Jan Stühmer

Shell Xu Hu, Da Li, Jan Stühmer et al.

Few-shot learning (FSL) is an important and topical problem in computer vision that has motivated extensive research into numerous methods spanning from sophisticated meta-learning methods to simple transfer learning baselines. We seek to push the limits of a simple-but-effective pipeline for more realistic and practical settings of few-shot image classification. To this end, we explore few-shot learning from the perspective of neural network architecture, as well as a three stage pipeline of network updates under different data supplies, where unsupervised external data is considered for pre-training, base categories are used to simulate few-shot tasks for meta-training, and the scarcely labelled data of an novel task is taken for fine-tuning. We investigate questions such as: (1) How pre-training on external data benefits FSL? (2) How state-of-the-art transformer architectures can be exploited? and (3) How fine-tuning mitigates domain shift? Ultimately, we show that a simple transformer-based pipeline yields surprisingly good performance on standard benchmarks such as Mini-ImageNet, CIFAR-FS, CDFSL and Meta-Dataset. Our code and demo are available at https://hushell.github.io/pmf.

Robin Ruff, Patrick Reiser, Jan Stühmer et al.

Graph neural networks (GNNs) have been applied to a large variety of applications in materials science and chemistry. Here, we recapitulate the graph construction for crystalline (periodic) materials and investigate its impact on the GNNs model performance. We suggest the asymmetric unit cell as a representation to reduce the number of atoms by using all symmetries of the system. This substantially reduced the computational cost and thus time needed to train large graph neural networks without any loss in accuracy. Furthermore, with a simple but systematically built GNN architecture based on message passing and line graph templates, we introduce a general architecture (Nested Graph Network, NGN) that is applicable to a wide range of tasks. We show that our suggested models systematically improve state-of-the-art results across all tasks within the MatBench benchmark. Further analysis shows that optimized connectivity and deeper message functions are responsible for the improvement. Asymmetric unit cells and connectivity optimization can be generally applied to (crystal) graph networks, while our suggested nested graph framework will open new ways of systematic comparison of GNN architectures.

Ruchika Chavhan, Henry Gouk, Jan Stühmer et al.

Providing invariances in a given learning task conveys a key inductive bias that can lead to sample-efficient learning and good generalisation, if correctly specified. However, the ideal invariances for many problems of interest are often not known, which has led both to a body of engineering lore as well as attempts to provide frameworks for invariance learning. However, invariance learning is expensive and data intensive for popular neural architectures. We introduce the notion of amortizing invariance learning. In an up-front learning phase, we learn a low-dimensional manifold of feature extractors spanning invariance to different transformations using a hyper-network. Then, for any problem of interest, both model and invariance learning are rapid and efficient by fitting a low-dimensional invariance descriptor an output head. Empirically, this framework can identify appropriate invariances in different downstream tasks and lead to comparable or better test performance than conventional approaches. Our HyperInvariance framework is also theoretically appealing as it enables generalisation-bounds that provide an interesting new operating point in the trade-off between model fit and complexity.

Torben Berndt, Elyes Farjallah, Leif Seute et al.

Recent work on the sequence universality of State Space Models (SSMs) has introduced efficient, maximally expressive continuous-time approaches for time-series modelling. While these works focus on discriminative settings, we extend this perspective to generative time-series modelling by proving that maximally expressive Structured Linear Controlled Differential Equations (SLiCEs) are universal time-series generators, in the sense that they can approximate the induced path laws of continuous causal pushforwards on compact latent sets in $W_\infty$. Building on these theoretical results, we propose Generative SLiCEs (G-SLiCEs), a maximally expressive continuous-time model for flow matching on path-space. Empirically, we show that expressivity improves performance in probabilistic forecasting and downstream tasks, while retaining the advantages of continuous-time models such as generalising to arbitrary observation grids. This is particularly beneficial for irregular grids, where fixed-grid models often struggle.

Nicolas Wolf, Leif Seute, Vsevolod Viliuga et al.

Deep generative models have recently been proposed for sampling protein conformations from the Boltzmann distribution, as an alternative to often prohibitively expensive Molecular Dynamics simulations. However, current state-of-the-art approaches rely on fine-tuning pre-trained folding models and evolutionary sequence information, limiting their applicability and efficiency, and introducing potential biases. In this work, we propose a flow matching model for sampling protein conformations based solely on backbone geometry - BBFlow. We introduce a geometric encoding of the backbone equilibrium structure as input and propose to condition not only the flow but also the prior distribution on the respective equilibrium structure, eliminating the need for evolutionary information. The resulting model is orders of magnitudes faster than current state-of-the-art approaches at comparable accuracy, is transferable to multi-chain proteins, and can be trained from scratch in a few GPU days. In our experiments, we demonstrate that the proposed model achieves competitive performance with reduced inference time, across not only an established benchmark of naturally occurring proteins but also de novo proteins, for which evolutionary information is scarce or absent. BBFlow is available at https://github.com/graeter-group/bbflow.

Moritz Feik, Sebastian Lerch, Jan Stühmer

Ensemble forecasts from numerical weather prediction models show systematic errors that require correction via post-processing. While there has been substantial progress in flexible neural network-based post-processing methods over the past years, most station-based approaches still treat every input data point separately which limits the capabilities for leveraging spatial structures in the forecast errors. In order to improve information sharing across locations, we propose a graph neural network architecture for ensemble post-processing, which represents the station locations as nodes on a graph and utilizes an attention mechanism to identify relevant predictive information from neighboring locations. In a case study on 2-m temperature forecasts over Europe, the graph neural network model shows substantial improvements over a highly competitive neural network-based post-processing method.

Vsevolod Viliuga, Leif Seute, Nicolas Wolf et al.

Recent advances in geometric deep learning and generative modeling have enabled the design of novel proteins with a wide range of desired properties. However, current state-of-the-art approaches are typically restricted to generating proteins with only static target properties, such as motifs and symmetries. In this work, we take a step towards overcoming this limitation by proposing a framework to condition structure generation on flexibility, which is crucial for key functionalities such as catalysis or molecular recognition. We first introduce BackFlip, an equivariant neural network for predicting per-residue flexibility from an input backbone structure. Relying on BackFlip, we propose FliPS, an SE(3)-equivariant conditional flow matching model that solves the inverse problem, that is, generating backbones that display a target flexibility profile. In our experiments, we show that FliPS is able to generate novel and diverse protein backbones with the desired flexibility, verified by Molecular Dynamics (MD) simulations. FliPS and BackFlip are available at https://github.com/graeter-group/flips .

Dorin Ungureanu, Federica Bogo, Silvano Galliani et al.

Mixed reality headsets, such as the Microsoft HoloLens 2, are powerful sensing devices with integrated compute capabilities, which makes it an ideal platform for computer vision research. In this technical report, we present HoloLens 2 Research Mode, an API and a set of tools enabling access to the raw sensor streams. We provide an overview of the API and explain how it can be used to build mixed reality applications based on processing sensor data. We also show how to combine the Research Mode sensor data with the built-in eye and hand tracking capabilities provided by HoloLens 2. By releasing the Research Mode API and a set of open-source tools, we aim to foster further research in the fields of computer vision as well as robotics and encourage contributions from the research community.

Torben Berndt, Jan Stühmer

Equivariance is a powerful inductive bias in neural networks, improving generalisation and physical consistency. Recently, however, non-equivariant models have regained attention, due to their better runtime performance and imperfect symmetries that might arise in real-world applications. This has motivated the development of approximately equivariant models that strike a middle ground between respecting symmetries and fitting the data distribution. Existing approaches in this field usually apply sample-based regularisers which depend on data augmentation at training time, incurring a high sample complexity, in particular for continuous groups such as $SO(3)$. This work instead approaches approximate equivariance via a projection-based regulariser which leverages the orthogonal decomposition of linear layers into equivariant and non-equivariant components. In contrast to existing methods, this penalises non-equivariance at an operator level across the full group orbit, rather than point-wise. We present a mathematical framework for computing the non-equivariance penalty exactly and efficiently in both the spatial and spectral domain. In our experiments, our method consistently outperforms prior approximate equivariance approaches in both model performance and efficiency, achieving substantial runtime gains over sample-based regularisers.

Leif Seute, Eric Hartmann, Jan Stühmer et al.

Simulating large molecular systems over long timescales requires force fields that are both accurate and efficient. In recent years, E(3) equivariant neural networks have lifted the tension between computational efficiency and accuracy of force fields, but they are still several orders of magnitude more expensive than established molecular mechanics (MM) force fields. Here, we propose Grappa, a machine learning framework to predict MM parameters from the molecular graph, employing a graph attentional neural network and a transformer with symmetry-preserving positional encoding. The resulting Grappa force field outperformstabulated and machine-learned MM force fields in terms of accuracy at the same computational efficiency and can be used in existing Molecular Dynamics (MD) engines like GROMACS and OpenMM. It predicts energies and forces of small molecules, peptides, RNA and - showcasing its extensibility to uncharted regions of chemical space - radicals at state-of-the-art MM accuracy. We demonstrate Grappa's transferability to macromolecules in MD simulations from a small fast folding protein up to a whole virus particle. Our force field sets the stage for biomolecular simulations closer to chemical accuracy, but with the same computational cost as established protein force fields.

Simon Wagner, Leif Seute, Vsevolod Viliuga et al.

We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA) architecture from AlphaFold2, in which the backbone residue frames and geometric features are represented in the projective geometric algebra. This enables to construct geometrically expressive messages between residues, including higher order terms, using the bilinear operations of the algebra. We evaluate our architecture by incorporating it into the framework of FrameFlow, a state-of-the-art flow matching model for protein backbone generation. The proposed model achieves high designability, diversity and novelty, while also sampling protein backbones that follow the statistical distribution of secondary structure elements found in naturally occurring proteins, a property so far only insufficiently achieved by many state-of-the-art generative models.

Beni Egressy, Jan Stühmer

While large language models (LLMs) demonstrate impressive capabilities across numerous applications, their robustness remains a critical concern. This paper is motivated by a specific vulnerability: the order sensitivity of LLMs. This vulnerability manifests itself as the order bias observed when LLMs decide between possible options (for example, a preference for the first option) and the tendency of LLMs to provide different answers when options are reordered. The use cases for this scenario extend beyond the classical case of multiple-choice question answering to the use of LLMs as automated evaluators in AI pipelines, comparing output generated by different models. We introduce Set-LLM, a novel architectural adaptation for pretrained LLMs that enables the processing of mixed set-text inputs with permutation invariance guarantees. The adaptations involve a new attention mask and new positional encodings specifically designed for sets. We provide a theoretical proof of invariance and demonstrate through experiments that Set-LLM can be trained effectively, achieving comparable or improved performance and maintaining the runtime of the original model, while eliminating order sensitivity.

Torben Berndt, Benjamin Walker, Tiexin Qin et al.

Dynamic graphs exhibit complex temporal dynamics due to the interplay between evolving node features and changing network structures. Recently, Graph Neural Controlled Differential Equations (Graph Neural CDEs) successfully adapted Neural CDEs from paths on Euclidean domains to paths on graph domains. Building on this foundation, we introduce Permutation Equivariant Neural Graph CDEs, which project Graph Neural CDEs onto permutation equivariant function spaces. This significantly reduces the model's parameter count without compromising representational power, resulting in more efficient training and improved generalisation. We empirically demonstrate the advantages of our approach through experiments on simulated dynamical systems and real-world tasks, showing improved performance in both interpolation and extrapolation scenarios.

Jan Stühmer, Richard E. Turner, Sebastian Nowozin

Recently there has been an increased interest in unsupervised learning of disentangled representations using the Variational Autoencoder (VAE) framework. Most of the existing work has focused largely on modifying the variational cost function to achieve this goal. We first show that these modifications, e.g. beta-VAE, simplify the tendency of variational inference to underfit causing pathological over-pruning and over-orthogonalization of learned components. Second we propose a complementary approach: to modify the probabilistic model with a structured latent prior. This prior allows to discover latent variable representations that are structured into a hierarchy of independent vector spaces. The proposed prior has three major advantages: First, in contrast to the standard VAE normal prior the proposed prior is not rotationally invariant. This resolves the problem of unidentifiability of the standard VAE normal prior. Second, we demonstrate that the proposed prior encourages a disentangled latent representation which facilitates learning of disentangled representations. Third, extensive quantitative experiments demonstrate that the prior significantly mitigates the trade-off between reconstruction loss and disentanglement over the state of the art.

Sebastian Tschiatschek, Kai Arulkumaran, Jan Stühmer et al.

Partially observable Markov decision processes (POMDPs) are a powerful abstraction for tasks that require decision making under uncertainty, and capture a wide range of real world tasks. Today, effective planning approaches exist that generate effective strategies given black-box models of a POMDP task. Yet, an open question is how to acquire accurate models for complex domains. In this paper we propose DELIP, an approach to model learning for POMDPs that utilizes amortized structured variational inference. We empirically show that our model leads to effective control strategies when coupled with state-of-the-art planners. Intuitively, model-based approaches should be particularly beneficial in environments with changing reward structures, or where rewards are initially unknown. Our experiments confirm that DELIP is particularly effective in this setting.