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Researcher profile

Ender Konukoglu

Ender Konukoglu contributes to research discovery and scholarly infrastructure.

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Computer Visioneess.IVMachine LearningApplicationsArtificial Intelligenceeess.SP

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Published work

13 published item(s)

preprint2026arXiv

A Single-Parameter Factor-Graph Image Prior

We propose a novel piecewise smooth image model with piecewise constant local parameters that are automatically adapted to each image. Technically, the model is formulated in terms of factor graphs with NUP (normal with unknown parameters) priors, and the pertinent computations amount to iterations of conjugate-gradient steps and Gaussian message passing. The proposed model and algorithms are demonstrated with applications to denoising and contrast enhancement.

0 citations0 reviewsNo code linkedOpen access
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
preprint2022arXiv

ISNAS-DIP: Image-Specific Neural Architecture Search for Deep Image Prior

Recent works show that convolutional neural network (CNN) architectures have a spectral bias towards lower frequencies, which has been leveraged for various image restoration tasks in the Deep Image Prior (DIP) framework. The benefit of the inductive bias the network imposes in the DIP framework depends on the architecture. Therefore, researchers have studied how to automate the search to determine the best-performing model. However, common neural architecture search (NAS) techniques are resource and time-intensive. Moreover, best-performing models are determined for a whole dataset of images instead of for each image independently, which would be prohibitively expensive. In this work, we first show that optimal neural architectures in the DIP framework are image-dependent. Leveraging this insight, we then propose an image-specific NAS strategy for the DIP framework that requires substantially less training than typical NAS approaches, effectively enabling image-specific NAS. We justify the proposed strategy's effectiveness by (1) demonstrating its performance on a NAS Dataset for DIP that includes 522 models from a particular search space (2) conducting extensive experiments on image denoising, inpainting, and super-resolution tasks. Our experiments show that image-specific metrics can reduce the search space to a small cohort of models, of which the best model outperforms current NAS approaches for image restoration. Codes and datasets are available at https://github.com/ozgurkara99/ISNAS-DIP.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Rethinking Semantic Segmentation: A Prototype View

Prevalent semantic segmentation solutions, despite their different network designs (FCN based or attention based) and mask decoding strategies (parametric softmax based or pixel-query based), can be placed in one category, by considering the softmax weights or query vectors as learnable class prototypes. In light of this prototype view, this study uncovers several limitations of such parametric segmentation regime, and proposes a nonparametric alternative based on non-learnable prototypes. Instead of prior methods learning a single weight/query vector for each class in a fully parametric manner, our model represents each class as a set of non-learnable prototypes, relying solely on the mean features of several training pixels within that class. The dense prediction is thus achieved by nonparametric nearest prototype retrieving. This allows our model to directly shape the pixel embedding space, by optimizing the arrangement between embedded pixels and anchored prototypes. It is able to handle arbitrary number of classes with a constant amount of learnable parameters. We empirically show that, with FCN based and attention based segmentation models (i.e., HRNet, Swin, SegFormer) and backbones (i.e., ResNet, HRNet, Swin, MiT), our nonparametric framework yields compelling results over several datasets (i.e., ADE20K, Cityscapes, COCO-Stuff), and performs well in the large-vocabulary situation. We expect this work will provoke a rethink of the current de facto semantic segmentation model design.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Sampling possible reconstructions of undersampled acquisitions in MR imaging

Undersampling the k-space during MR acquisitions saves time, however results in an ill-posed inversion problem, leading to an infinite set of images as possible solutions. Traditionally, this is tackled as a reconstruction problem by searching for a single "best" image out of this solution set according to some chosen regularization or prior. This approach, however, misses the possibility of other solutions and hence ignores the uncertainty in the inversion process. In this paper, we propose a method that instead returns multiple images which are possible under the acquisition model and the chosen prior to capture the uncertainty in the inversion process. To this end, we introduce a low dimensional latent space and model the posterior distribution of the latent vectors given the acquisition data in k-space, from which we can sample in the latent space and obtain the corresponding images. We use a variational autoencoder for the latent model and the Metropolis adjusted Langevin algorithm for the sampling. We evaluate our method on two datasets; with images from the Human Connectome Project and in-house measured multi-coil images. We compare to five alternative methods. Results indicate that the proposed method produces images that match the measured k-space data better than the alternatives, while showing realistic structural variability. Furthermore, in contrast to the compared methods, the proposed method yields higher uncertainty in the undersampled phase encoding direction, as expected. Keywords: Magnetic Resonance image reconstruction, uncertainty estimation, inverse problems, sampling, MCMC, deep learning, unsupervised learning.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Zero Pixel Directional Boundary by Vector Transform

Boundaries are among the primary visual cues used by human and computer vision systems. One of the key problems in boundary detection is the label representation, which typically leads to class imbalance and, as a consequence, to thick boundaries that require non-differential post-processing steps to be thinned. In this paper, we re-interpret boundaries as 1-D surfaces and formulate a one-to-one vector transform function that allows for training of boundary prediction completely avoiding the class imbalance issue. Specifically, we define the boundary representation at any point as the unit vector pointing to the closest boundary surface. Our problem formulation leads to the estimation of direction as well as richer contextual information of the boundary, and, if desired, the availability of zero-pixel thin boundaries also at training time. Our method uses no hyper-parameter in the training loss and a fixed stable hyper-parameter at inference. We provide theoretical justification/discussions of the vector transform representation. We evaluate the proposed loss method using a standard architecture and show the excellent performance over other losses and representations on several datasets. Code is available at https://github.com/edomel/BoundaryVT.

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

Joint reconstruction and bias field correction for undersampled MR imaging

Undersampling the k-space in MRI allows saving precious acquisition time, yet results in an ill-posed inversion problem. Recently, many deep learning techniques have been developed, addressing this issue of recovering the fully sampled MR image from the undersampled data. However, these learning based schemes are susceptible to differences between the training data and the image to be reconstructed at test time. One such difference can be attributed to the bias field present in MR images, caused by field inhomogeneities and coil sensitivities. In this work, we address the sensitivity of the reconstruction problem to the bias field and propose to model it explicitly in the reconstruction, in order to decrease this sensitivity. To this end, we use an unsupervised learning based reconstruction algorithm as our basis and combine it with a N4-based bias field estimation method, in a joint optimization scheme. We use the HCP dataset as well as in-house measured images for the evaluations. We show that the proposed method improves the reconstruction quality, both visually and in terms of RMSE.

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
preprint2020arXiv

Unsupervised Lesion Detection via Image Restoration with a Normative Prior

Unsupervised lesion detection is a challenging problem that requires accurately estimating normative distributions of healthy anatomy and detecting lesions as outliers without training examples. Recently, this problem has received increased attention from the research community following the advances in unsupervised learning with deep learning. Such advances allow the estimation of high-dimensional distributions, such as normative distributions, with higher accuracy than previous methods.The main approach of the recently proposed methods is to learn a latent-variable model parameterized with networks to approximate the normative distribution using example images showing healthy anatomy, perform prior-projection, i.e. reconstruct the image with lesions using the latent-variable model, and determine lesions based on the differences between the reconstructed and original images. While being promising, the prior-projection step often leads to a large number of false positives. In this work, we approach unsupervised lesion detection as an image restoration problem and propose a probabilistic model that uses a network-based prior as the normative distribution and detect lesions pixel-wise using MAP estimation. The probabilistic model punishes large deviations between restored and original images, reducing false positives in pixel-wise detections. Experiments with gliomas and stroke lesions in brain MRI using publicly available datasets show that the proposed approach outperforms the state-of-the-art unsupervised methods by a substantial margin, +0.13 (AUC), for both glioma and stroke detection. Extensive model analysis confirms the effectiveness of MAP-based image restoration.

0 citations0 reviewsNo code linkedOpen access