Doruk Öner

Doruk Oner, Hussein Osman, Mateusz Kozinski et al.

Many biological and medical tasks require the delineation of 3D curvilinear structures such as blood vessels and neurites from image volumes. This is typically done using neural networks trained by minimizing voxel-wise loss functions that do not capture the topological properties of these structures. As a result, the connectivity of the recovered structures is often wrong, which lessens their usefulness. In this paper, we propose to improve the 3D connectivity of our results by minimizing a sum of topology-aware losses on their 2D projections. This suffices to increase the accuracy and to reduce the annotation effort required to provide the required annotated training data. Code is available at https://github.com/doruk-oner/ConnectivityOnProjections.

Doruk Oner, Leonardo Citraro, Mateusz Koziński et al.

Deep learning-based approaches to delineating 3D structure depend on accurate annotations to train the networks. Yet, in practice, people, no matter how conscientious, have trouble precisely delineating in 3D and on a large scale, in part because the data is often hard to interpret visually and in part because the 3D interfaces are awkward to use. In this paper, we introduce a method that explicitly accounts for annotation inaccuracies. To this end, we treat the annotations as active contour models that can deform themselves while preserving their topology. This enables us to jointly train the network and correct potential errors in the original annotations. The result is an approach that boosts performance of deep networks trained with potentially inaccurate annotations. Code has been released at https://github.com/doruk-oner/AdjustingAnnotationswithSnakes.

Doruk Oner, Adélie Garin, Mateusz Koziński et al.

Persistent Homology (PH) has been successfully used to train networks to detect curvilinear structures and to improve the topological quality of their results. However, existing methods are very global and ignore the location of topological features. In this paper, we remedy this by introducing a new filtration function that fuses two earlier approaches: thresholding-based filtration, previously used to train deep networks to segment medical images, and filtration with height functions, typically used to compare 2D and 3D shapes. We experimentally demonstrate that deep networks trained using our PH-based loss function yield reconstructions of road networks and neuronal processes that reflect ground-truth connectivity better than networks trained with existing loss functions based on PH. Code is available at https://github.com/doruk-oner/PH-TopoLoss.

Nikita Durasov, Doruk Oner, Jonathan Donier et al.

Turning pass-through network architectures into iterative ones, which use their own output as input, is a well-known approach for boosting performance. In this paper, we argue that such architectures offer an additional benefit: The convergence rate of their successive outputs is highly correlated with the accuracy of the value to which they converge. Thus, we can use the convergence rate as a useful proxy for uncertainty. This results in an approach to uncertainty estimation that provides state-of-the-art estimates at a much lower computational cost than techniques like Ensembles, and without requiring any modifications to the original iterative model. We demonstrate its practical value by embedding it in two application domains: road detection in aerial images and the estimation of aerodynamic properties of 2D and 3D shapes.

Elyar Esmaeilzadeh, Ehsan Garaaghaji, Farzad Hallaji Azad et al.

Promoting the connectivity of curvilinear structures, such as neuronal processes in biomedical scans and blood vessels in CT images, remains a key challenge in semantic segmentation. Traditional pixel-wise loss functions, including cross-entropy and Dice losses, often fail to capture high-level topological connectivity, resulting in topological mistakes in graphs obtained from prediction maps. In this paper, we propose CAPE (Connectivity-Aware Path Enforcement), a novel loss function designed to enforce connectivity in graphs obtained from segmentation maps by optimizing a graph connectivity metric. CAPE uses the graph representation of the ground truth to select node pairs and determine their corresponding paths within the predicted segmentation through a shortest-path algorithm. Using this, we penalize both disconnections and false positive connections, effectively promoting the model to preserve topological correctness. Experiments on 2D and 3D datasets, including neuron and blood vessel tracing demonstrate that CAPE significantly improves topology-aware metrics and outperforms state-of-the-art methods.

Doruk Oner, Mateusz Koziński, Leonardo Citraro et al.

We propose a novel, connectivity-oriented loss function for training deep convolutional networks to reconstruct network-like structures, like roads and irrigation canals, from aerial images. The main idea behind our loss is to express the connectivity of roads, or canals, in terms of disconnections that they create between background regions of the image. In simple terms, a gap in the predicted road causes two background regions, that lie on the opposite sides of a ground truth road, to touch in prediction. Our loss function is designed to prevent such unwanted connections between background regions, and therefore close the gaps in predicted roads. It also prevents predicting false positive roads and canals by penalizing unwarranted disconnections of background regions. In order to capture even short, dead-ending road segments, we evaluate the loss in small image crops. We show, in experiments on two standard road benchmarks and a new data set of irrigation canals, that convnets trained with our loss function recover road connectivity so well, that it suffices to skeletonize their output to produce state of the art maps. A distinct advantage of our approach is that the loss can be plugged in to any existing training setup without further modifications.

Doruk Öner, Altuğ Karakurt, Atilla Eryılmaz et al.

In this paper, we introduce the COmbinatorial Multi-Objective Multi-Armed Bandit (COMO-MAB) problem that captures the challenges of combinatorial and multi-objective online learning simultaneously. In this setting, the goal of the learner is to choose an action at each time, whose reward vector is a linear combination of the reward vectors of the arms in the action, to learn the set of super Pareto optimal actions, which includes the Pareto optimal actions and actions that become Pareto optimal after adding an arbitrary small positive number to their expected reward vectors. We define the Pareto regret performance metric and propose a fair learning algorithm whose Pareto regret is $O(N L^3 \log T)$, where $T$ is the time horizon, $N$ is the number of arms and $L$ is the maximum number of arms in an action. We show that COMO-MAB has a wide range of applications, including recommending bundles of items to users and network routing, and focus on a resource-allocation application for multi-user communication in the presence of multidimensional performance metrics, where we show that our algorithm outperforms existing MAB algorithms.

Eralp Turğay, Doruk Öner, Cem Tekin

In this paper we propose the multi-objective contextual bandit problem with similarity information. This problem extends the classical contextual bandit problem with similarity information by introducing multiple and possibly conflicting objectives. Since the best arm in each objective can be different given the context, learning the best arm based on a single objective can jeopardize the rewards obtained from the other objectives. In order to evaluate the performance of the learner in this setup, we use a performance metric called the contextual Pareto regret. Essentially, the contextual Pareto regret is the sum of the distances of the arms chosen by the learner to the context dependent Pareto front. For this problem, we develop a new online learning algorithm called Pareto Contextual Zooming (PCZ), which exploits the idea of contextual zooming to learn the arms that are close to the Pareto front for each observed context by adaptively partitioning the joint context-arm set according to the observed rewards and locations of the context-arm pairs selected in the past. Then, we prove that PCZ achieves $\tilde O (T^{(1+d_p)/(2+d_p)})$ Pareto regret where $d_p$ is the Pareto zooming dimension that depends on the size of the set of near-optimal context-arm pairs. Moreover, we show that this regret bound is nearly optimal by providing an almost matching $Ω(T^{(1+d_p)/(2+d_p)})$ lower bound.