Bulat Ibragimov

Sepideh Amiri, Bulat Ibragimov

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}

Tudor Dascalu, Shaqayeq Ramezanzade, Azam Bakhshandeh et al.

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.

Malte Silbernagel, Albert Alonso, Jens Petersen et al.

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.

Aleksandr Nesterov, Bulat Ibragimov, Dmitriy Umerenkov et al.

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.

Ehsan Yousefzadeh-Asl-Miandoab, Reza Karimzadeh, Danyal Yorulmaz et al.

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.

Reza Karimzadeh, Albert Alonso, Frans Zdyb et al.

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.

Danis Alukaev, Semen Kiselev, Ilya Pershin et al.

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.

Shengyuan Liu, Zanting Ye, Yunrui Lin et al.

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 to maintain or even exceed their original performance while retaining fewer than 5% of visual tokens, thereby drastically reducing computational overhead and validating the necessity of dynamic token selection for practical clinical deployment. Our code will be released.

Anna Anikina, Leila Khaertdinova, Trine Balschmidt et al.

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.

Ibrahim Ethem Hamamci, Sezgin Er, Omer Faruk Durugol et al.

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

Achraf Ben-Hamadou, Oussama Smaoui, Ahmed Rekik et al.

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

Leila Khaertdinova, Ilya Pershin, Tatiana Shmykova et al.

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.

Ehsan Yousefzadeh-Asl-Miandoab, Reza Karimzadeh, Bulat Ibragimov et al.

GPUs running deep learning (DL) workloads are frequently underutilized. Collocating multiple DL training tasks on the same GPU can improve utilization but introduces two key risks: (1) out-of-memory (OOM) crashes for newly scheduled tasks, and (2) severe performance interference among co-running tasks, which can negate any throughput gains. These issues reduce system robustness, quality of service, and energy efficiency. We present CARMA, a task-level, collocation-aware resource management system for the server-scale. CARMA addresses collocation challenges via (1) fine-grained monitoring and bookkeeping of GPUs and a collocation risk analysis that filters out the high-risk GPUs; (2) task placement policies that cap GPU utilization to avoid OOMs and limit interference; (3) integration of GPU memory need estimators for DL tasks to minimize OOMs during collocation; and (4) a lightweight recovery method that relaunches jobs crashed due to OOMs. Our evaluation on a DL training workload derived from real-world traces shows that CARMA uses GPUs more efficiently by making more informed collocation decisions: for the best-performing collocation policy, CARMA increases GPU streaming multiprocessor (SM) utilization by 54%, the parallelism achieved per SM by 61%, and memory use by 62%. This results in a $\sim$35% and $\sim$15% reduction in the end-to-end execution time (makespan) and GPU energy consumption, respectively, for this workload.

Bulat Ibragimov, Gleb Gusev

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.