arXiv subjects

Ender Konukoglu

Publications and source records attributed to Ender Konukoglu.

At least 55 records · Page 3Linked to original sources

arXiv2024

Implicit-Zoo: A Large-Scale Dataset of Neural Implicit Functions for 2D Images and 3D Scenes

Neural implicit functions have demonstrated significant importance in various areas such as computer vision, graphics. Their advantages include the ability to represent complex shapes and scenes with high fidelity, smooth interpolation capabilities, and continuous representations. Despite these benefits, the development and analysis of implicit functions have been limited by the lack of comprehensive datasets and the substantial computational resources required for their implementation and evaluation. To address these challenges, we introduce "Implicit-Zoo": a large-scale dataset requiring thousands of GPU training days designed to facilitate research and development in this field. Our dataset includes diverse 2D and 3D scenes, such as CIFAR-10, ImageNet-1K, and Cityscapes for 2D image tasks, and the OmniObject3D dataset for 3D vision tasks. We ensure high quality through strict checks, refining or filtering out low-quality data. Using Implicit-Zoo, we showcase two immediate benefits as it enables to: (1) learn token locations for transformer models; (2) directly regress 3D cameras poses of 2D images with respect to NeRF models. This in turn leads to an improved performance in all three task of image classification, semantic segmentation, and 3D pose regression, thereby unlocking new avenues for research.

cs.CV↗

arXiv2024

QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT; various organs such as the brain, prostate, kidney, and pancreas; and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks.

eess.IV↗

arXiv2024

Vision-Based Neurosurgical Guidance: Unsupervised Localization and Camera-Pose Prediction

Localizing oneself during endoscopic procedures can be problematic due to the lack of distinguishable textures and landmarks, as well as difficulties due to the endoscopic device such as a limited field of view and challenging lighting conditions. Expert knowledge shaped by years of experience is required for localization within the human body during endoscopic procedures. In this work, we present a deep learning method based on anatomy recognition, that constructs a surgical path in an unsupervised manner from surgical videos, modelling relative location and variations due to different viewing angles. At inference time, the model can map an unseen video's frames on the path and estimate the viewing angle, aiming to provide guidance, for instance, to reach a particular destination. We test the method on a dataset consisting of surgical videos of transsphenoidal adenomectomies, as well as on a synthetic dataset. An online tool that lets researchers upload their surgical videos to obtain anatomy detections and the weights of the trained YOLOv7 model are available at: https://surgicalvision.bmic.ethz.ch.

cs.CV↗

arXiv2023

Expert load matters: operating networks at high accuracy and low manual effort

In human-AI collaboration systems for critical applications, in order to ensure minimal error, users should set an operating point based on model confidence to determine when the decision should be delegated to human experts. Samples for which model confidence is lower than the operating point would be manually analysed by experts to avoid mistakes. Such systems can become truly useful only if they consider two aspects: models should be confident only for samples for which they are accurate, and the number of samples delegated to experts should be minimized. The latter aspect is especially crucial for applications where available expert time is limited and expensive, such as healthcare. The trade-off between the model accuracy and the number of samples delegated to experts can be represented by a curve that is similar to an ROC curve, which we refer to as confidence operating characteristic (COC) curve. In this paper, we argue that deep neural networks should be trained by taking into account both accuracy and expert load and, to that end, propose a new complementary loss function for classification that maximizes the area under this COC curve. This promotes simultaneously the increase in network accuracy and the reduction in number of samples delegated to humans. We perform experiments on multiple computer vision and medical image datasets for classification. Our results demonstrate that the proposed loss improves classification accuracy and delegates less number of decisions to experts, achieves better out-of-distribution samples detection and on par calibration performance compared to existing loss functions.

cs.AI↗

arXiv2023

Quantification of Predictive Uncertainty via Inference-Time Sampling

Predictive variability due to data ambiguities has typically been addressed via construction of dedicated models with built-in probabilistic capabilities that are trained to predict uncertainty estimates as variables of interest. These approaches require distinct architectural components and training mechanisms, may include restrictive assumptions and exhibit overconfidence, i.e., high confidence in imprecise predictions. In this work, we propose a post-hoc sampling strategy for estimating predictive uncertainty accounting for data ambiguity. The method can generate different plausible outputs for a given input and does not assume parametric forms of predictive distributions. It is architecture agnostic and can be applied to any feed-forward deterministic network without changes to the architecture or training procedure. Experiments on regression tasks on imaging and non-imaging input data show the method's ability to generate diverse and multi-modal predictive distributions, and a desirable correlation of the estimated uncertainty with the prediction error.

cs.LG↗

arXiv2023

Explicitly Minimizing the Blur Error of Variational Autoencoders

Variational autoencoders (VAEs) are powerful generative modelling methods, however they suffer from blurry generated samples and reconstructions compared to the images they have been trained on. Significant research effort has been spent to increase the generative capabilities by creating more flexible models but often flexibility comes at the cost of higher complexity and computational cost. Several works have focused on altering the reconstruction term of the evidence lower bound (ELBO), however, often at the expense of losing the mathematical link to maximizing the likelihood of the samples under the modeled distribution. Here we propose a new formulation of the reconstruction term for the VAE that specifically penalizes the generation of blurry images while at the same time still maximizing the ELBO under the modeled distribution. We show the potential of the proposed loss on three different data sets, where it outperforms several recently proposed reconstruction losses for VAEs.

cs.CV↗

arXiv2023

Neural Vector Fields for Implicit Surface Representation and Inference

Implicit fields have recently shown increasing success in representing and learning 3D shapes accurately. Signed distance fields and occupancy fields are decades old and still the preferred representations, both with well-studied properties, despite their restriction to closed surfaces. With neural networks, several other variations and training principles have been proposed with the goal to represent all classes of shapes. In this paper, we develop a novel and yet a fundamental representation considering unit vectors in 3D space and call it Vector Field (VF): at each point in $\mathbb{R}^3$, VF is directed at the closest point on the surface. We theoretically demonstrate that VF can be easily transformed to surface density by computing the flux density. Unlike other standard representations, VF directly encodes an important physical property of the surface, its normal. We further show the advantages of VF representation, in learning open, closed, or multi-layered as well as piecewise planar surfaces. We compare our method on several datasets including ShapeNet where the proposed new neural implicit field shows superior accuracy in representing any type of shape, outperforming other standard methods. Code is available at https://github.com/edomel/ImplicitVF.

cs.CV↗

arXiv2023

Live image-based neurosurgical guidance and roadmap generation using unsupervised embedding

Advanced minimally invasive neurosurgery navigation relies mainly on Magnetic Resonance Imaging (MRI) guidance. MRI guidance, however, only provides pre-operative information in the majority of the cases. Once the surgery begins, the value of this guidance diminishes to some extent because of the anatomical changes due to surgery. Guidance with live image feedback coming directly from the surgical device, e.g., endoscope, can complement MRI-based navigation or be an alternative if MRI guidance is not feasible. With this motivation, we present a method for live image-only guidance leveraging a large data set of annotated neurosurgical videos.First, we report the performance of a deep learning-based object detection method, YOLO, on detecting anatomical structures in neurosurgical images. Second, we present a method for generating neurosurgical roadmaps using unsupervised embedding without assuming exact anatomical matches between patients, presence of an extensive anatomical atlas, or the need for simultaneous localization and mapping. A generated roadmap encodes the common anatomical paths taken in surgeries in the training set. At inference, the roadmap can be used to map a surgeon's current location using live image feedback on the path to provide guidance by being able to predict which structures should appear going forward or backward, much like a mapping application. Even though the embedding is not supervised by position information, we show that it is correlated to the location inside the brain and on the surgical path. We trained and evaluated the proposed method with a data set of 166 transsphenoidal adenomectomy procedures.

cs.CV↗

arXiv2023

InOR-Net: Incremental 3D Object Recognition Network for Point Cloud Representation

3D object recognition has successfully become an appealing research topic in the real-world. However, most existing recognition models unreasonably assume that the categories of 3D objects cannot change over time in the real-world. This unrealistic assumption may result in significant performance degradation for them to learn new classes of 3D objects consecutively, due to the catastrophic forgetting on old learned classes. Moreover, they cannot explore which 3D geometric characteristics are essential to alleviate the catastrophic forgetting on old classes of 3D objects. To tackle the above challenges, we develop a novel Incremental 3D Object Recognition Network (i.e., InOR-Net), which could recognize new classes of 3D objects continuously via overcoming the catastrophic forgetting on old classes. Specifically, a category-guided geometric reasoning is proposed to reason local geometric structures with distinctive 3D characteristics of each class by leveraging intrinsic category information. We then propose a novel critic-induced geometric attention mechanism to distinguish which 3D geometric characteristics within each class are beneficial to overcome the catastrophic forgetting on old classes of 3D objects, while preventing the negative influence of useless 3D characteristics. In addition, a dual adaptive fairness compensations strategy is designed to overcome the forgetting brought by class imbalance, by compensating biased weights and predictions of the classifier. Comparison experiments verify the state-of-the-art performance of the proposed InOR-Net model on several public point cloud datasets.

cs.CV↗

arXiv2023

FedFA: Federated Feature Augmentation

Federated learning is a distributed paradigm that allows multiple parties to collaboratively train deep models without exchanging the raw data. However, the data distribution among clients is naturally non-i.i.d., which leads to severe degradation of the learnt model. The primary goal of this paper is to develop a robust federated learning algorithm to address feature shift in clients' samples, which can be caused by various factors, e.g., acquisition differences in medical imaging. To reach this goal, we propose FedFA to tackle federated learning from a distinct perspective of federated feature augmentation. FedFA is based on a major insight that each client's data distribution can be characterized by statistics (i.e., mean and standard deviation) of latent features; and it is likely to manipulate these local statistics globally, i.e., based on information in the entire federation, to let clients have a better sense of the underlying distribution and therefore alleviate local data bias. Based on this insight, we propose to augment each local feature statistic probabilistically based on a normal distribution, whose mean is the original statistic and variance quantifies the augmentation scope. Key to our approach is the determination of a meaningful Gaussian variance, which is accomplished by taking into account not only biased data of each individual client, but also underlying feature statistics characterized by all participating clients. We offer both theoretical and empirical justifications to verify the effectiveness of FedFA. Our code is available at https://github.com/tfzhou/FedFA.

cs.LG↗

arXiv2022

Unsupervised Superpixel Generation using Edge-Sparse Embedding

Partitioning an image into superpixels based on the similarity of pixels with respect to features such as colour or spatial location can significantly reduce data complexity and improve subsequent image processing tasks. Initial algorithms for unsupervised superpixel generation solely relied on local cues without prioritizing significant edges over arbitrary ones. On the other hand, more recent methods based on unsupervised deep learning either fail to properly address the trade-off between superpixel edge adherence and compactness or lack control over the generated number of superpixels. By using random images with strong spatial correlation as input, \ie, blurred noise images, in a non-convolutional image decoder we can reduce the expected number of contrasts and enforce smooth, connected edges in the reconstructed image. We generate edge-sparse pixel embeddings by encoding additional spatial information into the piece-wise smooth activation maps from the decoder's last hidden layer and use a standard clustering algorithm to extract high quality superpixels. Our proposed method reaches state-of-the-art performance on the BSDS500, PASCAL-Context and a microscopy dataset.

cs.CV↗

arXiv2022

Assessing radiomics feature stability with simulated CT acquisitions

Medical imaging quantitative features had once disputable usefulness in clinical studies. Nowadays, advancements in analysis techniques, for instance through machine learning, have enabled quantitative features to be progressively useful in diagnosis and research. Tissue characterisation is improved via the 'radiomics' features, whose extraction can be automated. Despite the advances, stability of quantitative features remains an important open problem. As features can be highly sensitive to variations of acquisition details, it is not trivial to quantify stability and efficiently select stable features. In this work, we develop and validate a Computed Tomography (CT) simulator environment based on the publicly available ASTRA toolbox (www.astra-toolbox.com). We show that the variability, stability and discriminative power of the radiomics features extracted from the virtual phantom images generated by the simulator are similar to those observed in a tandem phantom study. Additionally, we show that the variability is matched between a multi-center phantom study and simulated results. Consequently, we demonstrate that the simulator can be utilised to assess radiomics features' stability and discriminative power.

physics.comp-ph↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

cs.CV↗

arXiv2022

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.

eess.IV↗

arXiv2022

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.

cs.LG↗