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Erik Bekkers

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Published work

5 published item(s)

preprint2026arXiv

Flowing with Confidence

Generative models can produce nonsensical text, unrealistic images, and unstable materials faster than simulation or human review can absorb; without per-sample confidence, trust erodes. Existing fixes run $k$ ensembles or stochastic trajectories at $k\times$ compute, measuring variability between models, not model confidence. We propose Flow Matching with Confidence (FMwC). FMwC injects input-dependent multiplicative noise at selected layers, propagates its variance through the network in closed form, and integrates it along the ODE trajectory, yielding a per-sample confidence score at standard sampling cost. The score supports multiple uses: filtering improves image quality and thermodynamic stability of crystals; editing rewinds trajectories to the points where the model commits and redirects them; and adaptive stepping concentrates ODE compute where the flow is ambiguous. We find that the confidence score correlates with the magnitude of the divergence of the learned velocity field, which gives us a window to understand the generative process, opening up surgical forms of guidance that target the moments that matter, new sampling algorithms and interpretability of generative models.

preprint2022arXiv

PDE-based Group Equivariant Convolutional Neural Networks

We present a PDE-based framework that generalizes Group equivariant Convolutional Neural Networks (G-CNNs). In this framework, a network layer is seen as a set of PDE-solvers where geometrically meaningful PDE-coefficients become the layer's trainable weights. Formulating our PDEs on homogeneous spaces allows these networks to be designed with built-in symmetries such as rotation in addition to the standard translation equivariance of CNNs. Having all the desired symmetries included in the design obviates the need to include them by means of costly techniques such as data augmentation. We will discuss our PDE-based G-CNNs (PDE-G-CNNs) in a general homogeneous space setting while also going into the specifics of our primary case of interest: roto-translation equivariance. We solve the PDE of interest by a combination of linear group convolutions and non-linear morphological group convolutions with analytic kernel approximations that we underpin with formal theorems. Our kernel approximations allow for fast GPU-implementation of the PDE-solvers, we release our implementation with this article in the form of the LieTorch extension to PyTorch, available at https://gitlab.com/bsmetsjr/lietorch . Just like for linear convolution a morphological convolution is specified by a kernel that we train in our PDE-G-CNNs. In PDE-G-CNNs we do not use non-linearities such as max/min-pooling and ReLUs as they are already subsumed by morphological convolutions. We present a set of experiments to demonstrate the strength of the proposed PDE-G-CNNs in increasing the performance of deep learning based imaging applications with far fewer parameters than traditional CNNs.

preprint2015arXiv

Sub-Riemannian Fast Marching in SE(2)

We propose a Fast Marching based implementation for computing sub-Riemanninan (SR) geodesics in the roto-translation group SE(2), with a metric depending on a cost induced by the image data. The key ingredient is a Riemannian approximation of the SR-metric. Then, a state of the art Fast Marching solver that is able to deal with extreme anisotropies is used to compute a SR-distance map as the solution of a corresponding eikonal equation. Subsequent backtracking on the distance map gives the geodesics. To validate the method, we consider the uniform cost case in which exact formulas for SR-geodesics are known and we show remarkable accuracy of the numerically computed SR-spheres. We also show a dramatic decrease in computational time with respect to a previous PDE-based iterative approach. Regarding image analysis applications, we show the potential of considering these data adaptive geodesics for a fully automated retinal vessel tree segmentation.

preprint2014arXiv

Vesselness via Multiple Scale Orientation Scores

The multi-scale Frangi vesselness filter is an established tool in (retinal) vascular imaging. However, it cannot cope with crossings or bifurcations, since it only looks for elongated structures. Therefore, we disentangle crossing structures in the image via (multiple scale) invertible orientation scores. The described vesselness filter via scale-orientation scores performs considerably better at enhancing vessels throughout crossings and bifurcations than the Frangi version. Both methods are evaluated on a public dataset. Performance is measured by comparing ground truth data to the segmentation results obtained by basic thresholding and morphological component analysis of the filtered images.

preprint2013arXiv

A Multi-Orientation Analysis Approach to Retinal Vessel Tracking

This paper presents a method for retinal vasculature extraction based on biologically inspired multi-orientation analysis. We apply multi-orientation analysis via so-called invertible orientation scores, modeling the cortical columns in the visual system of higher mammals. This allows us to generically deal with many hitherto complex problems inherent to vessel tracking, such as crossings, bifurcations, parallel vessels, vessels of varying widths and vessels with high curvature. Our approach applies tracking in invertible orientation scores via a novel geometrical principle for curve optimization in the Euclidean motion group SE(2). The method runs fully automatically and provides a detailed model of the retinal vasculature, which is crucial as a sound basis for further quantitative analysis of the retina, especially in screening applications.