Mahmut S. Gokmen

Mahmut S. Gokmen, Moneera N. Haque, Steve W. Leung et al.

Coronary artery calcium (CAC) scoring is a key predictor of cardiovascular risk, but it relies on ECG-gated CT scans, restricting its use to specialized cardiac imaging settings. We introduce an automated framework for CAC detection and lesion-specific Agatston scoring that operates across both gated and non-gated CT scans. At its core is CARD-ViT, a self-supervised Vision Transformer trained exclusively on gated CT data using DINO. Without any non-gated training data, our framework achieves 0.707 accuracy and a Cohen's kappa of 0.528 on the Stanford non-gated dataset, matching models trained directly on non-gated scans. On gated test sets, the framework achieves 0.910 accuracy with Cohen's kappa scores of 0.871 and 0.874 across independent datasets, demonstrating robust risk stratification. These results demonstrate the feasibility of cross-domain CAC scoring from gated to non-gated domains, supporting scalable cardiovascular screening in routine chest imaging without additional scans or annotations.

Mahmut S. Gokmen, Mitchell A. Klusty, Peter T. Nelson et al.

Whole-slide images (WSIs) contain tissue information distributed across multiple magnification levels, yet most self-supervised methods treat these scales as independent views. This separation prevents models from learning representations that remain stable when resolution changes, a key requirement for practical neuropathology workflows. This study introduces Magnification-Aware Distillation (MAD), a self-supervised strategy that links low-magnification context with spatially aligned high-magnification detail, enabling the model to learn how coarse tissue structure relates to fine cellular patterns. The resulting foundation model, MAD-NP, is trained entirely through this cross-scale correspondence without annotations. A linear classifier trained only on 10x embeddings maintains 96.7% of its performance when applied to unseen 40x tiles, demonstrating strong resolution-invariant representation learning. Segmentation outputs remain consistent across magnifications, preserving anatomical boundaries and minimizing noise. These results highlight the feasibility of scalable, magnification-robust WSI analysis using a unified embedding space

V. K. Cody Bumgardner, Mitchell A. Klusty, Mahmut S. Gokmen et al.

Automated radiology report generation from 3D computed tomography (CT) volumes is challenging due to extreme sequence lengths, severe class imbalance, and the tendency of large language models (LLMs) to ignore visual tokens in favor of linguistic priors. We present Ker-VLJEPA-3B, a four-phase curriculum learning framework for free-text report generation from thoracic CT volumes. A phased training curriculum progressively adapts a Llama 3.2 3B decoder to ground its output in visual features from a frozen, self-supervised encoder. Our visual backbone (LeJEPA ViT-Large) is trained via self-supervised joint-embedding prediction on unlabeled CTs, without text supervision. Unlike contrastive models (CLIP, BiomedCLIP), this language-free backbone yields modality-pure representations. Vision-language alignment is deferred to the curriculum's bridge and generation phases. This modality-agnostic design can integrate any self-supervised encoder into an LLM without paired text during foundation training. Methodological innovations include: (1) zone-constrained cross-attention compressing slice embeddings into 32 spatially-grounded visual tokens; (2) PCA whitening of anisotropic LLM embeddings; (3) a positive-findings-only strategy eliminating posterior collapse; (4) warm bridge initialization transferring projection weights; and (5) selective cross-attention freezing with elastic weight consolidation to prevent catastrophic forgetting. Evaluated on the CT-RATE benchmark (2,984 validation volumes, 18 classes), Ker-VLJEPA-3B achieves a macro F1 of 0.429, surpassing the state-of-the-art (U-VLM, macro F1 = 0.414) by 3.6%, and reaching 0.448 (+8.2%) with threshold optimization. Ablation studies confirm 56.6% of generation quality derives from patient-specific visual content. Code and weights are available.

Mahmut S. Gokmen, Jie Zhang, Ge Wang et al.

Diffusion models have significant impact on wide range of generative tasks, especially on image inpainting and restoration. Although the improvements on aiming for decreasing number of function evaluations (NFE), the iterative results are still computationally expensive. Consistency models are as a new family of generative models, enable single-step sampling of high quality data without the need for adversarial training. In this paper, we introduce the beta noise distribution, which provides flexibility in adjusting noise levels. This is combined with a sinusoidal curriculum that enhances the learning of the trajectory between the noise distribution and the posterior distribution of interest, allowing High Noise Improved Consistency Training (HN-iCT) to be trained in a supervised fashion. Additionally, High Noise Improved Consistency Training with Image Condition (HN-iCT-CN) architecture is introduced, enables to take Low Dose images as a condition for extracting significant features by Weighted Attention Gates (WAG).Our results indicate that unconditional image generation using HN-iCT significantly outperforms basic CT and iCT training techniques with NFE=1 on the CIFAR10 and CelebA datasets. Moreover, our image-conditioned model demonstrates exceptional performance in enhancing low-dose (LD) CT scans.

Mahmut S. Gokmen, Caner Ozcan, Moneera N. Haque et al.

Coronary artery disease (CAD), one of the leading causes of mortality worldwide, necessitates effective risk assessment strategies, with coronary artery calcium (CAC) scoring via computed tomography (CT) being a key method for prevention. Traditional methods, primarily based on UNET architectures implemented on pre-built models, face challenges like the scarcity of annotated CT scans containing CAC and imbalanced datasets, leading to reduced performance in segmentation and scoring tasks. In this study, we address these limitations by incorporating the self-supervised learning (SSL) technique of DINO (self-distillation with no labels), which trains without requiring CAC-specific annotations, enhancing its robustness in generating distinct features. The DINO-LG model, which leverages label guidance to focus on calcified areas, achieves significant improvements, with a sensitivity of 89% and specificity of 90% for detecting CAC-containing CT slices, compared to the standard DINO model's sensitivity of 79% and specificity of 77%. Additionally, false-negative and false-positive rates are reduced by 49% and 59%, respectively, instilling greater confidence in clinicians when ruling out calcification in low-risk patients and minimizing unnecessary imaging reviews by radiologists. Further, CAC scoring and segmentation tasks are conducted using a basic UNET architecture, applied specifically to CT slices identified by the DINO-LG model as containing calcified areas. This targeted approach enhances CAC scoring accuracy by feeding the UNET model with relevant slices, significantly improving diagnostic precision, reducing both false positives and false negatives, and ultimately lowering overall healthcare costs by minimizing unnecessary tests and treatments, presenting a valuable advancement in CAD risk assessment.

Mahmut S. Gokmen, Cody Bumgardner, Jie Zhang et al.

Consistency models possess high capabilities for image generation, advancing sampling steps to a single step through their advanced techniques. Current advancements move one step forward consistency training techniques and eliminates the limitation of distillation training. Even though the proposed curriculum and noise scheduling in improved training techniques yield better results than basic consistency models, it lacks well balanced noise distribution and its consistency between curriculum. In this study, it is investigated the balance between high and low noise levels in noise distribution and offered polynomial noise distribution to maintain the stability. This proposed polynomial noise distribution is also supported with a predefined Karras noises to prevent unique noise levels arises with Karras noise generation algorithm. Furthermore, by elimination of learned noisy steps with a curriculum based on sinusoidal function increase the performance of the model in denoising. To make a fair comparison with the latest released consistency model training techniques, experiments are conducted with same hyper-parameters except curriculum and noise distribution. The models utilized during experiments are determined with low depth to prove the robustness of our proposed technique. The results show that the polynomial noise distribution outperforms the model trained with log-normal noise distribution, yielding a 33.54 FID score after 100,000 training steps with constant discretization steps. Additionally, the implementation of a sinusoidal-based curriculum enhances denoising performance, resulting in a FID score of 30.48.