arXiv subjects

André Eberhard

Publications and source records attributed to André Eberhard.

4 recordsLinked to original sources

arXiv2026

Hyper-Dimensional Fingerprints as Molecular Representations

Computational molecular representations underpin virtual screening, property prediction, and materials discovery. Conventional fingerprints are efficient and deterministic but lose structural information through hash-based compression, particularly at low dimensionalities. Learned representations from graph neural networks recover this expressiveness but require task-specific training and substantial computational resources. Here we introduce hyperdimensional fingerprints (HDF), which replace the learned transformations of message-passing neural networks with algebraic operations on high-dimensional vectors, producing deterministic molecular representations without any training. Across diverse property prediction benchmarks, HDF outperforms conventional fingerprints in the majority of tasks while exhibiting greater consistency across datasets and models. Crucially, HDF embeddings preserve molecular similarity faithfully: at 32 dimensions, distances in HDF space achieve a 0.9 Pearson correlation with graph edit distance, compared to 0.55 for Morgan fingerprints at equivalent size. This structural fidelity persists at low dimensions where hash-based methods degrade, allowing simple nearest-neighbor regression to remain predictive with as few as 64 components. We further demonstrate the practical impact in Bayesian molecular optimization, where HDF-based surrogate models achieve substantially improved sample efficiency in regimes where Morgan fingerprints perform comparably to random search. HDF thus provides a general-purpose, training-free alternative to conventional molecular fingerprints, suggesting that the information loss long accepted as inherent to fixed-length fingerprints is a limitation of the hash-based encoding scheme rather than the fingerprint paradigm itself.

cs.LG↗

arXiv2026

Building Deep Graph Predictors with Graph Imitation Learning

Recent years have seen substantial progress in neural generation of text, images, and audio, supported by mature training pipelines and large-scale optimization. For graphs, however, comparable progress has been more limited. We attribute this gap to graph-specific optimization and representation challenges that undermine the effectiveness of training neural networks with backpropagation and gradient descent. We argue that representing graphs on a fixed-size Euclidean grid, as is common in recently proposed models for supervised graph prediction, may not be the optimal choice in these settings. To support our view, we provide an analysis of neural graph generation methods and identify theoretical challenges that lead to pitfalls when training neural networks to produce graphs as their output. Motivated by this analysis, we introduce \textbf{GRA}ph~\textbf{I}mitation~\textbf{L}earning~(GRAIL), a framework for training neural networks in supervised settings in which the supervision signal is a graph. GRAIL generates graphs sequentially through a Markov decision process over embeddings of partial graphs, thereby avoiding the representation issues associated with fixed-size grid graph representations. We empirically show that GRAIL achieves competitive results on supervised graph prediction across a comprehensive suite of 18 benchmarks, matching or surpassing state-of-the-art methods in several settings.

cs.CV↗

arXiv2022

Actively Learning Costly Reward Functions for Reinforcement Learning

Transfer of recent advances in deep reinforcement learning to real-world applications is hindered by high data demands and thus low efficiency and scalability. Through independent improvements of components such as replay buffers or more stable learning algorithms, and through massively distributed systems, training time could be reduced from several days to several hours for standard benchmark tasks. However, while rewards in simulated environments are well-defined and easy to compute, reward evaluation becomes the bottleneck in many real-world environments, e.g., in molecular optimization tasks, where computationally demanding simulations or even experiments are required to evaluate states and to quantify rewards. Therefore, training might become prohibitively expensive without an extensive amount of computational resources and time. We propose to alleviate this problem by replacing costly ground-truth rewards with rewards modeled by neural networks, counteracting non-stationarity of state and reward distributions during training with an active learning component. We demonstrate that using our proposed ACRL method (Actively learning Costly rewards for Reinforcement Learning), it is possible to train agents in complex real-world environments orders of magnitudes faster. By enabling the application of reinforcement learning methods to new domains, we show that we can find interesting and non-trivial solutions to real-world optimization problems in chemistry, materials science and engineering.

cs.LG↗

arXiv2022

Graph neural networks for materials science and chemistry

Machine learning plays an increasingly important role in many areas of chemistry and materials science, e.g. to predict materials properties, to accelerate simulations, to design new materials, and to predict synthesis routes of new materials. Graph neural networks (GNNs) are one of the fastest growing classes of machine learning models. They are of particular relevance for chemistry and materials science, as they directly work on a graph or structural representation of molecules and materials and therefore have full access to all relevant information required to characterize materials. In this review article, we provide an overview of the basic principles of GNNs, widely used datasets, and state-of-the-art architectures, followed by a discussion of a wide range of recent applications of GNNs in chemistry and materials science, and concluding with a road-map for the further development and application of GNNs.

physics.chem-ph↗