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Ertunc Erdil

Ertunc Erdil appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Computer Visioneess.IVMachine LearningArtificial Intelligence

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Published work

8 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
preprint2016arXiv

Dendritic Spine Shape Analysis: A Clustering Perspective

Functional properties of neurons are strongly coupled with their morphology. Changes in neuronal activity alter morphological characteristics of dendritic spines. First step towards understanding the structure-function relationship is to group spines into main spine classes reported in the literature. Shape analysis of dendritic spines can help neuroscientists understand the underlying relationships. Due to unavailability of reliable automated tools, this analysis is currently performed manually which is a time-intensive and subjective task. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. In this paper, we aim to address these issues by presenting a clustering perspective. In this context, clustering may serve both confirmation of known patterns and discovery of new ones. We perform cluster analysis on two-photon microscopic images of spines using morphological, shape, and appearance based features and gain insights into the spine shape analysis problem. We use histogram of oriented gradients (HOG), disjunctive normal shape models (DNSM), morphological features, and intensity profile based features for cluster analysis. We use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). For all features, this analysis produces 4 clusters and we observe the formation of at least one cluster consisting of spines which are difficult to be assigned to a known class. This observation supports the argument of intermediate shape types.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

MCMC Shape Sampling for Image Segmentation with Nonparametric Shape Priors

Segmenting images of low quality or with missing data is a challenging problem. Integrating statistical prior information about the shapes to be segmented can improve the segmentation results significantly. Most shape-based segmentation algorithms optimize an energy functional and find a point estimate for the object to be segmented. This does not provide a measure of the degree of confidence in that result, neither does it provide a picture of other probable solutions based on the data and the priors. With a statistical view, addressing these issues would involve the problem of characterizing the posterior densities of the shapes of the objects to be segmented. For such characterization, we propose a Markov chain Monte Carlo (MCMC) sampling-based image segmentation algorithm that uses statistical shape priors. In addition to better characterization of the statistical structure of the problem, such an approach would also have the potential to address issues with getting stuck at local optima, suffered by existing shape-based segmentation methods. Our approach is able to characterize the posterior probability density in the space of shapes through its samples, and to return multiple solutions, potentially from different modes of a multimodal probability density, which would be encountered, e.g., in segmenting objects from multiple shape classes. We present promising results on a variety of data sets. We also provide an extension for segmenting shapes of objects with parts that can go through independent shape variations. This extension involves the use of local shape priors on object parts and provides robustness to limitations in shape training data size.

0 citations0 reviewsNo code linkedOpen access