Erik Bekkers

Xuan Zhang, Limei Wang, Jacob Helwig et al. · cambridge, mit

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.

Floor Eijkelboom, Erik Bekkers, Michael Bronstein et al.

The most prevalent class of neural networks operating on graphs are message passing neural networks (MPNNs), in which the representation of a node is updated iteratively by aggregating information in the 1-hop neighborhood. Since this paradigm for computing node embeddings may prevent the model from learning coarse topological structures, the initial features are often augmented with structural information of the graph, typically in the form of Laplacian eigenvectors or Random Walk transition probabilities. In this work, we explore the contribution of message passing when strong structural encodings are provided. We introduce a novel way of modeling the interaction between feature and structural information based on their tensor product rather than the standard concatenation. The choice of interaction is compared in common scenarios and in settings where the capacity of the message-passing layer is severely reduced and ultimately the message-passing phase is removed altogether. Our results indicate that using tensor-based encodings is always at least on par with the concatenation-based encoding and that it makes the model much more robust when the message passing layers are removed, on some tasks incurring almost no drop in performance. This suggests that the importance of message passing is limited when the model can construct strong structural encodings.

Guillermo Bernárdez, Lev Telyatnikov, Marco Montagna et al.

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings.

Friso de Kruiff, Dario Coscia, Max Welling et al.

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.

Tin Hadži Veljković, Erik Bekkers, Michael Tiemann et al.

Many learning problems require predicting sets of objects when the number of objects is not known beforehand. Examples include object detection, molecular modeling, and scientific inference tasks such as astrophysical source detection. Existing methods often rely on padded representations or must explicitly infer the set size, which often poses challenges. We present a novel strategy for addressing this challenge by casting prediction of variable-sized sets as a continuous inference problem. Our approach, CORDS (Continuous Representations of Discrete Structures), provides an invertible mapping that transforms a set of spatial objects into continuous fields: a density field that encodes object locations and count, and a feature field that carries their attributes over the same support. Because the mapping is invertible, models operate entirely in field space while remaining exactly decodable to discrete sets. We evaluate CORDS across molecular generation and regression, object detection, simulation-based inference, and a mathematical task involving recovery of local maxima, demonstrating robust handling of unknown set sizes with competitive accuracy.

Martin Carrasco, Olga Zaghen, Erik Bekkers et al.

For far too long, expressivity of graph neural networks has been measured \emph{only} in terms of combinatorial properties. In this work we stray away from this tradition and provide a principled way to measure similarity between vertex attributed graphs. We denote this measure as the \emph{graph homomorphism distortion}. We show it can \emph{completely characterize} graphs and thus is also a \emph{complete graph embedding}. However, somewhere along the road, we run into the graph canonization problem. To circumvent this obstacle, we devise to efficiently compute this measure via sampling, which in expectation ensures \emph{completeness}. Additionally, we also discovered that we can obtain a metric from this measure. We validate our claims empirically and find that the \emph{graph homomorphism distortion}: (1.) fully distinguishes the \texttt{BREC} dataset with up to $4$-WL non-distinguishable graphs, and (2.) \emph{outperforms} previous methods inspired in homomorphisms under the \texttt{ZINC-12k} dataset. These theoretical results, (and their empirical validation), pave the way for future characterization of graphs, extending the graph theoretic tradition to new frontiers.

Sharvaree Vadgama, Mohammad Mohaiminul Islam, Domas Buracas et al.

In this work, we explore the trade-offs of explicit structural priors, particularly group equivariance. We address this through theoretical analysis and a comprehensive empirical study. To enable controlled and fair comparisons, we introduce \texttt{Rapidash}, a unified group convolutional architecture that allows for different variants of equivariant and non-equivariant models. Our results suggest that more constrained equivariant models outperform less constrained alternatives when aligned with the geometry of the task, and increasing representation capacity does not fully eliminate performance gaps. We see improved performance of models with equivariance and symmetry-breaking through tasks like segmentation, regression, and generation across diverse datasets. Explicit \textit{symmetry breaking} via geometric reference frames consistently improves performance, while \textit{breaking equivariance} through geometric input features can be helpful when aligned with task geometry. Our results provide task-specific performance trends that offer a more nuanced way for model selection.

Maksim Zhdanov, Nabil Iqbal, Erik Bekkers et al.

Conformal symmetries, i.e.\ coordinate transformations that preserve angles, play a key role in many fields, including physics, mathematics, computer vision and (geometric) machine learning. Here we build a neural network that is equivariant under general conformal transformations. To achieve this, we lift data from flat Euclidean space to Anti de Sitter (AdS) space. This allows us to exploit a known correspondence between conformal transformations of flat space and isometric transformations on the AdS space. We then build upon the fact that such isometric transformations have been extensively studied on general geometries in the geometric deep learning literature. We employ message-passing layers conditioned on the proper distance, yielding a computationally efficient framework. We validate our model on tasks from computer vision and statistical physics, demonstrating strong performance, improved generalization capacities, and the ability to extract conformal data such as scaling dimensions from the trained network.

Cong Liu, Sharvaree Vadgama, David Ruhe et al.

This paper explores leveraging the Clifford algebra's expressive power for $\E(n)$-equivariant diffusion models. We utilize the geometric products between Clifford multivectors and the rich geometric information encoded in Clifford subspaces in \emph{Clifford Diffusion Models} (CDMs). We extend the diffusion process beyond just Clifford one-vectors to incorporate all higher-grade multivector subspaces. The data is embedded in grade-$k$ subspaces, allowing us to apply latent diffusion across complete multivectors. This enables CDMs to capture the joint distribution across different subspaces of the algebra, incorporating richer geometric information through higher-order features. We provide empirical results for unconditional molecular generation on the QM9 dataset, showing that CDMs provide a promising avenue for generative modeling.

Andrew Draganov, Sharvaree Vadgama, Sebastian Damrich et al.

Self-supervised learning (SSL) allows training data representations without a supervised signal and has become an important paradigm in machine learning. Most SSL methods employ the cosine similarity between embedding vectors and hence effectively embed data on a hypersphere. While this seemingly implies that embedding norms cannot play any role in SSL, a few recent works have suggested that embedding norms have properties related to network convergence and confidence. In this paper, we resolve this apparent contradiction and systematically establish the embedding norm's role in SSL training. Using theoretical analysis, simulations, and experiments, we show that embedding norms (i) govern SSL convergence rates and (ii) encode network confidence, with smaller norms corresponding to unexpected samples. Additionally, we show that manipulating embedding norms can have large effects on convergence speed. Our findings demonstrate that SSL embedding norms are integral to understanding and optimizing network behavior.

Floor Eijkelboom, Rob Hesselink, Erik Bekkers

This paper presents $\mathrm{E}(n)$ Equivariant Message Passing Simplicial Networks (EMPSNs), a novel approach to learning on geometric graphs and point clouds that is equivariant to rotations, translations, and reflections. EMPSNs can learn high-dimensional simplex features in graphs (e.g. triangles), and use the increase of geometric information of higher-dimensional simplices in an $\mathrm{E}(n)$ equivariant fashion. EMPSNs simultaneously generalize $\mathrm{E}(n)$ Equivariant Graph Neural Networks to a topologically more elaborate counterpart and provide an approach for including geometric information in Message Passing Simplicial Networks. The results indicate that EMPSNs can leverage the benefits of both approaches, leading to a general increase in performance when compared to either method. Furthermore, the results suggest that incorporating geometric information serves as an effective measure against over-smoothing in message passing networks, especially when operating on high-dimensional simplicial structures. Last, we show that EMPSNs are on par with state-of-the-art approaches for learning on geometric graphs.

Melle B. Vessies, Sharvaree P. Vadgama, Rutger R. van de Leur et al.

Electrocardiography (ECG) is an effective and non-invasive diagnostic tool that measures the electrical activity of the heart. Interpretation of ECG signals to detect various abnormalities is a challenging task that requires expertise. Recently, the use of deep neural networks for ECG classification to aid medical practitioners has become popular, but their black box nature hampers clinical implementation. Several saliency-based interpretability techniques have been proposed, but they only indicate the location of important features and not the actual features. We present a novel interpretability technique called qLST, a query-based latent space traversal technique that is able to provide explanations for any ECG classification model. With qLST, we train a neural network that learns to traverse in the latent space of a variational autoencoder trained on a large university hospital dataset with over 800,000 ECGs annotated for 28 diseases. We demonstrate through experiments that we can explain different black box classifiers by generating ECGs through these traversals.

Bart Smets, Jim Portegies, Erik Bekkers et al.

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.

Gonzalo Sanguinetti, Erik Bekkers, Remco Duits et al.

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.

Julius Hannink, Remco Duits, Erik Bekkers

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.