogeneous datasets. Experimental results demonstrate that our approach enhances segmentation accuracy and reduces the impact of domain shift compared to conventional FL methods while maintaining privacy-preserving capabilities. Significant performance improvements are observed across multiple hospitals (centers).

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arXiv2025

Shifts in Doctors' Eye Movements Between Real and AI-Generated Medical Images

Eye-tracking analysis plays a vital role in medical imaging, providing key insights into how radiologists visually interpret and diagnose clinical cases. In this work, we first analyze radiologists' attention and agreement by measuring the distribution of various eye-movement patterns, including saccades direction, amplitude, and their joint distribution. These metrics help uncover patterns in attention allocation and diagnostic strategies. Furthermore, we investigate whether and how doctors' gaze behavior shifts when viewing authentic (Real) versus deep-learning-generated (Fake) images. To achieve this, we examine fixation bias maps, focusing on first, last, short, and longest fixations independently, along with detailed saccades patterns, to quantify differences in gaze distribution and visual saliency between authentic and synthetic images.

cs.CV↗

arXiv2025

Eyes Tell the Truth: GazeVal Highlights Shortcomings of Generative AI in Medical Imaging

The demand for high-quality synthetic data for model training and augmentation has never been greater in medical imaging. However, current evaluations predominantly rely on computational metrics that fail to align with human expert recognition. This leads to synthetic images that may appear realistic numerically but lack clinical authenticity, posing significant challenges in ensuring the reliability and effectiveness of AI-driven medical tools. To address this gap, we introduce GazeVal, a practical framework that synergizes expert eye-tracking data with direct radiological evaluations to assess the quality of synthetic medical images. GazeVal leverages gaze patterns of radiologists as they provide a deeper understanding of how experts perceive and interact with synthetic data in different tasks (i.e., diagnostic or Turing tests). Experiments with sixteen radiologists revealed that 96.6% of the generated images (by the most recent state-of-the-art AI algorithm) were identified as fake, demonstrating the limitations of generative AI in producing clinically accurate images.

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