Andreas Mayr

Richard Freinschlag, Timo Bertram, Erich Kobler et al.

Reasoning problems such as Sudoku and ARC-AGI remain challenging for neural networks. The structured problem solving architecture family of Recurrent Reasoning Models (RRMs), including Hierarchical Reasoning Model (HRM) and Tiny Recursive Model (TRM), offer a compact alternative to large language models, but currently handle symbol symmetries only implicitly via costly data augmentation. We introduce Symbol-Equivariant Recurrent Reasoning Models (SE-RRMs), which enforce permutation equivariance at the architectural level through symbol-equivariant layers, guaranteeing identical solutions under symbol or color permutations. SE-RRMs outperform prior RRMs on 9x9 Sudoku and generalize from just training on 9x9 to smaller 4x4 and larger 16x16 and 25x25 instances, to which existing RRMs cannot extrapolate. On ARC-AGI-1 and ARC-AGI-2, SE-RRMs achieve competitive performance with substantially less data augmentation and only 2 million parameters, demonstrating that explicitly encoding symmetry improves the robustness and scalability of neural reasoning. Code is available at https://github.com/ml-jku/SE-RRM.

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 .

Thomas Adler, Johannes Brandstetter, Michael Widrich et al.

In order to quickly adapt to new data, few-shot learning aims at learning from few examples, often by using already acquired knowledge. The new data often differs from the previously seen data due to a domain shift, that is, a change of the input-target distribution. While several methods perform well on small domain shifts like new target classes with similar inputs, larger domain shifts are still challenging. Large domain shifts may result in high-level concepts that are not shared between the original and the new domain, whereas low-level concepts like edges in images might still be shared and useful. For cross-domain few-shot learning, we suggest representation fusion to unify different abstraction levels of a deep neural network into one representation. We propose Cross-domain Hebbian Ensemble Few-shot learning (CHEF), which achieves representation fusion by an ensemble of Hebbian learners acting on different layers of a deep neural network. Ablation studies show that representation fusion is a decisive factor to boost cross-domain few-shot learning. On the few-shot datasets miniImagenet and tieredImagenet with small domain shifts, CHEF is competitive with state-of-the-art methods. On cross-domain few-shot benchmark challenges with larger domain shifts, CHEF establishes novel state-of-the-art results in all categories. We further apply CHEF on a real-world cross-domain application in drug discovery. We consider a domain shift from bioactive molecules to environmental chemicals and drugs with twelve associated toxicity prediction tasks. On these tasks, that are highly relevant for computational drug discovery, CHEF significantly outperforms all its competitors. Github: https://github.com/ml-jku/chef

Günter Klambauer, Thomas Unterthiner, Andreas Mayr et al.

Deep Learning has revolutionized vision via convolutional neural networks (CNNs) and natural language processing via recurrent neural networks (RNNs). However, success stories of Deep Learning with standard feed-forward neural networks (FNNs) are rare. FNNs that perform well are typically shallow and, therefore cannot exploit many levels of abstract representations. We introduce self-normalizing neural networks (SNNs) to enable high-level abstract representations. While batch normalization requires explicit normalization, neuron activations of SNNs automatically converge towards zero mean and unit variance. The activation function of SNNs are "scaled exponential linear units" (SELUs), which induce self-normalizing properties. Using the Banach fixed-point theorem, we prove that activations close to zero mean and unit variance that are propagated through many network layers will converge towards zero mean and unit variance -- even under the presence of noise and perturbations. This convergence property of SNNs allows to (1) train deep networks with many layers, (2) employ strong regularization, and (3) to make learning highly robust. Furthermore, for activations not close to unit variance, we prove an upper and lower bound on the variance, thus, vanishing and exploding gradients are impossible. We compared SNNs on (a) 121 tasks from the UCI machine learning repository, on (b) drug discovery benchmarks, and on (c) astronomy tasks with standard FNNs and other machine learning methods such as random forests and support vector machines. SNNs significantly outperformed all competing FNN methods at 121 UCI tasks, outperformed all competing methods at the Tox21 dataset, and set a new record at an astronomy data set. The winning SNN architectures are often very deep. Implementations are available at: github.com/bioinf-jku/SNNs.

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.

Andreas Mayr, Sebastian Lehner, Arno Mayrhofer et al.

Recently, the application of machine learning models has gained momentum in natural sciences and engineering, which is a natural fit due to the abundance of data in these fields. However, the modeling of physical processes from simulation data without first principle solutions remains difficult. Here, we present a Graph Neural Networks approach towards accurate modeling of complex 3D granular flow simulation processes created by the discrete element method LIGGGHTS and concentrate on simulations of physical systems found in real world applications like rotating drums and hoppers. We discuss how to implement Graph Neural Networks that deal with 3D objects, boundary conditions, particle - particle, and particle - boundary interactions such that an accurate modeling of relevant physical quantities is made possible. Finally, we compare the machine learning based trajectories to LIGGGHTS trajectories in terms of particle flows and mixing entropies.

Thomas Unterthiner, Andreas Mayr, Günter Klambauer et al.

Everyday we are exposed to various chemicals via food additives, cleaning and cosmetic products and medicines -- and some of them might be toxic. However testing the toxicity of all existing compounds by biological experiments is neither financially nor logistically feasible. Therefore the government agencies NIH, EPA and FDA launched the Tox21 Data Challenge within the "Toxicology in the 21st Century" (Tox21) initiative. The goal of this challenge was to assess the performance of computational methods in predicting the toxicity of chemical compounds. State of the art toxicity prediction methods build upon specifically-designed chemical descriptors developed over decades. Though Deep Learning is new to the field and was never applied to toxicity prediction before, it clearly outperformed all other participating methods. In this application paper we show that deep nets automatically learn features resembling well-established toxicophores. In total, our Deep Learning approach won both of the panel-challenges (nuclear receptors and stress response) as well as the overall Grand Challenge, and thereby sets a new standard in tox prediction.

Djork-Arné Clevert, Andreas Mayr, Thomas Unterthiner et al.

We propose rectified factor networks (RFNs) to efficiently construct very sparse, non-linear, high-dimensional representations of the input. RFN models identify rare and small events in the input, have a low interference between code units, have a small reconstruction error, and explain the data covariance structure. RFN learning is a generalized alternating minimization algorithm derived from the posterior regularization method which enforces non-negative and normalized posterior means. We proof convergence and correctness of the RFN learning algorithm. On benchmarks, RFNs are compared to other unsupervised methods like autoencoders, RBMs, factor analysis, ICA, and PCA. In contrast to previous sparse coding methods, RFNs yield sparser codes, capture the data's covariance structure more precisely, and have a significantly smaller reconstruction error. We test RFNs as pretraining technique for deep networks on different vision datasets, where RFNs were superior to RBMs and autoencoders. On gene expression data from two pharmaceutical drug discovery studies, RFNs detected small and rare gene modules that revealed highly relevant new biological insights which were so far missed by other unsupervised methods.