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Researcher profile

Ertunc Erdil

Ertunc Erdil contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer Visioneess.IVMachine LearningArtificial Intelligence

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Published work

6 published item(s)

preprint2026arXiv

VoxCor: Training-Free Volumetric Features for Multimodal Voxel Correspondence

Cross-modal 3D medical image analysis requires voxelwise representations that remain anatomically consistent across imaging contrasts, scanners, and acquisition protocols. Recent work has shown that frozen 2D Vision Transformer (ViT) foundation models can support such representations, but typical pipelines extract features along a single anatomical axis and adapt those features inside a registration solver for one image pair at a time, leaving complementary viewing directions unused and producing representations that do not transfer to new volumes. We introduce VoxCor, a training-free fit--transform method for reusable volumetric feature representations from frozen 2D ViT foundation models. During an offline fitting phase, VoxCor combines triplanar ViT inference with a compact closed-form weighted partial least squares (WPLS) projection that uses fitting-time voxel correspondences to select modality-stable anatomical directions in the triplanar feature space. At transform time, new volumes are mapped by triplanar ViT inference and linear projection alone, without fine-tuning or registration. Voxel correspondences can then be queried directly by nearest-neighbor search. We evaluate VoxCor on intra-subject Abdomen MR--CT and inter-subject HCP T2w--T1w tasks using deformable registration, voxelwise k-nearest-neighbor segmentation, and segmentation-center landmark localization. VoxCor improves the hardest cross-subject, cross-modality transfer settings, reduces encoder sensitivity for dense correspondence transfer, and yields registration performance competitive with handcrafted descriptors and learned 3D features. This positions VoxCor as a reusable feature layer for downstream multimodal analysis beyond pairwise registration. Code, configuration files, and implementation details are publicly available on GitHub at \href{https://github.com/guneytombak/VoxCor}{guneytombak/VoxCor}.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A Field of Experts Prior for Adapting Neural Networks at Test Time

Performance of convolutional neural networks (CNNs) in image analysis tasks is often marred in the presence of acquisition-related distribution shifts between training and test images. Recently, it has been proposed to tackle this problem by fine-tuning trained CNNs for each test image. Such test-time-adaptation (TTA) is a promising and practical strategy for improving robustness to distribution shifts as it requires neither data sharing between institutions nor annotating additional data. Previous TTA methods use a helper model to increase similarity between outputs and/or features extracted from a test image with those of the training images. Such helpers, which are typically modeled using CNNs, can be task-specific and themselves vulnerable to distribution shifts in their inputs. To overcome these problems, we propose to carry out TTA by matching the feature distributions of test and training images, as modelled by a field-of-experts (FoE) prior. FoEs model complicated probability distributions as products of many simpler expert distributions. We use 1D marginal distributions of a trained task CNN's features as experts in the FoE model. Further, we compute principal components of patches of the task CNN's features, and consider the distributions of PCA loadings as additional experts. We validate the method on 5 MRI segmentation tasks (healthy tissues in 4 anatomical regions and lesions in 1 one anatomy), using data from 17 clinics, and on a MRI registration task, using data from 3 clinics. We find that the proposed FoE-based TTA is generically applicable in multiple tasks, and outperforms all previous TTA methods for lesion segmentation. For healthy tissue segmentation, the proposed method outperforms other task-agnostic methods, but a previous TTA method which is specifically designed for segmentation performs the best for most of the tested datasets. Our code is publicly available.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Constrained Optimization to Train Neural Networks on Critical and Under-Represented Classes

Deep neural networks (DNNs) are notorious for making more mistakes for the classes that have substantially fewer samples than the others during training. Such class imbalance is ubiquitous in clinical applications and very crucial to handle because the classes with fewer samples most often correspond to critical cases (e.g., cancer) where misclassifications can have severe consequences. Not to miss such cases, binary classifiers need to be operated at high True Positive Rates (TPRs) by setting a higher threshold, but this comes at the cost of very high False Positive Rates (FPRs) for problems with class imbalance. Existing methods for learning under class imbalance most often do not take this into account. We argue that prediction accuracy should be improved by emphasizing reducing FPRs at high TPRs for problems where misclassification of the positive, i.e. critical, class samples are associated with higher cost. To this end, we pose the training of a DNN for binary classification as a constrained optimization problem and introduce a novel constraint that can be used with existing loss functions to enforce maximal area under the ROC curve (AUC) through prioritizing FPR reduction at high TPR. We solve the resulting constrained optimization problem using an Augmented Lagrangian method (ALM). Going beyond binary, we also propose two possible extensions of the proposed constraint for multi-class classification problems. We present experimental results for image-based binary and multi-class classification applications using an in-house medical imaging dataset, CIFAR10, and CIFAR100. Our results demonstrate that the proposed method improves the baselines in majority of the cases by attaining higher accuracy on critical classes while reducing the misclassification rate for the non-critical class samples.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Test-Time Adaptable Neural Networks for Robust Medical Image Segmentation

Convolutional Neural Networks (CNNs) work very well for supervised learning problems when the training dataset is representative of the variations expected to be encountered at test time. In medical image segmentation, this premise is violated when there is a mismatch between training and test images in terms of their acquisition details, such as the scanner model or the protocol. Remarkable performance degradation of CNNs in this scenario is well documented in the literature. To address this problem, we design the segmentation CNN as a concatenation of two sub-networks: a relatively shallow image normalization CNN, followed by a deep CNN that segments the normalized image. We train both these sub-networks using a training dataset, consisting of annotated images from a particular scanner and protocol setting. Now, at test time, we adapt the image normalization sub-network for \emph{each test image}, guided by an implicit prior on the predicted segmentation labels. We employ an independently trained denoising autoencoder (DAE) in order to model such an implicit prior on plausible anatomical segmentation labels. We validate the proposed idea on multi-center Magnetic Resonance imaging datasets of three anatomies: brain, heart and prostate. The proposed test-time adaptation consistently provides performance improvement, demonstrating the promise and generality of the approach. Being agnostic to the architecture of the deep CNN, the second sub-network, the proposed design can be utilized with any segmentation network to increase robustness to variations in imaging scanners and protocols. Our code is available at: \url{https://github.com/neerakara/test-time-adaptable-neural-networks-for-domain-generalization}.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Modelling the Distribution of 3D Brain MRI using a 2D Slice VAE

Probabilistic modelling has been an essential tool in medical image analysis, especially for analyzing brain Magnetic Resonance Images (MRI). Recent deep learning techniques for estimating high-dimensional distributions, in particular Variational Autoencoders (VAEs), opened up new avenues for probabilistic modeling. Modelling of volumetric data has remained a challenge, however, because constraints on available computation and training data make it difficult effectively leverage VAEs, which are well-developed for 2D images. We propose a method to model 3D MR brain volumes distribution by combining a 2D slice VAE with a Gaussian model that captures the relationships between slices. We do so by estimating the sample mean and covariance in the latent space of the 2D model over the slice direction. This combined model lets us sample new coherent stacks of latent variables to decode into slices of a volume. We also introduce a novel evaluation method for generated volumes that quantifies how well their segmentations match those of true brain anatomy. We demonstrate that our proposed model is competitive in generating high quality volumes at high resolutions according to both traditional metrics and our proposed evaluation.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

RevPHiSeg: A Memory-Efficient Neural Network for Uncertainty Quantification in Medical Image Segmentation

Quantifying segmentation uncertainty has become an important issue in medical image analysis due to the inherent ambiguity of anatomical structures and its pathologies. Recently, neural network-based uncertainty quantification methods have been successfully applied to various problems. One of the main limitations of the existing techniques is the high memory requirement during training; which limits their application to processing smaller field-of-views (FOVs) and/or using shallower architectures. In this paper, we investigate the effect of using reversible blocks for building memory-efficient neural network architectures for quantification of segmentation uncertainty. The reversible architecture achieves memory saving by exactly computing the activations from the outputs of the subsequent layers during backpropagation instead of storing the activations for each layer. We incorporate the reversible blocks into a recently proposed architecture called PHiSeg that is developed for uncertainty quantification in medical image segmentation. The reversible architecture, RevPHiSeg, allows training neural networks for quantifying segmentation uncertainty on GPUs with limited memory and processing larger FOVs. We perform experiments on the LIDC-IDRI dataset and an in-house prostate dataset, and present comparisons with PHiSeg. The results demonstrate that RevPHiSeg consumes ~30% less memory compared to PHiSeg while achieving very similar segmentation accuracy.

0 citations0 reviewsNo code linkedOpen access