Showing 1–19 of 19 results for author: Aktas, H E

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

Authors: Max A. Nelson, Eminenur Sen Tasci, Zhixiang Wang, Zongwei Zhou, Halil Ertugrul Aktas, Andrea M. Bejar, Elif Keles, Ziliang Hong, Sıtkı Safa Taflan, Muhammed Enes Tasci, Frank H. Miller, Michael B. Wallace, Rajesh N. Keswani, Gorkem Durak, Ulas Bagci

Abstract: 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… ▽ More 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. △ Less

Submitted 11 August, 2026; originally announced August 2026.

Comments: Accepted at the International Workshop on Machine Learning in Medical Imaging (MLMI 2026), held in conjunction with MICCAI 2026. This is the authors' accepted manuscript; the final version will appear in Springer Lecture Notes in Computer Science (LNCS). 11 pages, 3 figures

BreastMammo and DenseMammo: Benchmarks for Mammography Domain Generalization

Authors: Hongyi Pan, Gorkem Durak, Halil Ertugrul Aktas, Andrea Mia Bejar, Mustafa Ege Seker, Nebile Alibeyoglu, Rumeysa Guclu, Rana Gunoz Comert Bozkurt, Sibel Ozkan Gurdal, Neslihan Cabioglu, Beyza Ozcinar, Ravza Yilmaz, Vahit Ozmen, Erkin Aribal, Sukru Mehmet Erturk, Yalda Zafari, Mohamed Mabrok, Kayhan Batmanghelich, Mohammad Yaqub, Ziyue Xu, Ulas Bagci

Abstract: 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… ▽ More 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. △ Less

Submitted 10 August, 2026; originally announced August 2026.

Comments: This paper was accepted to the MICCAI 2026 workshop Deep-Brea3th

Revisiting LLM Adaptation for 3D CT Report Generation: A Study of Scaling and Diagnostic Priors

Authors: Vanshali Sharma, Andrea M. Bejar, Halil Ertugrul Aktas, Quoc-Huy Trinh, Debesh Jha, Gorkem Durak, Ulas Bagci

Abstract: Recent advances in multimodal learning, including large language models (LLMs) and vision-language models (VLMs), have demonstrated strong adaptability to natural images. However, extending their use to the medical domain, particularly for volumetric (3D) images, is challenging due to high computational complexity, volumetric dependencies and the semantic gap between visual features and clinical t… ▽ More Recent advances in multimodal learning, including large language models (LLMs) and vision-language models (VLMs), have demonstrated strong adaptability to natural images. However, extending their use to the medical domain, particularly for volumetric (3D) images, is challenging due to high computational complexity, volumetric dependencies and the semantic gap between visual features and clinical terminology. Naively fine-tuning LLMs on limited medical data often leads to overfitting and clinical hallucination, where linguistic fluency is prioritized over clinical factuality. In this study, we investigate parameter-efficient adaptation strategies for volumetric CT report generation and introduce RAD3D-Prefix, a lightweight diagnostic-prior conditioning framework that minimizes the need for extensive parameter training. This module integrates image embeddings with multi-label diagnostic classification logits, preserving critical clinical details while bridging the semantic gap. By keeping the LLM frozen, our method requires minimal trainable parameters and mitigates the risk of overfitting on small, domain-specific datasets. Through a systematic study spanning LLMs from 96.1M to 1.6B parameters, we find that fine-tuning is most beneficial for smaller LLMs, whereas freezing larger (~1B+ LLMs and training only lightweight projection layers provides a superior trade-off between performance, generalization, and computational efficiency. Across multiple automatic metrics and a clinical reader study, RAD3D-Prefix outperforms comparable parameter-efficient baselines and demonstrates strong out-of-domain generalization while using substantially fewer trainable parameters than fully fine-tuned alternatives. △ Less

Submitted 15 June, 2026; originally announced June 2026.

CrossPan: A Comprehensive Benchmark for Cross-Sequence Pancreas MRI Segmentation and Generalization

Authors: Linkai Peng, Cuiling Sun, Zheyuan Zhang, Wanying Dou, Halil Ertugrul Aktas, Andrea M Bejar, Elif Keles, Tamas Gonda, Michael B Wallace, Zongwei Zhou, Gorkem Durak, Rajesh N Keswani, Ulas Bagci

Abstract: Automatic pancreas segmentation is fundamental to abdominal MRI analysis, yet deep learning models trained on one MRI sequence often fail catastrophically when applied to another-a challenge that has received little systematic investigation. We introduce CrossPan, a multi-institutional benchmark comprising 1,386 3D scans across three routinely acquired sequences (T1-weighted, T2-weighted, and Out-… ▽ More Automatic pancreas segmentation is fundamental to abdominal MRI analysis, yet deep learning models trained on one MRI sequence often fail catastrophically when applied to another-a challenge that has received little systematic investigation. We introduce CrossPan, a multi-institutional benchmark comprising 1,386 3D scans across three routinely acquired sequences (T1-weighted, T2-weighted, and Out-of-Phase) from eight centers. Our experiments reveal three key findings. First, cross-sequence domain shifts are far more severe than cross-center variability: models achieving Dice scores above 0.85 in-domain collapse to near-zero (<0.02) when transferred across sequences. Second, state-of-the-art domain generalization methods provide negligible benefit under these physics-driven contrast inversions, whereas foundation models like MedSAM2 maintain moderate zero-shot performance through contrast-invariant shape priors. Third, semi-supervised learning offers gains only under stable intensity distributions and becomes unstable on sequences with high intra-organ variability. These results establish cross-sequence generalization-not model architecture or center diversity-as the primary barrier to clinically deployable pancreas MRI segmentation. Dataset and code are available at https://crosspan.netlify.app/. △ Less

Submitted 20 April, 2026; originally announced April 2026.

Comments: Accepted to MIDL 2026

Align then Refine: Text-Guided 3D Prostate Lesion Segmentation

Authors: Cuiling Sun, Linkai Peng, Adam Murphy, Elif Keles, Hiten D. Patel, Ashley Ross, Frank Miller, Baris Turkbey, Andrea Mia Bejar, Halil Ertugrul Aktas, Gorkem Durak, Ulas Bagci

Abstract: Automated 3D segmentation of prostate lesions from biparametric MRI (bp-MRI) is essential for reliable algorithmic analysis, but achieving high precision remains challenging. Volumetric methods must combine multiple modalities while ensuring anatomical consistency, but current models struggle to integrate cross-modal information reliably. While vision-language models (VLMs) are replacing the curre… ▽ More Automated 3D segmentation of prostate lesions from biparametric MRI (bp-MRI) is essential for reliable algorithmic analysis, but achieving high precision remains challenging. Volumetric methods must combine multiple modalities while ensuring anatomical consistency, but current models struggle to integrate cross-modal information reliably. While vision-language models (VLMs) are replacing the currently used architectural designs, they still lack the fine-grained, lesion-level semantics required for effective localized guidance. To address these limitations, we propose a new multi-encoder U-Net architecture incorporating three key innovations: (1) an alignment loss that enhances foreground text-image similarity to inject lesion semantics; (2) a heatmap loss that calibrates the similarity map and suppresses spurious background activations; and (3) a final-stage, confidence-gated multi-head cross-attention refiner that performs localized boundary edits in high-confidence regions. A phase-scheduled training regime stabilizes the optimization of these components. Our method consistently outperforms prior approaches, establishing a new state-of-the-art on the PI-CAI dataset through enhanced multi-modal fusion and localized text guidance. Our code is available at https://github.com/NUBagciLab/Prostate-Lesion-Segmentation. △ Less

Submitted 20 April, 2026; originally announced April 2026.

Comments: Accepted to EMBC 2026

GazeVaLM: A Multi-Observer Eye-Tracking Benchmark for Evaluating Clinical Realism in AI-Generated X-Rays

Authors: David Wong, Zeynep Isik, Bin Wang, Marouane Tliba, Gorkem Durak, Elif Keles, Halil Ertugrul Aktas, Aladine Chetouani, Cagdas Topel, Nicolo Gennaro, Camila Lopes Vendrami, Tugce Agirlar Trabzonlu, Amir Ali Rahsepar, Laetitia Perronne, Matthew Antalek, Onural Ozturk, Gokcan Okur, Andrew C. Gordon, Ayis Pyrros, Frank H. Miller, Amir Borhani, Hatice Savas, Eric Hart, Elizabeth Krupinski, Ulas Bagci

Abstract: We introduce GazeVaLM, a public eye-tracking dataset for studying clinical perception during chest radiograph authenticity assessment. The dataset comprises 960 gaze recordings from 16 expert radiologists interpreting 30 real and 30 synthetic chest X-rays (generated by diffusion based generative AI) under two conditions: diagnostic assessment and real-fake classification (Visual Turing test). For… ▽ More We introduce GazeVaLM, a public eye-tracking dataset for studying clinical perception during chest radiograph authenticity assessment. The dataset comprises 960 gaze recordings from 16 expert radiologists interpreting 30 real and 30 synthetic chest X-rays (generated by diffusion based generative AI) under two conditions: diagnostic assessment and real-fake classification (Visual Turing test). For each image-observer pair, we provide raw gaze samples, fixation maps, scanpaths, saliency density maps, structured diagnostic labels, and authenticity judgments. We extend the protocol to 6 state-of-the-art multimodal LLMs, releasing their predicted diagnoses, authenticity labels, and confidence scores under matched conditions - enabling direct human-AI comparison at both decision and uncertainty levels. We further provide analyses of gaze agreement, inter-observer consistency, and benchmarking of radiologists versus LLMs in diagnostic accuracy and authenticity detection. GazeVaLM supports research in gaze modeling, clinical decision-making, human-AI comparison, generative image realism assessment, and uncertainty quantification. By jointly releasing visual attention data, clinical labels, and model predictions, we aim to facilitate reproducible research on how experts and AI systems perceive, interpret, and evaluate medical images. The dataset is available at https://huggingface.co/datasets/davidcwong/GazeVaLM. △ Less

Submitted 13 April, 2026; originally announced April 2026.

Comments: This work appears in ACM ETRA 2026

CORA: Generalizable coronary artery disease assessment and risk stratification from coronary CT angiography using pathology-centric representation learning

Authors: Jinkui Hao, Gorkem Durak, Halil Ertugrul Aktas, Ulas Bagci, Bradley D. Allen, Nilay S. Shah, Bo Zhou

Abstract: Coronary artery disease, a leading cause of cardiovascular mortality worldwide, can be assessed non-invasively by coronary computed tomography angiography (CCTA). Although deep learning has advanced automated CCTA analysis, clinical translation remains constrained by the scarcity of expert-annotated data and by the spatial sparsity of coronary pathology, which occupies only a small fraction of eac… ▽ More Coronary artery disease, a leading cause of cardiovascular mortality worldwide, can be assessed non-invasively by coronary computed tomography angiography (CCTA). Although deep learning has advanced automated CCTA analysis, clinical translation remains constrained by the scarcity of expert-annotated data and by the spatial sparsity of coronary pathology, which occupies only a small fraction of each scan. Widely used label-free pretraining strategies, such as masked image modeling and contrastive learning, optimize for global anatomical reconstruction and tend to under-represent these tiny localized pathological features. Here we present CORA, an annotation-efficient model for comprehensive coronary artery disease assessment. Rather than reconstructing background anatomy, CORA learns from volumetric CCTA through a synthesis-driven self-supervised strategy: an anatomy-guided engine inserts diverse synthetic calcified and non-calcified lesions into unlabeled scans, reframing pretraining as an abnormality-detection task that biases representation learning toward clinically relevant disease features. We pretrained CORA on 10,138 unlabeled CCTA volumes and evaluated it across datasets from nine independent hospitals. Across plaque characterization, stenosis detection, and coronary artery segmentation, CORA consistently outperformed strong self-supervised pretraining baselines, with the largest gains on external multi-center data, indicating robust generalization under distributional shift. Coupling the imaging encoder with structured clinical variables further enabled near-term major adverse cardiac event (MACE) risk stratification. Our results show that pathology-centric, synthesis-driven pretraining is an effective and scalable strategy for annotation-efficient coronary artery disease assessment from CCTA. △ Less

Submitted 3 July, 2026; v1 submitted 25 March, 2026; originally announced March 2026.

Comments: Code is available at: https://github.com/Advanced-AI-in-Medicine-and-Physics-Lab/CORA

LUMINA: A Multi-Vendor Mammography Benchmark with Energy Harmonization Protocol

Authors: Hongyi Pan, Gorkem Durak, Halil Ertugrul Aktas, Andrea M. Bejar, Baver Tutun, Emre Uysal, Ezgi Bulbul, Mehmet Fatih Dogan, Berrin Erok, Berna Akkus Yildirim, Sukru Mehmet Erturk, Ulas Bagci

Abstract: Publicly available full-field digital mammography (FFDM) datasets remain limited in size, clinical annotations, and vendor diversity, hindering the development of robust models. We introduce LUMINA, a curated, multi-vendor FFDM dataset that explicitly encodes acquisition energy and vendor metadata to capture clinically relevant appearance variations often overlooked in existing benchmarks. This da… ▽ More Publicly available full-field digital mammography (FFDM) datasets remain limited in size, clinical annotations, and vendor diversity, hindering the development of robust models. We introduce LUMINA, a curated, multi-vendor FFDM dataset that explicitly encodes acquisition energy and vendor metadata to capture clinically relevant appearance variations often overlooked in existing benchmarks. This dataset contains 1824 images from 468 patients (960 benign, 864 malignant), with pathology-confirmed labels, BI-RADS assessments, and breast-density annotations. LUMINA spans six acquisition systems and includes both high- and low-energy imaging styles, enabling systematic analysis of vendor- and energy-induced domain shifts. To address these variations, we propose a foreground-only pixel-space alignment method (''energy harmonization'') that maps images to a low-energy reference while preserving lesion morphology. We benchmark CNN and transformer models on three clinically relevant tasks: diagnosis (benign vs. malignant), BI-RADS classification, and density estimation. Two-view models consistently outperform single-view models. EfficientNet-B0 achieves an AUC of 93.54% for diagnosis, while Swin-T achieves the best macro-AUC of 89.43% for density prediction. Harmonization improves performance across architectures and produces more localized Grad-CAM responses. Overall, LUMINA provides (1) a vendor-diverse benchmark and (2) a model-agnostic harmonization framework for reliable and deployable mammography AI. △ Less

Submitted 27 May, 2026; v1 submitted 15 March, 2026; originally announced March 2026.

Comments: This paper was accepted to CVPR 2026

Beyond Medical Diagnostics: How Medical Multimodal Large Language Models Think in Space

Authors: Quoc-Huy Trinh, Xi Ding, Yang Liu, Zhenyue Qin, Xingjian Li, Gorkem Durak, Halil Ertugrul Aktas, Andrea M. Bejar, Ulas Bagci, Min Xu

Abstract: Visual spatial intelligence is critical for medical image interpretation, yet remains largely unexplored in Multimodal Large Language Models (MLLMs) for 3D imaging. This gap persists due to a systemic lack of datasets featuring structured 3D spatial annotations beyond basic labels. In this study, we introduce an agentic pipeline that autonomously synthesizes spatial visual question-answering (VQA)… ▽ More Visual spatial intelligence is critical for medical image interpretation, yet remains largely unexplored in Multimodal Large Language Models (MLLMs) for 3D imaging. This gap persists due to a systemic lack of datasets featuring structured 3D spatial annotations beyond basic labels. In this study, we introduce an agentic pipeline that autonomously synthesizes spatial visual question-answering (VQA) data by orchestrating computational tools such as volume estimation and bounding boxes extraction with multi-agent collaboration and expert radiologist validation. We present SpatialMed, the first comprehensive benchmark for evaluating 3D spatial intelligence in medical MLLMs, comprising 31,253 question-answer pairs across multiple organs and tumor types. Our evaluations on 24 state-of-the-art MLLMs and extensive analyses reveal that current models lack robust spatial reasoning capabilities for medical imaging. △ Less

Submitted 16 July, 2026; v1 submitted 14 March, 2026; originally announced March 2026.

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

Authors: Xinran Gong, Gorkem Durak, Halil Ertugrul Aktas, Vedat Cicek, Jinkui Hao, Ulas Bagci, Nilay S. Shah, Bo Zhou

Abstract: 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 populatio… ▽ More 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. △ Less

Submitted 31 December, 2025; originally announced December 2025.

Comments: 21 pages, 8 figures

Upstream Probabilistic Meta-Imputation for Multimodal Pediatric Pancreatitis Classification

Authors: Max A. Nelson, Elif Keles, Eminenur Sen Tasci, Merve Yazol, Halil Ertugrul Aktas, Ziliang Hong, Andrea Mia Bejar, Gorkem Durak, Oznur Leman Boyunaga, Ulas Bagci

Abstract: 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… ▽ More 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). △ Less

Submitted 19 November, 2025; originally announced November 2025.

Comments: 5 pages, 5 figures

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

Authors: Alec K. Peltekian, Halil Ertugrul Aktas, Gorkem Durak, Kevin Grudzinski, Bradford C. Bemiss, Carrie Richardson, Jane E. Dematte, G. R. Scott Budinger, Anthony J. Esposito, Alexander Misharin, Alok Choudhary, Ankit Agrawal, Ulas Bagci

Abstract: 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… ▽ More 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. △ Less

Submitted 30 March, 2026; v1 submitted 6 October, 2025; originally announced October 2025.

Comments: 13 pages, 4 figures, 5 tables

Pancreas Part Segmentation under Federated Learning Paradigm

Authors: Ziliang Hong, Halil Ertugrul Aktas, Andrea Mia Bejar, Katherine Wu, Hongyi Pan, Gorkem Durak, Zheyuan Zhang, Sait Kayali, Temel Tirkes, Federica Proietto Salanitri, Concetto Spampinato, Michael Goggins, Tamas Gonda, Candice Bolan, Raj Keswani, Frank Miller, Michael Wallace, Ulas Bagci

Abstract: 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,… ▽ More 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. △ Less

Submitted 27 September, 2025; originally announced September 2025.

Rethink Domain Generalization in Heterogeneous Sequence MRI Segmentation

Authors: Zheyuan Zhang, Linkai Peng, Wanying Dou, Cuiling Sun, Halil Ertugrul Aktas, Andrea M. Bejar, Elif Keles, Gorkem Durak, Ulas Bagci

Abstract: 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 or… ▽ More 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. △ Less

Submitted 30 July, 2025; originally announced July 2025.

Cyst-X: A Multi-Center MRI Benchmark and Federated Learning Framework for Malignancy-Risk Stratification of Pancreatic Cystic Neoplasm

Authors: Hongyi Pan, Gorkem Durak, Elif Keles, Ziliang Hong, Deniz Seyithanoglu, Zheyuan Zhang, Alpay Medetalibeyoglu, Halil Ertugrul Aktas, Andrea Mia Bejar, Yavuz Taktak, Gulbiz Dagoglu Kartal, Mehmet Sukru Erturk, Timurhan Cebeci, Yury Velichko, Lili Zhao, Emil Agarunov, Federica Proietto Salanitri, Concetto Spampinato, Pallavi Tiwari, Ziyue Xu, Sachin Jambawalikar, Ivo G. Schoots, Marco J. Bruno, Chenchan Huang, Candice W. Bolan , et al. (5 additional authors not shown)

Abstract: Pancreatic cancer is projected to be the second-deadliest cancer by 2030, making early detection critical. Intraductal papillary mucinous neoplasms (IPMNs), key cancer precursors, present a clinical dilemma, as current guidelines struggle to stratify malignancy risk, leading to unnecessary surgeries or missed diagnoses. Here, we introduce Cyst-X, a multi-center MRI benchmark and a federated learni… ▽ More Pancreatic cancer is projected to be the second-deadliest cancer by 2030, making early detection critical. Intraductal papillary mucinous neoplasms (IPMNs), key cancer precursors, present a clinical dilemma, as current guidelines struggle to stratify malignancy risk, leading to unnecessary surgeries or missed diagnoses. Here, we introduce Cyst-X, a multi-center MRI benchmark and a federated learning framework for IPMN malignancy-risk stratification. The dataset comprises 1,461 abdominal MRI scans from 764 patients at seven international centers, with three-tier malignancy labels anchored in histopathology or three-year imaging follow-up and expert pancreas segmentations. The pipeline couples the PanSegNet pancreas segmenter with a 3D DenseNet-121 classifier and a parallel radiomics predictor. On internal cross-validation, the deep learning classifier reached a mean area under the receiver operating characteristic curve (AUC) of 0.85 (95% confidence interval 0.84-0.86) on T2-weighted MRI for high-risk versus low- or no-risk discrimination, with the average precision rising from a prevalence baseline of 0.23 to 0.64. This performance was preserved (AUC 0.85, FedProx) when training was distributed across institutions without exchange of raw patient images. Benchmarked against three blinded radiologists on a 629-case reader subset evaluated under imaging-only conditions, the classifier matched or exceeded sensitivity at comparable specificity. To accelerate research in early pancreatic cancer detection, we publicly release the Cyst-X dataset, segmentation masks, and trained models as the first large-scale, multi-centre MRI resource for pancreatic cystic neoplasm analysis. △ Less

Submitted 8 June, 2026; v1 submitted 29 July, 2025; originally announced July 2025.

Pediatric Pancreas Segmentation from MRI Scans with Deep Learning

Authors: Elif Keles, Merve Yazol, Gorkem Durak, Ziliang Hong, Halil Ertugrul Aktas, Zheyuan Zhang, Linkai Peng, Onkar Susladkar, Necati Guzelyel, Oznur Leman Boyunaga, Cemal Yazici, Mark Lowe, Aliye Uc, Ulas Bagci

Abstract: 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… ▽ More 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. △ Less

Submitted 18 June, 2025; originally announced June 2025.

Comments: Code and MRI data available for public

IPMN Risk Assessment under Federated Learning Paradigm

Authors: Hongyi Pan, Ziliang Hong, Gorkem Durak, Elif Keles, Halil Ertugrul Aktas, Yavuz Taktak, Alpay Medetalibeyoglu, Zheyuan Zhang, Yury Velichko, Concetto Spampinato, Ivo Schoots, Marco J. Bruno, Pallavi Tiwari, Candice Bolan, Tamas Gonda, Frank Miller, Rajesh N. Keswani, Michael B. Wallace, Ziyue Xu, Ulas Bagci

Abstract: Accurate classification of Intraductal Papillary Mucinous Neoplasms (IPMN) is essential for identifying high-risk cases that require timely intervention. In this study, we develop a federated learning framework for multi-center IPMN classification utilizing a comprehensive pancreas MRI dataset. This dataset includes 652 T1-weighted and 655 T2-weighted MRI images, accompanied by corresponding IPMN… ▽ More Accurate classification of Intraductal Papillary Mucinous Neoplasms (IPMN) is essential for identifying high-risk cases that require timely intervention. In this study, we develop a federated learning framework for multi-center IPMN classification utilizing a comprehensive pancreas MRI dataset. This dataset includes 652 T1-weighted and 655 T2-weighted MRI images, accompanied by corresponding IPMN risk scores from 7 leading medical institutions, making it the largest and most diverse dataset for IPMN classification to date. We assess the performance of DenseNet-121 in both centralized and federated settings for training on distributed data. Our results demonstrate that the federated learning approach achieves high classification accuracy comparable to centralized learning while ensuring data privacy across institutions. This work marks a significant advancement in collaborative IPMN classification, facilitating secure and high-accuracy model training across multiple centers. △ Less

Submitted 22 January, 2025; v1 submitted 8 November, 2024; originally announced November 2024.

Comments: This paper has been accepted to ISBI 2025

Adaptive Aggregation Weights for Federated Segmentation of Pancreas MRI

Authors: Hongyi Pan, Gorkem Durak, Zheyuan Zhang, Yavuz Taktak, Elif Keles, Halil Ertugrul Aktas, Alpay Medetalibeyoglu, Yury Velichko, Concetto Spampinato, Ivo Schoots, Marco J. Bruno, Rajesh N. Keswani, Pallavi Tiwari, Candice Bolan, Tamas Gonda, Michael G. Goggins, Michael B. Wallace, Ziyue Xu, Ulas Bagci

Abstract: 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 part… ▽ More 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). △ Less

Submitted 6 May, 2025; v1 submitted 29 October, 2024; originally announced October 2024.

Comments: This paper has been accepted to ISBI 2025

Large Scale MRI Collection and Segmentation of Cirrhotic Liver

Authors: Debesh Jha, Onkar Kishor Susladkar, Vandan Gorade, Elif Keles, Matthew Antalek, Deniz Seyithanoglu, Timurhan Cebeci, Halil Ertugrul Aktas, Gulbiz Dagoglu Kartal, Sabahattin Kaymakoglu, Sukru Mehmet Erturk, Yuri Velichko, Daniela Ladner, Amir A. Borhani, Alpay Medetalibeyoglu, Gorkem Durak, Ulas Bagci

Abstract: 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 lea… ▽ More 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. △ Less

Submitted 7 May, 2025; v1 submitted 6 October, 2024; originally announced October 2024.