arXiv subjects

Bulat Ibragimov

Publications and source records attributed to Bulat Ibragimov.

16 recordsLinked to original sources

arXiv2026

Predicting Radiologist Expertise from 3D Gaze Patterns During CT Interpretation

Accurate interpretation of volumetric CT requires efficient navigation of 3D image volumes and attention to diagnostically relevant regions. While eye-tracking has been widely studied in 2D medical imaging, its use for expertise assessment in CT settings remains limited. We propose a gaze-informed transformer framework for expertise classification in thoracic CT. Using a DINOv2 backbone, radiologist fixation patterns are integrated into volumetric feature learning through (1) a learnable log-space bias in self-attention and (2) gaze-weighted pooling of patch embeddings. We trained and evaluated our approach on 182 CT reading sessions from five radiologists with varying levels of experience. On a held-out test set, the model achieves an ROC-AUC of 0.91 and F1 score of 0.86, outperforming adapted methods. These findings suggest that incorporating visual search behavior into transformers may support objective, process-based expertise assessment in radiology. Code is available via https://github.com/leiluk1/GazeToSkill.

cs.CV↗

arXiv2026

MedPruner: Training-Free Hierarchical Token Pruning for Efficient 3D Medical Image Understanding in Vision-Language Models

While specialized Medical Vision-Language Models (VLMs) have achieved remarkable success in interpreting 2D and 3D medical modalities, their deployment for 3D volumetric data remains constrained by significant computational inefficiencies. Current architectures typically suffer from massive anatomical redundancy due to the direct concatenation of consecutive 2D slices and lack the flexibility to handle heterogeneous information densities across different slices using fixed pruning ratios. To address these challenges, we propose MedPruner, a training-free and model-agnostic hierarchical token pruning framework specifically designed for efficient 3D medical image understanding. MedPruner introduces a two-stage mechanism: an Inter-slice Anchor-based Filtering module to eliminate slice-level temporal redundancy, followed by a Dynamic Information Nucleus Selection strategy that achieves adaptive token-level compression by quantifying cumulative attention weights. Extensive experiments on three 3D medical benchmarks and across three diverse medical VLMs reveal massive token redundancy in existing architectures. Notably, MedPruner enables models such as MedGemma-1.5 to maintain or even exceed their original performance while retaining fewer than 5\% of visual tokens, thereby reducing visual-token overhead and validating the necessity of dynamic token selection for practical clinical deployment. Our code is available at https://github.com/CUHK-AIM-Group/MedPruner.

cs.CV↗

arXiv2026

Visual Search Patterns in 3D Pancreatic Imaging: An Eye Tracking Study

Eye tracking has emerged as a powerful tool for examining visual perception and search strategies in various domains, including medicine. While it is relatively straightforward to apply in 2D settings, its use in 3D medical imaging remains challenging and not yet well explored. This gap is particularly relevant for radiology, where volumetric images such as computed tomography (CT) scans are routinely read by medical experts. Radiologists typically interpret these images by navigating through hundreds of 2D slices, most often viewed in the axial projection. A taxonomy of eye movement data during navigation through a CT volume could be valuable to understand how radiologists approach diagnostic tasks. As an example of the derived taxonomy, we asked two radiologists to search abdominal CTs of the pancreas. We collect eye tracking data and align eye gaze movements with slice navigation to visualize the representation of the pancreas through volume and analyze clinicians' gaze behavior in both space and time.

cs.CV↗

arXiv2026

GPU Memory and Utilization Estimation for Training-Aware Resource Management: Opportunities and Limitations

Collocating deep learning training tasks improves GPU utilization but risks resource contention, severe slowdowns, and out-of-memory (OOM) failures. Accurate memory estimation is essential for robust collocation, and GPU utilization estimation -- a key proxy for contention -- enables interference-aware scheduling. Existing GPU memory estimators span three paradigms -- analytical models, CPU-side libraries, and ML-based estimators -- each with distinct limitations: dependence on detailed model specifications, intrusive integration, poor generalization, and varying latency overhead. GPU heterogeneity further complicates estimation, as identical tasks can exhibit different memory footprints across hardware generations. GPU utilization remains comparatively understudied, further complicated by non-additive utilization metrics and GPU heterogeneity. We conduct a systematic analysis of representative estimators from each paradigm -- Horus, PyTorch FakeTensor, and our lightweight ML-based estimator -- evaluating accuracy, generalizability, and overhead. We construct a synthetic dataset spanning MLPs, CNNs, and Transformers with controlled architectural variations, and train MLP- and Transformer-based estimators for memory prediction, and experiment with utilization estimation. Our evaluation reveals key tradeoffs and validates estimators against real-world unseen models. Significant challenges remain: analytical models lack generalization and cannot easily be extended to new GPU architectures or accurately reflect memory optimization savings; CPU-side libraries impose intrusive integration overhead; and both analytical and ML-based estimators rely on model specifications or computation graphs, limiting generalization across diverse architectures and hardware variants. We release all datasets, tools, and artifacts to support further research.

cs.DC↗

arXiv2025

rNCA: Self-Repairing Segmentation Masks

Accurately predicting topologically correct masks remains a difficult task for general segmentation models, which often produce fragmented or disconnected outputs. Fixing these artifacts typically requires hand-crafted refinement rules or architectures specialized to a particular task. Here, we show that Neural Cellular Automata (NCA) can be directly re-purposed as an effective refinement mechanism, using local, iterative updates guided by image context to repair segmentation masks. By training on imperfect masks and ground truths, the automaton learns the structural properties of the target shape while relying solely on local information. When applied to coarse, globally predicted masks, the learned dynamics progressively reconnect broken regions, prune loose fragments and converge towards stable, topologically consistent results. We show how refinement NCA (rNCA) can be easily applied to repair common topological errors produced by different base segmentation models and tasks: for fragmented retinal vessels, it yields 2-3% gains in Dice/clDice and improves Betti errors, reducing $β_0$ errors by 60% and $β_1$ by 20%; for myocardium, it repairs 61.5% of broken cases in a zero-shot setting while lowering ASSD and HD by 19% and 16%, respectively. This showcases NCA as effective and broadly applicable refiners.

cs.CV↗

arXiv2025

DENTEX: Dental Enumeration and Tooth Pathosis Detection Benchmark for Panoramic X-ray

Panoramic X-rays are frequently used in dentistry for treatment planning, but their interpretation can be both time-consuming and prone to error. Artificial intelligence (AI) has the potential to aid in the analysis of these X-rays, thereby improving the accuracy of dental diagnoses and treatment plans. Nevertheless, designing automated algorithms for this purpose poses significant challenges, mainly due to the scarcity of annotated data and variations in anatomical structure. To address these issues, we organized the Dental Enumeration and Diagnosis on Panoramic X-rays Challenge (DENTEX) in association with the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) in 2023. This challenge aims to promote the development of algorithms for multi-label detection of abnormal teeth, using three types of hierarchically annotated data: partially annotated quadrant data, partially annotated quadrant-enumeration data, and fully annotated quadrant-enumeration-diagnosis data, inclusive of four different diagnoses. In this paper, we present a comprehensive analysis of the methods and results from the challenge. Our findings reveal that top performers succeeded through diverse, specialized strategies, from segmentation-guided pipelines to highly-engineered single-stage detectors, using advanced Transformer and diffusion models. These strategies significantly outperformed traditional approaches, particularly for the challenging tasks of tooth enumeration and subtle disease classification. By dissecting the architectural choices that drove success, this paper provides key insights for future development of AI-powered tools that can offer more precise and efficient diagnosis and treatment planning in dentistry. The evaluation code and datasets can be accessed at https://github.com/ibrahimethemhamamci/DENTEX

cs.CV↗

arXiv2025

Extremal Contours: Gradient-driven contours for compact visual attribution

Faithful yet compact explanations for vision models remain a challenge, as commonly used dense perturbation masks are often fragmented and overfitted, needing careful post-processing. Here, we present a training-free explanation method that replaces dense masks with smooth tunable contours. A star-convex region is parameterized by a truncated Fourier series and optimized under an extremal preserve/delete objective using the classifier gradients. The approach guarantees a single, simply connected mask, cuts the number of free parameters by orders of magnitude, and yields stable boundary updates without cleanup. Restricting solutions to low-dimensional, smooth contours makes the method robust to adversarial masking artifacts. On ImageNet classifiers, it matches the extremal fidelity of dense masks while producing compact, interpretable regions with improved run-to-run consistency. Explicit area control also enables importance contour maps, yielding a transparent fidelity-area profiles. Finally, we extend the approach to multi-contour and show how it can localize multiple objects within the same framework. Across benchmarks, the method achieves higher relevance mass and lower complexity than gradient and perturbation based baselines, with especially strong gains on self-supervised DINO models where it improves relevance mass by over 15% and maintains positive faithfulness correlations.

cs.CV↗

arXiv2024

Gaze-Assisted Medical Image Segmentation

The annotation of patient organs is a crucial part of various diagnostic and treatment procedures, such as radiotherapy planning. Manual annotation is extremely time-consuming, while its automation using modern image analysis techniques has not yet reached levels sufficient for clinical adoption. This paper investigates the idea of semi-supervised medical image segmentation using human gaze as interactive input for segmentation correction. In particular, we fine-tuned the Segment Anything Model in Medical Images (MedSAM), a public solution that uses various prompt types as additional input for semi-automated segmentation correction. We used human gaze data from reading abdominal images as a prompt for fine-tuning MedSAM. The model was validated on a public WORD database, which consists of 120 CT scans of 16 abdominal organs. The results of the gaze-assisted MedSAM were shown to be superior to the results of the state-of-the-art segmentation models. In particular, the average Dice coefficient for 16 abdominal organs was 85.8%, 86.7%, 81.7%, and 90.5% for nnUNetV2, ResUNet, original MedSAM, and our gaze-assisted MedSAM model, respectively.

cs.CV↗

arXiv2024

Generating Synthetic Computed Tomography for Radiotherapy: SynthRAD2023 Challenge Report

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>97.3%/97.0%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

physics.med-ph↗

arXiv2024

Building an AI Support Tool for Real-time Ulcerative Colitis Diagnosis

Ulcerative Colitis (UC) is a chronic inflammatory bowel disease decreasing life quality through symptoms such as bloody diarrhoea and abdominal pain. Endoscopy is a cornerstone of diagnosis and monitoring of UC. The Mayo endoscopic subscore (MES) index is the standard for measuring UC severity during endoscopic evaluation. However, the MES is subject to high inter-observer variability leading to misdiagnosis and suboptimal treatment. We propose using a machine-learning based MES classification system to support the endoscopic process and to mitigate the observer-variability. The system runs real-time in the clinic and augments doctors' decision-making during the endoscopy. This project report outlines the process of designing, creating and evaluating our system. We describe our initial evaluation, which is a combination of a standard non-clinical model test and a first clinical test of the system on a real patient.

eess.IV↗

arXiv2023

Cross-Modal Conceptualization in Bottleneck Models

Concept Bottleneck Models (CBMs) assume that training examples (e.g., x-ray images) are annotated with high-level concepts (e.g., types of abnormalities), and perform classification by first predicting the concepts, followed by predicting the label relying on these concepts. The main difficulty in using CBMs comes from having to choose concepts that are predictive of the label and then having to label training examples with these concepts. In our approach, we adopt a more moderate assumption and instead use text descriptions (e.g., radiology reports), accompanying the images in training, to guide the induction of concepts. Our cross-modal approach treats concepts as discrete latent variables and promotes concepts that (1) are predictive of the label, and (2) can be predicted reliably from both the image and text. Through experiments conducted on datasets ranging from synthetic datasets (e.g., synthetic images with generated descriptions) to realistic medical imaging datasets, we demonstrate that cross-modal learning encourages the induction of interpretable concepts while also facilitating disentanglement. Our results also suggest that this guidance leads to increased robustness by suppressing the reliance on shortcut features.

cs.CL↗

arXiv2023

A Sequential Framework for Detection and Classification of Abnormal Teeth in Panoramic X-rays

This paper describes our solution for the Dental Enumeration and Diagnosis on Panoramic X-rays Challenge at MICCAI 2023. Our approach consists of a multi-step framework tailored to the task of detecting and classifying abnormal teeth. The solution includes three sequential stages: dental instance detection, healthy instance filtering, and abnormal instance classification. In the first stage, we employed a Faster-RCNN model for detecting and identifying teeth. In subsequent stages, we designed a model that merged the encoding pathway of a pretrained U-net, optimized for dental lesion detection, with the Vgg16 architecture. The resulting model was first used for filtering out healthy teeth. Then, any identified abnormal teeth were categorized, potentially falling into one or more of the following conditions: embedded, periapical lesion, caries, deep caries. The model performing dental instance detection achieved an AP score of 0.49. The model responsible for identifying healthy teeth attained an F1 score of 0.71. Meanwhile, the model trained for multi-label dental disease classification achieved an F1 score of 0.76. The code is available at https://github.com/tudordascalu/2d-teeth-detection-challenge.

eess.IV↗

arXiv2023

3DTeethSeg'22: 3D Teeth Scan Segmentation and Labeling Challenge

Teeth localization, segmentation, and labeling from intra-oral 3D scans are essential tasks in modern dentistry to enhance dental diagnostics, treatment planning, and population-based studies on oral health. However, developing automated algorithms for teeth analysis presents significant challenges due to variations in dental anatomy, imaging protocols, and limited availability of publicly accessible data. To address these challenges, the 3DTeethSeg'22 challenge was organized in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2022, with a call for algorithms tackling teeth localization, segmentation, and labeling from intraoral 3D scans. A dataset comprising a total of 1800 scans from 900 patients was prepared, and each tooth was individually annotated by a human-machine hybrid algorithm. A total of 6 algorithms were evaluated on this dataset. In this study, we present the evaluation results of the 3DTeethSeg'22 challenge. The 3DTeethSeg'22 challenge code can be accessed at: https://github.com/abenhamadou/3DTeethSeg22_challenge

cs.CV↗

arXiv2022

Improved automated lesion segmentation in whole-body FDG/PET-CT via Test-Time Augmentation

Numerous oncology indications have extensively quantified metabolically active tumors using positron emission tomography (PET) and computed tomography (CT). F-fluorodeoxyglucose-positron emission tomography (FDG-PET) is frequently utilized in clinical practice and clinical drug research to detect and measure metabolically active malignancies. The assessment of tumor burden using manual or computer-assisted tumor segmentation in FDG-PET images is widespread. Deep learning algorithms have also produced effective solutions in this area. However, there may be a need to improve the performance of a pre-trained deep learning network without the opportunity to modify this network. We investigate the potential benefits of test-time augmentation for segmenting tumors from PET-CT pairings. We applied a new framework of multilevel and multimodal tumor segmentation techniques that can simultaneously consider PET and CT data. In this study, we improve the network using a learnable composition of test time augmentations. We trained U-Net and Swin U-Netr on the training database to determine how different test time augmentation improved segmentation performance. We also developed an algorithm that finds an optimal test time augmentation contribution coefficient set. Using the newly trained U-Net and Swin U-Netr results, we defined an optimal set of coefficients for test-time augmentation and utilized them in combination with a pre-trained fixed nnU-Net. The ultimate idea is to improve performance at the time of testing when the model is fixed. Averaging the predictions with varying ratios on the augmented data can improve prediction accuracy. Our code will be available at \url{https://github.com/sepidehamiri/pet\_seg\_unet}

eess.IV↗

arXiv2022

NeuralSympCheck: A Symptom Checking and Disease Diagnostic Neural Model with Logic Regularization

The symptom checking systems inquire users for their symptoms and perform a rapid and affordable medical assessment of their condition. The basic symptom checking systems based on Bayesian methods, decision trees, or information gain methods are easy to train and do not require significant computational resources. However, their drawbacks are low relevance of proposed symptoms and insufficient quality of diagnostics. The best results on these tasks are achieved by reinforcement learning models. Their weaknesses are the difficulty of developing and training such systems and limited applicability to cases with large and sparse decision spaces. We propose a new approach based on the supervised learning of neural models with logic regularization that combines the advantages of the different methods. Our experiments on real and synthetic data show that the proposed approach outperforms the best existing methods in the accuracy of diagnosis when the number of diagnoses and symptoms is large.

cs.CL↗

arXiv2019

Minimal Variance Sampling in Stochastic Gradient Boosting

Stochastic Gradient Boosting (SGB) is a widely used approach to regularization of boosting models based on decision trees. It was shown that, in many cases, random sampling at each iteration can lead to better generalization performance of the model and can also decrease the learning time. Different sampling approaches were proposed, where probabilities are not uniform, and it is not currently clear which approach is the most effective. In this paper, we formulate the problem of randomization in SGB in terms of optimization of sampling probabilities to maximize the estimation accuracy of split scoring used to train decision trees. This optimization problem has a closed-form nearly optimal solution, and it leads to a new sampling technique, which we call Minimal Variance Sampling (MVS). The method both decreases the number of examples needed for each iteration of boosting and increases the quality of the model significantly as compared to the state-of-the art sampling methods. The superiority of the algorithm was confirmed by introducing MVS as a new default option for subsampling in CatBoost, a gradient boosting library achieving state-of-the-art quality on various machine learning tasks.

stat.ML↗