arXiv subjects

Baris Turkbey

Publications and source records attributed to Baris Turkbey.

At least 19 recordsLinked to original sources

arXiv2026

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

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.

cs.CV↗

arXiv2025

Reasoning Visual Language Model for Chest X-Ray Analysis

Vision-language models (VLMs) have shown strong promise for medical image analysis, but most remain opaque, offering predictions without the transparent, stepwise reasoning clinicians rely on. We present a framework that brings chain-of-thought (CoT) reasoning to chest X-ray interpretation. Inspired by reasoning-first training paradigms, our approach is designed to learn how experts reason, not just what they conclude, by aligning intermediate steps with observable image evidence and radiology workflow. Beyond accuracy, the explicit reasoning traces support clinical auditability: they reveal why a conclusion was reached, which alternatives were considered, and where uncertainty remains, enabling quality assurance, error analysis, and safer human-AI collaboration. Our model couples high-fidelity visual encoding with a two-stage training recipe: a reasoning-style supervised fine-tuning (SFT) followed by reinforcement learning (RL) that uses verifiable rewards over a list of X-ray abnormalities. The model outputs reasoning that mirrors radiologists systematic thought process, uncertainty, and differential diagnosis. In out-of-distribution evaluation, the approach achieves competitive multi-label classification while improving interpretability. In a reader study with expert radiologists, full reasoning traces increased confidence, supported error auditing, and reduced time to finalize reports. We release code and the model NV-Reason-CXR-3B to support community progress toward trustworthy, explainable AI in chest radiography and other medical imaging tasks where reasoning quality is as critical as prediction quality.

cs.CV↗

arXiv2025

MAISI-v2: Accelerated 3D High-Resolution Medical Image Synthesis with Rectified Flow and Region-specific Contrastive Loss

Medical image synthesis is an important topic for both clinical and research applications. Recently, diffusion models have become a leading approach in this area. Despite their strengths, many existing methods struggle with (1) limited generalizability that only work for specific body regions or voxel spacings, (2) slow inference, which is a common issue for diffusion models, and (3) weak alignment with input conditions, which is a critical issue for medical imaging. MAISI, a previously proposed framework, addresses generalizability issues but still suffers from slow inference and limited condition consistency. In this work, we present MAISI-v2, the first accelerated 3D medical image synthesis framework that integrates rectified flow to enable fast and high quality generation. To further enhance condition fidelity, we introduce a novel region-specific contrastive loss to enhance the sensitivity to region of interest. Our experiments show that MAISI-v2 can achieve SOTA image quality with $33 \times$ acceleration for latent diffusion model. We also conducted a downstream segmentation experiment to show that the synthetic images can be used for data augmentation. We release our code, training details, model weights, and a GUI demo to facilitate reproducibility and promote further development within the community.

cs.CV↗

arXiv2025

Scaling Artificial Intelligence for Prostate Cancer Detection on MRI towards Organized Screening and Primary Diagnosis in a Global, Multiethnic Population (Study Protocol)

In this intercontinental, confirmatory study, we include a retrospective cohort of 22,481 MRI examinations (21,288 patients; 46 cities in 22 countries) to train and externally validate the PI-CAI-2B model, i.e., an efficient, next-generation iteration of the state-of-the-art AI system that was developed for detecting Gleason grade group $\geq$2 prostate cancer on MRI during the PI-CAI study. Of these examinations, 20,471 cases (19,278 patients; 26 cities in 14 countries) from two EU Horizon projects (ProCAncer-I, COMFORT) and 12 independent centers based in Europe, North America, Asia and Africa, are used for training and internal testing. Additionally, 2010 cases (2010 patients; 20 external cities in 12 countries) from population-based screening (STHLM3-MRI, IP1-PROSTAGRAM trials) and primary diagnostic settings (PRIME trial) based in Europe, North and South Americas, Asia and Australia, are used for external testing. Primary endpoint is the proportion of AI-based assessments in agreement with the standard of care diagnoses (i.e., clinical assessments made by expert uropathologists on histopathology, if available, or at least two expert urogenital radiologists in consensus; with access to patient history and peer consultation) in the detection of Gleason grade group $\geq$2 prostate cancer within the external testing cohorts. Our statistical analysis plan is prespecified with a hypothesis of diagnostic interchangeability to the standard of care at the PI-RADS $\geq$3 (primary diagnosis) or $\geq$4 (screening) cut-off, considering an absolute margin of 0.05 and reader estimates derived from the PI-CAI observer study (62 radiologists reading 400 cases). Secondary measures comprise the area under the receiver operating characteristic curve (AUROC) of the AI system stratified by imaging quality, patient age and patient ethnicity to identify underlying biases (if any).

eess.IV↗

arXiv2025

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

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

eess.IV↗

arXiv2025

OpenPros: A Large-Scale Dataset for Limited View Prostate Ultrasound Computed Tomography

Prostate cancer is one of the most prevalent and deadly cancers among men, motivating the development of accurate and accessible imaging technologies for early detection. Ultrasound computed tomography (USCT) reconstructs quantitative tissue parameters such as speed-of-sound (SOS) and is a promising low-cost alternative to existing modalities. However, prostate USCT remains challenging due to limited-angle acquisition, strong tissue heterogeneity, bone-induced wave distortion, and the lack of large-scale, anatomically realistic datasets for method development and evaluation. We introduce OPENPROS, the first large-scale benchmark dataset for limited-angle prostate USCT, designed to systematically evaluate machine learning methods for quantitative inverse problems. OPENPROS contains over 280,000 paired samples of realistic 2D SOS maps and corresponding ultrasound full-waveform data, generated from anatomically accurate 3D digital prostate models derived from 4 clinical MRI/CT scans and 62 ex vivo prostate specimens with experimental ultrasound measurements. Wave propagation is simulated under clinically realistic configurations using open-source finite-difference time-domain and Runge-Kutta solvers. We provide standardized training, in-distribution, and out-of-distribution benchmarks and evaluate representative deep learning baselines. While learning-based methods substantially improve inference speed and reconstruction accuracy over physics-based approaches, results highlight persistent challenges in robustness, generalization, and high-resolution reconstruction quality. By publicly releasing OPENPROS, we establish a rigorous benchmark to support research in inverse problems, physics-guided learning, and operator learning, and to bridge the gap between machine learning research and practical USCT deployment. The dataset is available at https://open-pros.github.io/.

physics.med-ph↗

arXiv2025

Text2CT: Towards 3D CT Volume Generation from Free-text Descriptions Using Diffusion Model

Generating 3D CT volumes from descriptive free-text inputs presents a transformative opportunity in diagnostics and research. In this paper, we introduce Text2CT, a novel approach for synthesizing 3D CT volumes from textual descriptions using the diffusion model. Unlike previous methods that rely on fixed-format text input, Text2CT employs a novel prompt formulation that enables generation from diverse, free-text descriptions. The proposed framework encodes medical text into latent representations and decodes them into high-resolution 3D CT scans, effectively bridging the gap between semantic text inputs and detailed volumetric representations in a unified 3D framework. Our method demonstrates superior performance in preserving anatomical fidelity and capturing intricate structures as described in the input text. Extensive evaluations show that our approach achieves state-of-the-art results, offering promising potential applications in diagnostics, and data augmentation.

eess.IV↗

arXiv2024

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data$-$features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

cs.CV↗

arXiv2024

MAISI: Medical AI for Synthetic Imaging

Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns. This paper introduces the Medical AI for Synthetic Imaging (MAISI), an innovative approach using the diffusion model to generate synthetic 3D computed tomography (CT) images to address those challenges. MAISI leverages the foundation volume compression network and the latent diffusion model to produce high-resolution CT images (up to a landmark volume dimension of 512 x 512 x 768 ) with flexible volume dimensions and voxel spacing. By incorporating ControlNet, MAISI can process organ segmentation, including 127 anatomical structures, as additional conditions and enables the generation of accurately annotated synthetic images that can be used for various downstream tasks. Our experiment results show that MAISI's capabilities in generating realistic, anatomically accurate images for diverse regions and conditions reveal its promising potential to mitigate challenges using synthetic data.

eess.IV↗

arXiv2024

Location-based Radiology Report-Guided Semi-supervised Learning for Prostate Cancer Detection

Prostate cancer is one of the most prevalent malignancies in the world. While deep learning has potential to further improve computer-aided prostate cancer detection on MRI, its efficacy hinges on the exhaustive curation of manually annotated images. We propose a novel methodology of semisupervised learning (SSL) guided by automatically extracted clinical information, specifically the lesion locations in radiology reports, allowing for use of unannotated images to reduce the annotation burden. By leveraging lesion locations, we refined pseudo labels, which were then used to train our location-based SSL model. We show that our SSL method can improve prostate lesion detection by utilizing unannotated images, with more substantial impacts being observed when larger proportions of unannotated images are used.

cs.CV↗

arXiv2024

VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging

Foundation models for interactive segmentation in 2D natural images and videos have sparked significant interest in building 3D foundation models for medical imaging. However, the domain gaps and clinical use cases for 3D medical imaging require a dedicated model that diverges from existing 2D solutions. Specifically, such foundation models should support a full workflow that can actually reduce human effort. Treating 3D medical images as sequences of 2D slices and reusing interactive 2D foundation models seems straightforward, but 2D annotation is too time-consuming for 3D tasks. Moreover, for large cohort analysis, it's the highly accurate automatic segmentation models that reduce the most human effort. However, these models lack support for interactive corrections and lack zero-shot ability for novel structures, which is a key feature of "foundation". While reusing pre-trained 2D backbones in 3D enhances zero-shot potential, their performance on complex 3D structures still lags behind leading 3D models. To address these issues, we present VISTA3D, Versatile Imaging SegmenTation and Annotation model, that targets to solve all these challenges and requirements with one unified foundation model. VISTA3D is built on top of the well-established 3D segmentation pipeline, and it is the first model to achieve state-of-the-art performance in both 3D automatic (supporting 127 classes) and 3D interactive segmentation, even when compared with top 3D expert models on large and diverse benchmarks. Additionally, VISTA3D's 3D interactive design allows efficient human correction, and a novel 3D supervoxel method that distills 2D pretrained backbones grants VISTA3D top 3D zero-shot performance. We believe the model, recipe, and insights represent a promising step towards a clinically useful 3D foundation model. Code and weights are publicly available at https://github.com/Project-MONAI/VISTA.

cs.CV↗

arXiv2024

Large-Scale Multi-Center CT and MRI Segmentation of Pancreas with Deep Learning

Automated volumetric segmentation of the pancreas on cross-sectional imaging is needed for diagnosis and follow-up of pancreatic diseases. While CT-based pancreatic segmentation is more established, MRI-based segmentation methods are understudied, largely due to a lack of publicly available datasets, benchmarking research efforts, and domain-specific deep learning methods. In this retrospective study, we collected a large dataset (767 scans from 499 participants) of T1-weighted (T1W) and T2-weighted (T2W) abdominal MRI series from five centers between March 2004 and November 2022. We also collected CT scans of 1,350 patients from publicly available sources for benchmarking purposes. We developed a new pancreas segmentation method, called PanSegNet, combining the strengths of nnUNet and a Transformer network with a new linear attention module enabling volumetric computation. We tested PanSegNet's accuracy in cross-modality (a total of 2,117 scans) and cross-center settings with Dice and Hausdorff distance (HD95) evaluation metrics. We used Cohen's kappa statistics for intra and inter-rater agreement evaluation and paired t-tests for volume and Dice comparisons, respectively. For segmentation accuracy, we achieved Dice coefficients of 88.3% (std: 7.2%, at case level) with CT, 85.0% (std: 7.9%) with T1W MRI, and 86.3% (std: 6.4%) with T2W MRI. There was a high correlation for pancreas volume prediction with R^2 of 0.91, 0.84, and 0.85 for CT, T1W, and T2W, respectively. We found moderate inter-observer (0.624 and 0.638 for T1W and T2W MRI, respectively) and high intra-observer agreement scores. All MRI data is made available at https://osf.io/kysnj/. Our source code is available at https://github.com/NUBagciLab/PaNSegNet.

eess.IV↗

arXiv2024

Detection of Peri-Pancreatic Edema using Deep Learning and Radiomics Techniques

Identifying peri-pancreatic edema is a pivotal indicator for identifying disease progression and prognosis, emphasizing the critical need for accurate detection and assessment in pancreatitis diagnosis and management. This study \textit{introduces a novel CT dataset sourced from 255 patients with pancreatic diseases, featuring annotated pancreas segmentation masks and corresponding diagnostic labels for peri-pancreatic edema condition}. With the novel dataset, we first evaluate the efficacy of the \textit{LinTransUNet} model, a linear Transformer based segmentation algorithm, to segment the pancreas accurately from CT imaging data. Then, we use segmented pancreas regions with two distinctive machine learning classifiers to identify existence of peri-pancreatic edema: deep learning-based models and a radiomics-based eXtreme Gradient Boosting (XGBoost). The LinTransUNet achieved promising results, with a dice coefficient of 80.85\%, and mIoU of 68.73\%. Among the nine benchmarked classification models for peri-pancreatic edema detection, \textit{Swin-Tiny} transformer model demonstrated the highest recall of $98.85 \pm 0.42$ and precision of $98.38\pm 0.17$. Comparatively, the radiomics-based XGBoost model achieved an accuracy of $79.61\pm4.04$ and recall of $91.05\pm3.28$, showcasing its potential as a supplementary diagnostic tool given its rapid processing speed and reduced training time. Our code is available \url{https://github.com/NUBagciLab/Peri-Pancreatic-Edema-Detection}.

eess.IV↗

arXiv2024

A Probabilistic Hadamard U-Net for MRI Bias Field Correction

Magnetic field inhomogeneity correction remains a challenging task in MRI analysis. Most established techniques are designed for brain MRI by supposing that image intensities in the identical tissue follow a uniform distribution. Such an assumption cannot be easily applied to other organs, especially those that are small in size and heterogeneous in texture (large variations in intensity), such as the prostate. To address this problem, this paper proposes a probabilistic Hadamard U-Net (PHU-Net) for prostate MRI bias field correction. First, a novel Hadamard U-Net (HU-Net) is introduced to extract the low-frequency scalar field, multiplied by the original input to obtain the prototypical corrected image. HU-Net converts the input image from the time domain into the frequency domain via Hadamard transform. In the frequency domain, high-frequency components are eliminated using the trainable filter (scaling layer), hard-thresholding layer, and sparsity penalty. Next, a conditional variational autoencoder is used to encode possible bias field-corrected variants into a low-dimensional latent space. Random samples drawn from latent space are then incorporated with a prototypical corrected image to generate multiple plausible images. Experimental results demonstrate the effectiveness of PHU-Net in correcting bias-field in prostate MRI with a fast inference speed. It has also been shown that prostate MRI segmentation accuracy improves with the high-quality corrected images from PHU-Net. The code will be available in the final version of this manuscript.

eess.IV↗

arXiv2024

Using YOLO v7 to Detect Kidney in Magnetic Resonance Imaging

Introduction This study explores the use of the latest You Only Look Once (YOLO V7) object detection method to enhance kidney detection in medical imaging by training and testing a modified YOLO V7 on medical image formats. Methods Study includes 878 patients with various subtypes of renal cell carcinoma (RCC) and 206 patients with normal kidneys. A total of 5657 MRI scans for 1084 patients were retrieved. 326 patients with 1034 tumors recruited from a retrospective maintained database, and bounding boxes were drawn around their tumors. A primary model was trained on 80% of annotated cases, with 20% saved for testing (primary test set). The best primary model was then used to identify tumors in the remaining 861 patients and bounding box coordinates were generated on their scans using the model. Ten benchmark training sets were created with generated coordinates on not-segmented patients. The final model used to predict the kidney in the primary test set. We reported the positive predictive value (PPV), sensitivity, and mean average precision (mAP). Results The primary training set showed an average PPV of 0.94 +/- 0.01, sensitivity of 0.87 +/- 0.04, and mAP of 0.91 +/- 0.02. The best primary model yielded a PPV of 0.97, sensitivity of 0.92, and mAP of 0.95. The final model demonstrated an average PPV of 0.95 +/- 0.03, sensitivity of 0.98 +/- 0.004, and mAP of 0.95 +/- 0.01. Conclusion Using a semi-supervised approach with a medical image library, we developed a high-performing model for kidney detection. Further external validation is required to assess the model's generalizability.

eess.IV↗

arXiv2023

GazeGNN: A Gaze-Guided Graph Neural Network for Chest X-ray Classification

Eye tracking research is important in computer vision because it can help us understand how humans interact with the visual world. Specifically for high-risk applications, such as in medical imaging, eye tracking can help us to comprehend how radiologists and other medical professionals search, analyze, and interpret images for diagnostic and clinical purposes. Hence, the application of eye tracking techniques in disease classification has become increasingly popular in recent years. Contemporary works usually transform gaze information collected by eye tracking devices into visual attention maps (VAMs) to supervise the learning process. However, this is a time-consuming preprocessing step, which stops us from applying eye tracking to radiologists' daily work. To solve this problem, we propose a novel gaze-guided graph neural network (GNN), GazeGNN, to leverage raw eye-gaze data without being converted into VAMs. In GazeGNN, to directly integrate eye gaze into image classification, we create a unified representation graph that models both images and gaze pattern information. With this benefit, we develop a real-time, real-world, end-to-end disease classification algorithm for the first time in the literature. This achievement demonstrates the practicality and feasibility of integrating real-time eye tracking techniques into the daily work of radiologists. To our best knowledge, GazeGNN is the first work that adopts GNN to integrate image and eye-gaze data. Our experiments on the public chest X-ray dataset show that our proposed method exhibits the best classification performance compared to existing methods. The code is available at https://github.com/ukaukaaaa/GazeGNN.

cs.CV↗

arXiv2023

Automatic segmentation of clear cell renal cell tumors, kidney, and cysts in patients with von Hippel-Lindau syndrome using U-net architecture on magnetic resonance images

We demonstrate automated segmentation of clear cell renal cell carcinomas (ccRCC), cysts, and surrounding normal kidney parenchyma in patients with von Hippel-Lindau (VHL) syndrome using convolutional neural networks (CNN) on Magnetic Resonance Imaging (MRI). We queried 115 VHL patients and 117 scans (3 patients have two separate scans) with 504 ccRCCs and 1171 cysts from 2015 to 2021. Lesions were manually segmented on T1 excretory phase, co-registered on all contrast-enhanced T1 sequences and used to train 2D and 3D U-Net. The U-Net performance was evaluated on 10 randomized splits of the cohort. The models were evaluated using the dice similarity coefficient (DSC). Our 2D U-Net achieved an average ccRCC lesion detection Area under the curve (AUC) of 0.88 and DSC scores of 0.78, 0.40, and 0.46 for segmentation of the kidney, cysts, and tumors, respectively. Our 3D U-Net achieved an average ccRCC lesion detection AUC of 0.79 and DSC scores of 0.67, 0.32, and 0.34 for kidney, cysts, and tumors, respectively. We demonstrated good detection and moderate segmentation results using U-Net for ccRCC on MRI. Automatic detection and segmentation of normal renal parenchyma, cysts, and masses may assist radiologists in quantifying the burden of disease in patients with VHL.

q-bio.QM↗

arXiv2022

Distance Map Supervised Landmark Localization for MR-TRUS Registration

In this work, we propose to explicitly use the landmarks of prostate to guide the MR-TRUS image registration. We first train a deep neural network to automatically localize a set of meaningful landmarks, and then directly generate the affine registration matrix from the location of these landmarks. For landmark localization, instead of directly training a network to predict the landmark coordinates, we propose to regress a full-resolution distance map of the landmark, which is demonstrated effective in avoiding statistical bias to unsatisfactory performance and thus improving performance. We then use the predicted landmarks to generate the affine transformation matrix, which outperforms the clinicians' manual rigid registration by a significant margin in terms of TRE.

cs.CV↗