Florian Sestak

Florian Sestak, Artur Toshev, Andreas Fürst et al.

Generative models are spearheading recent progress in deep learning, showcasing strong promise for trajectory sampling in dynamical systems as well. However, whereas latent space modeling paradigms have transformed image and video generation, similar approaches are more difficult for most dynamical systems. Such systems -- from chemical molecule structures to collective human behavior -- are described by interactions of entities, making them inherently linked to connectivity patterns, entity conservation, and the traceability of entities over time. Our approach, LaM-SLidE (Latent Space Modeling of Spatial Dynamical Systems via Linked Entities), bridges the gap between: (1) keeping the traceability of individual entities in a latent system representation, and (2) leveraging the efficiency and scalability of recent advances in image and video generation, where pre-trained encoder and decoder enable generative modeling directly in latent space. The core idea of LaM-SLidE is the introduction of identifier representations (IDs) that enable the retrieval of entity properties and entity composition from latent system representations, thus fostering traceability. Experimentally, across different domains, we show that LaM-SLidE performs favorably in terms of speed, accuracy, and generalizability. Code is available at https://github.com/ml-jku/LaM-SLidE .

Florian Sestak, Lisa Schneckenreiter, Johannes Brandstetter et al.

Being able to identify regions within or around proteins, to which ligands can potentially bind, is an essential step to develop new drugs. Binding site identification methods can now profit from the availability of large amounts of 3D structures in protein structure databases or from AlphaFold predictions. Current binding site identification methods heavily rely on graph neural networks (GNNs), usually designed to output E(3)-equivariant predictions. Such methods turned out to be very beneficial for physics-related tasks like binding energy or motion trajectory prediction. However, the performance of GNNs at binding site identification is still limited potentially due to the lack of dedicated nodes that model hidden geometric entities, such as binding pockets. In this work, we extend E(n)-Equivariant Graph Neural Networks (EGNNs) by adding virtual nodes and applying an extended message passing scheme. The virtual nodes in these graphs are dedicated quantities to learn representations of binding sites, which leads to improved predictive performance. In our experiments, we show that our proposed method VN-EGNN sets a new state-of-the-art at locating binding site centers on COACH420, HOLO4K and PDBbind2020.

Lisa Schneckenreiter, Richard Freinschlag, Florian Sestak et al.

Graph neural networks (GNNs), and especially message-passing neural networks, excel in various domains such as physics, drug discovery, and molecular modeling. The expressivity of GNNs with respect to their ability to discriminate non-isomorphic graphs critically depends on the functions employed for message aggregation and graph-level readout. By applying signal propagation theory, we propose a variance-preserving aggregation function (VPA) that maintains expressivity, but yields improved forward and backward dynamics. Experiments demonstrate that VPA leads to increased predictive performance for popular GNN architectures as well as improved learning dynamics. Our results could pave the way towards normalizer-free or self-normalizing GNNs.

Michael Aich, Andreas Fürst, Florian Sestak et al.

Deep learning has revolutionized weather and climate modeling, yet the current landscape remains fragmented: highly specialized models are typically trained individually for distinct tasks. To unify this landscape, we introduce WIND, a single pre-trained foundation model capable of replacing specialized baselines across a vast array of tasks. Crucially, in contrast to previous atmospheric foundation models, we achieve this without any task-specific fine-tuning. To learn a robust, task-agnostic prior of the atmosphere, we pre-train WIND with a self-supervised video reconstruction objective, utilizing an unconditional video diffusion model to iteratively reconstruct atmospheric dynamics from a noisy state. At inference, we frame diverse domain-specific problems strictly as inverse problems and solve them via posterior sampling. This unified approach allows us to tackle highly relevant weather and climate problems, including probabilistic forecasting, spatial and temporal downscaling, sparse reconstruction and enforcing conservation laws purely with our pre-trained model. We further demonstrate the model's capacity to generate physically consistent counterfactual storylines of extreme weather events under global warming scenarios. By combining generative video modeling with inverse problem solving, WIND offers a computationally efficient paradigm shift in AI-based atmospheric modeling.