arXiv subjects

Ulas Bagci

Publications and source records attributed to Ulas Bagci.

At least 19 recordsLinked to original sources

arXiv2026

Cyst-X: A Multicenter MRI Benchmark for Pancreatic Cyst Risk Stratification and Cross-Institutional AI

Intraductal papillary mucinous neoplasms (IPMNs) are pancreatic cancer precursors, and guideline-based risk stratification both over-treats indolent lesions and misses progression. We present Cyst-X, a public benchmark of 1,461 T1-weighted (T1W) and T2-weighted (T2W) MRI volumes from 764 patients at seven centers, with expert pancreas masks, risk labels, splits and reference AI risk-prediction models. PanSegNet segmented the pancreas with Dice of 86.34% (T1W) and 89.26% (T2W) on held-out centers. For the primary task, high-risk versus low-risk IPMN, a 3D DenseNet-121 achieved cross-validated AUCs of 74.59% and 73.45%; complementary broad binary and three-class tasks reached 78.67--81.28% and 73.47--75.76%. Because patient images often cannot be pooled across institutions, we also simulated federated learning across the seven centers. On T2W MRI, FedProx was similar to centralized training in center-averaged external AUC (71.00% versus 71.18%) but not in pooled AUC (62.35% versus 77.49%). Radiologist comparisons showed cohort-dependent sensitivity--specificity tradeoffs. Cyst-X supports reproducible method development and identifies within-IPMN risk discrimination and cross-center score comparability as open challenges.

eess.IV↗

arXiv2026

Zonal-Aware Prostate Cancer Detection and Classification via Hadamard-Fused Mamba-UNet

Accurate clinically significant prostate cancer (csPCa) detection from prostate MRI requires a detailed understanding of the prostate anatomical context. Deep learning approaches have achieved promising results in zonal and lesion segmentation; however, the joint analysis of prostate zonal anatomy and lesion morphology in a unified framework remains relatively underexplored. In this work, we propose ZH-Mamba, a multi-stage zonal-aware csPCa detection framework consisting of two H-Mamba UNets models for prostate zonal segmentation and lesion localization, followed by an anatomy-aware Convolutional Neural Network classifier for csPCa detection. The proposed model leverages a learnable Hadamard Transform-based fusion mechanism to enhance zonal and lesion feature representations without increasing computational complexity. The learned fusion patterns consistently emphasize prostate regions, suggesting that the proposed fusion captures anatomically relevant feature representations. We demonstrate a strong zonal segmentation performance on the PI-CAI dataset, reaching Dice scores of $\textbf{0.95}$, $\textbf{0.85}$, and $\textbf{0.95}$ for whole gland (WG), peripheral zone (PZ), and transition zone (TZ), respectively, providing robust anatomical priors for downstream csPCa detection. Experimental results on an independent internal dataset confirm the generalization capability of the proposed zonal segmentation model. For lesion localization, the H-Mamba UNet achieves a competitive Dice score of $\textbf{0.70}$. Integrating the zonal masks and lesion localization, the proposed ZH-Mamba framework achieves an AUC of $\textbf{0.86}$, Average Precision ($\mathrm{AP}_{\mathrm{Patient}}$) of $\textbf{0.72}$, and F1 score of $\textbf{0.76}$, demonstrating the effectiveness of zonal-aware csPCa detection.

eess.IV↗

arXiv2026

Anatomy-Aware Prediction of Bronchoscopic Accessibility from 3D CT

Pre-operative planning for bronchoscopy is critical for the diagnosis of lung lesions. Current accessibility assessment relies on subjective manual inspection of CT scans, which is time-consuming and prone to inter-observer variability. In this paper, we formalize bronchoscopy accessibility prediction as a novel supervised learning task and present the first end-to-end framework to address it. We propose an Anatomy-Aware Mixture-of-Experts (MoE) model that integrates specialized modules: a CT Expert for local morphological features, a Lobe Expert for anatomical priors, and a Path Geometry Expert that encodes the sequential constraints of the bronchial tree. To support this task, we curated the first clinical dataset of 438 cases with pre-operative CT scans and documented procedural outcomes. Experimental results demonstrate that our method achieves an AUROC of 0.8052, significantly outperforming both state-of-the-art baselines and experienced human experts. This work establishes a new benchmark for computer-aided interventional planning in pulmonary medicine. Our data and code will be publicly available at https://nubagcilab.github.io/BronchoAccess/.

cs.CV↗

arXiv2026

Decentralized Gossip Learning and Federated Averaging for Histopathology Image Classification

Breast histopathology analysis increasingly relies on distributed learning because direct data pooling across institutions is often restricted by privacy, governance, and communication constraints. This study compares server-based Federated Averaging (FedAvg), fully decentralized gossip learning, and Hybrid Gossip-FedAvg for invasive ductal carcinoma (IDC) patch classification. Experiments used 277,524 color image patches with patient-disjoint training, validation, and test partitions and a workload-balanced, Dirichlet-guided allocation across six nodes. Ring, random degree-3, and fully connected gossip topologies were evaluated together with sensitivity analyses for statistical heterogeneity, mixing coefficient, learning rate, model drift, prediction disagreement, calibration, clinically motivated operating points, communication payload, and patient-level IDC burden, together with auxiliary backbone robustness analyses. In the principal alpha=0.3 experiment, Hybrid Gossip-FedAvg achieved a test area under the receiver operating characteristic curve (ROC-AUC) of 0.8811, closely followed by FedAvg at 0.8801 and fully connected gossip at 0.8751. Across three independent patient-level repetitions, FedAvg and Hybrid Gossip-FedAvg obtained the same mean ROC-AUC of 0.9082, with standard deviations of 0.0037 and 0.0043, respectively. Hybrid achieved the highest mean area under the precision-recall curve of 0.8240, whereas FedAvg produced the lowest mean Brier score of 0.1335. Denser gossip graphs improved discrimination but increased theoretical model payload, while ring gossip remained sensitive to learning rate and mixing strength. Overall, FedAvg provided the most consistently reliable server-based baseline, topology-aware gossip offered a viable decentralized alternative, and Hybrid Gossip-FedAvg provided a balanced compromise between peer-to-peer diffusion and periodic global coordination.

cs.CV↗

arXiv2026

QwenVLConnector: A Fast, Unified Medical VLM Chatbot for Fine-Grained Clinical Perception and Text Generation

Most medical vision-language models (VLMs) excel at open-ended report generation and VQA but provide limited support for structured, fine-grained clinical perception within a unified interface. We present QwenVLConnector, a Qwen2.5-VL-based medical chatbot that unifies classification, multi-label classification, textualized detection, counting, regression, and free-form report generation under a single next-token objective. Our key component is a lightweight dense multi-layer Connector that aggregates low- and high-level visual features, aligns them through the pretrained vision Merger, and fuses them with the final visual representation without increasing sequence length. This design enriches visual tokens with complementary spatial and semantic cues while preserving efficiency. On FLARE-2D, QwenVLConnector improves detection F1 from 0.55 to 0.85, raises single-label classification from 0.37 to 0.51, and boosts report-generation GREEN by up to 18.3 points over the Qwen2.5-VL baseline. We further explore multimodal in-context learning for report generation, showing additional improvements without updating model parameters. Overall, QwenVLConnector offers a unified and efficient framework for combining structured medical perception with open-ended clinical text generation. Our code can be found at https://github.com/plnguyen2908/QwenConnector.

cs.CV↗

arXiv2026

Serverless gossip training of LSTM failure detectors: A matched-protocol comparison with federated, local and centralized learning on NASA C-MAPSS

Industrial predictive maintenance increasingly depends on learning from equipment spread across sites whose sensor data cannot easily be pooled. Federated averaging (FedAvg) solves this with a central aggregation server; gossip learning removes the server, but its behaviour for recurrent failure-detection models has not been measured under controlled conditions. We compare synchronous ring gossip with FedAvg, isolated local training and a centralized reference for a stacked LSTM that detects imminent failure on the NASA C-MAPSS turbofan benchmark. All methods share one open implementation, architecture, initialization, optimizer, data split and training budget, and the primary endpoint uses one terminal window per test engine to avoid the statistical dependence of overlapping windows. On FD001 (five seeds), gossip reached a terminal-window F1 of 89.6 +/- 1.3%, compared with 89.9 +/- 1.1% for FedAvg, 83.6 +/- 6.7% for local training and 93.5 +/- 2.1% for centralized training, while transmitting the same payload as FedAvg without a coordinator. Node models agreed closely but not exactly (1.8% pairwise decision disagreement versus 5.6% without communication). Across FD002-FD004, peer communication improved terminal-window F1 over local training by 13-28 points; gossip matched FedAvg on FD003 and FD004 but was 4.3 points lower on the multi-condition FD002 subset. Simulated message loss, node failure and server outage changed neither method appreciably, whereas larger rings degraded gossip faster. Ring gossip is therefore a practical serverless alternative when data heterogeneity is moderate, and faster-mixing topologies become important as heterogeneity grows.

cs.LG↗

arXiv2026

Patient-Level, Leakage-Aware Deep Learning for Cross-Center Periapical Radiograph Classification

Dental caries and endodontic disease are among the most common health conditions worldwide, and intraoral periapical radiographs are central to their detection, treatment planning, and follow-up. Automated tooth-level classification of these images, however, lacks reproducible benchmarks, is often evaluated with image-level splits that leak patients between training and test, and is rarely validated across clinics. This paper presents the first patient-level, leakage-aware classification benchmark for single-tooth intraoral periapical radiographs on the DentIRO dataset, which comprises 5,300 images from 3,243 patients across two clinics and four classes: Healthy, Caries, Crowned, and Root Canal. Five transfer-learning models are compared with patient-grouped stratified cross-validation, so that every patient remains within a single fold. DenseNet121 gave the strongest and most stable result at a mean macro-F1 of 0.9787, while the four ImageNet-initialized backbones performed comparably. A controlled comparison on a fixed architecture showed that chest-radiograph pretraining transferred less effectively than ImageNet initialization. Bidirectional cross-center validation produced a small average generalization gap of 0.0077, and Grad-CAM confirmed that predictions rely on clinically meaningful tooth regions rather than acquisition artifacts. The benchmark offers a rigorous and reproducible baseline for intraoral radiograph classification.

cs.CV↗

arXiv2026

Unified CT and MRI Pancreas Segmentation for Label-Efficient Cross-Modality Subregion Transfer

Robust medical image segmentation across imaging modalities is challenging because of large differences in appearance and intensity distributions. Models trained on a single modality often show substantial performance drops when applied to unseen domains. In this work, we develop a unified 3D pancreas segmentation framework that applies domain-adversarial learning to 4,604 heterogeneous CT and MRI scans to learn anatomical representations. A shared nnU-Net encoder-decoder is trained for whole-pancreas segmentation, with a latent domain discriminator encouraging CT-MRI feature alignment. The learned encoder is subsequently transferred to pancreatic head-body-tail segmentation using limited MRI-only subregion annotations. An average Dice score of 87.31% on the in-distribution test set and Dice scores ranging from 84.20% to 88.09% across external OOD datasets were achieved in whole pancreas segmentation. Dice scores of 80.53% on MRI and 83.05% on CT were achieved for downstream subregion segmentation, without using CT subregion annotations. These results demonstrate that a unified anatomical representation can support both cross-modality pancreas segmentation and label-efficient downstream transfer.

cs.CV↗

arXiv2026

TRIUNE-Net: Harmonizing Scale, Shape, and Efficiency in Pancreatic Tumor Segmentation

Pancreatic tumor segmentation in 3D CT volumes is challenged by extreme scale variability across both the pancreas and tumor, and highly irregular tumor morphology. While recent advances have pushed segmentation performance, existing methods do not explicitly address these challenges and come at the cost of excessive computational complexity, limiting their practicality in resource-constrained clinical environments. We propose TRIUNE-Net, a lightweight unified architecture that harmonizes scale, shape, and efficiency through three synergistic innovations. A multi-scale context aggregation module with stage-adaptive dilated convolutions enables the model to reason across the broad range of anatomical scales present in both organs. A serial linear-deformable attention mechanism combines large effective receptive fields with shapeadaptive deformable convolutions to capture irregular, non-convex tumor morphologies. Finally, an information-preserving downsampling module replaces conventional max pooling entirely, retaining all spatial information while adding negligible parameters, preventing small tumors from being discarded before they can be recognized. On both the MSD Pancreas and NVD Pancreas datasets, TRIUNE-Net achieves state-of-theart results with only 5.86 M parameters and no external pre-training, outperforming all baselines across all key tumor metrics. Specifically, it surpasses the next-best model by 0.45% in tumor Dice, 6.0 points in F1 score, 6.6 points in sensitivity, and 3.4 points in precision, simultaneously reflecting its ability to suppress both missed tumors and false alarms in clinically realistic conditions. Our code is available at: https://github.com/abdora-ai/TRIUNE-Net

cs.CV↗

arXiv2026

Improved Segmentation of Polyps and Visual Explainability Analysis

Colorectal cancer (CRC) remains one of the leading causes of cancer-related morbidity and mortality worldwide, with gastrointestinal (GI) polyps serving as critical precursors according to the World Health Organization (WHO). Early and accurate segmentation of polyps during colonoscopy is essential for reducing CRC progression, yet manual delineation is labor-intensive and prone to observer variability. Deep learning methods have demonstrated strong potential for automated polyp analysis, but their limited interpretability remains a barrier to clinical adoption. In this study, we present PolypSeg-GradCAM, an explainable deep learning framework that integrates a U-Net architecture with a pre-trained ResNet-34 backbone and Gradient-weighted Class Activation Mapping (Grad-CAM) for transparent polyp segmentation. To ensure rigorous benchmarking, the model was trained and evaluated using 5-Fold Cross-Validation on the Kvasir-SEG dataset of 1,000 annotated endoscopic images. Experimental results show a mean Dice coefficient of 0.8902 +/- 0.0125, a mean Intersection-over-Union (IoU) of 0.8023, and an Area Under the Receiver Operating Characteristic Curve (AUC-ROC) of 0.9722. Advanced quantitative analysis using an optimal threshold yielded a Sensitivity of 0.9058 and Precision of 0.9083. Additionally, Grad-CAM visualizations confirmed that predictions were guided by clinically relevant regions, offering insight into the model's decision-making process. This study demonstrates that integrating segmentation accuracy with interpretability can support the development of trustworthy AI-assisted colonoscopy tools.

cs.CV↗

arXiv2026

Asymmetric Paired-Annotation Learning for Multi-Structure ULF Pediatric Brain MRI Segmentation

Portable ultra-low-field (ULF) MRI can expand access to pediatric neuroimaging, but segmentation at 0.064 T remains challenging because anatomical boundaries are weakly delineated, small structures may be only partially visible, and high-field references can be locally misregistered. The LISA 2026 Challenge provides two non-equivalent annotations reflecting different sources of anatomical evidence: a highfield-derived (HF) mask defining the scored target and a low-field-edited (LF) mask aligned with visible ULF anatomy. In this challenge report, we describe AURA, an nnU-Net-based asymmetric supervision strategy that treats these annotations as distinct observations rather than interchangeable ground truths. AURA anchors training to the HF mask and incorporates the LF mask through a bounded reliability gate based on label disagreement, boundaries, predictive uncertainty, class reliability, and training stage. On a 16-case development split, the HF-supervised baseline, AURA, and their ensemble achieved Dice scores of 0.7984, 0.7950, and 0.7988, respectively, while the ensemble achieved an HD95 of 1.8892 and an ASSD of 0.7855. These results provide a preliminary evaluation of AURA within the LISA 2026 Challenge and motivate further assessment on the hidden test set and external ULF cohorts. Our code and pretrained models are available at https://github.com/minhdang050806/ A-nnU-Net-based-asymmetric-supervision-strategy.

cs.CV↗

arXiv2026

GazeRefine: Expert Gaze as a Test-Time Prompt for Training-Free Medical Image Segmentation

Medical image segmentation remains difficult to scale because high-performing methods typically rely on dense expert annotations and task-specific training. We introduce GazeRefine, a training-free framework that uses gaze as an inference-time prompt for zero-shot medical image segmentation. Sparse, duration-weighted fixations are converted into foreground and background priors that initialize semantic prototypes in frozen DINOv3 feature space. These prototypes are iteratively refined through foreground-background discrimination, feature-space affinity propagation, and anchoring to the initial gaze guidance, allowing segmentation to extend beyond directly fixated regions while limiting semantic drift. GazeRefine requires no segmentation masks, fine-tuning, adapters, prompt encoders, or gradient updates. We evaluate the method on gaze-annotated polyp segmentation and prostate MRI segmentation. The results show strong performance on colonoscopy images and competitive performance on prostate MRI, supporting gaze-guided prototype refinement as a promising approach for segmentation-label-efficient, human-in-the-loop medical image segmentation. Our tools and code can be found in the following repository: https://github.com/MohammedOussamaBEN/GazeRefine.git

eess.IV↗

arXiv2026

Hierarchical MoE for Multi-Modal ILD Diagnosis

Mixture-of-experts (MoE) models combine specialized predictors under learned routing, offering a principled mechanism for leveraging heterogeneity in medical data. We present a hierarchical multimodal MoE for interstitial lung disease (ILD) classification that integrates a frozen, pre-trained imaging expert with structured electronic health records (EHR) via two-stage gating. A modality-level gate assigns patient-specific weights to imaging and EHR predictions, while a sub-gating module decomposes the EHR branch into clinically defined feature groups with learned, group-specific contributions. This design preserves stable imaging representations while enabling input-dependent clinical weighting and explicit EHR specialization. Under strict patient-level cross-validation, the model achieved the highest mean AUC among the evaluated methods (0.8750 +- 0.0443), compared with 0.8646 for imaging-only REN and 0.7685 for SwinUNETR. The framework extends interpretability across anatomical regions, imaging--EHR utilization, and clinically defined EHR feature groups.

cs.AI↗

arXiv2026

Matched Outcomes, Divergent Gaze: How Foveated MLLMs Search Compared to Humans

Human visual search is serial: the fovea must land on a candidate to confirm it, and those landings form a scanpath. Whether multimodal large language models (MLLMs), given the same foveated input, search as humans do bears on their use as models of human vision and on attention-alignment scores. We compare three general-purpose MLLMs with human eye-movement scanpaths on goal-directed search (COCO-Search18), driving each model fixation by fixation through an identical, human-matched foveated view and assessing it along three axes: the decision of target presence, the efficiency of reaching the target, and the gaze process itself. The axes dissociate. On the decision and on target acquisition the models match or exceed humans, detecting present targets near ceiling and reaching them on the first saccade more often than people do. The gaze process is not human. Under the human-matched condition, all three share one signature: low-entropy, large-amplitude, self-consistent scanpaths that agree with themselves far more closely than two humans agree with each other. That is consistent with a single-pass, non-serial architecture rather than a limit of acuity. Matched retinal input reproduces where humans look but not how the looking unfolds in time, and no degradation regime recovers human-like search at human-like success. The gap sits on a process axis that answer-alignment and saliency metrics do not measure. Because they miss it, such metrics cannot certify human-like vision, and zero-shot models suit outcome and spatial questions but not temporal, process-level ones.

cs.CV↗

arXiv2026

A decodability criterion predicts when hidden-state selection beats majority voting in large language models

Combining the answers a large language model (LLM) samples for a question into one decision is a test-time information fusion problem, usually solved by majority voting. Voting is unreliable on difficult questions, where the sampled answers share correlated errors, so the wrong answer can win and drawing more samples makes the decision worse. Selecting a candidate by reading a correctness signal from the model's hidden states is a promising alternative, but its accuracy varies across models and tasks, and no measure indicates when it can be trusted. In this paper, we propose CASE (Correctness-Axis SElection), a dynamic selection combiner that trains a linear gate on the answer-token hidden state and selects the highest-scoring candidate. Its main contribution is decodability, a leakage-free measure of how well the gate ranks a question's correct candidates above its incorrect ones, which predicts whether hidden-state selection will outperform voting. A conventional probe appears accurate only because of question-identity leakage, which vanishes under question-grouped evaluation. On held-out data, decodability predicts the accuracy gain of selection over voting with a Pearson correlation r=0.75 and a decision threshold near AUC=0.60. Across general and medical LLMs, CASE improves over voting by up to 19 points on medium-difficulty questions and 16.8 points on hard questions. Decodability depends on the aligned knowledge a model must recall, not on its scale, and its prediction transfers to an unseen scientific domain within 3.8 points. It thus provides a practical criterion, measurable in advance for a given model and task, for choosing between learned selection and majority voting.

cs.AI↗

arXiv2026

Gaussian Meta-Space Augmentation for Stacking Ensembles in Multimodal IPMN Risk Stratification

Pancreatic cancer is among the most lethal malignancies; risk stratification of intraductal papillary mucinous neoplasms (IPMNs) offers a crucial opportunity for early intervention but typically requires invasive tissue biopsy. Dominant vision-based approaches, including radiomics and deep learning, provide promising but initially separate discrimination opportunities. Similarly, multisequence MRI (T1W/T2W) and anatomically decomposed (head, body and tail) analysis of the pancreas provide additional and potentially complementary signals. Effective fusion of this information is crucial in ordinal IPMN dysplasia risk prediction and can be accomplished via a meticulously regularized and calibrated ensemble stacking combiner. We present cUPMI, a class-conditional Gaussian augmentation of a combiner's log-probability meta-features, and test it on various prediction paradigms. In our multi-center analysis, we find cUPMI adds limited value to properly regularized L2-logistic binary classification stacks, but consistently regularizes higher-capacity tree combiners in the binary and radiomics-only setting (RF +0.015 and XGBoost +0.024 binary AUC, positive in all seeds). Its cleanest ordinal benefit appears for XGBoost on an 8-stream radiomics task (3-class no < low < high, +0.022 QWK in all seeds). Separately, fold-locked fusion of radiomics and 2.5D CNN streams yields the strongest overall model, an RF stack reaching QWK 0.595 (95% CI [0.54, 0.64]) and binary AUC 0.839, surpassing radiomics, 2.5D ResNet, and 3D DenseNet-121 baselines.

cs.CV↗

arXiv2026

BreastMammo and DenseMammo: Benchmarks for Mammography Domain Generalization

Breast density classification is a critical component of breast cancer risk assessment, yet AI models often struggle to generalize across clinical sites due to vendor-specific acquisition styles. In this work, we introduce two new datasets, BreastMammo and DenseMammo, to facilitate robust multi-view mammography research. We propose a domain generalization framework that utilizes a foreground-only histogram matching protocol to resolve the domain shift issue arising from disparate clinical sources. Internal evaluation using a 5-fold cross-validation protocol demonstrates the efficacy of our approach, with the Swin Transformer backbone achieving a peak AUC of 98.32% for density classification. External evaluation on the TNMammo and LUMINA datasets demonstrates that the proposed approach consistently reduces domain shift, significantly outperforming prominent domain generalization paradigms, including MixStyle and Discrete-Fourier-Transform-based frameworks.

eess.IV↗

arXiv2026

Ethical Framework for Responsible Foundational Models in Medical Imaging

The emergence of foundational models represents a paradigm shift in medical imaging, offering extraordinary capabilities in disease detection, diagnosis, and treatment planning. These large-scale artificial intelligence systems, trained on extensive multimodal and multi-center datasets, demonstrate remarkable versatility across diverse medical applications. However, their integration into clinical practice presents complex ethical challenges that extend beyond technical performance metrics. This study examines the critical ethical considerations at the intersection of healthcare and artificial intelligence. Patient data privacy remains a fundamental concern, particularly given these models' requirement for extensive training data and their potential to inadvertently memorize sensitive information. Algorithmic bias poses a significant challenge in healthcare, as historical disparities in medical data collection may perpetuate or exacerbate existing healthcare inequities across demographic groups. The complexity of foundational models presents significant challenges regarding transparency and explainability in medical decision-making. We propose a comprehensive ethical framework that addresses these challenges while promoting responsible innovation. This framework emphasizes robust privacy safeguards, systematic bias detection and mitigation strategies, and mechanisms for maintaining meaningful human oversight. By establishing clear guidelines for development and deployment, we aim to harness the transformative potential of foundational models while preserving the fundamental principles of medical ethics and patient-centered care.

cs.CY↗