MolGroup achieves this by utilizing a routing mechanismoptimized through abi-level optimization framework.

In molecular property prediction, the most valuable compounds (e.g., high potency) often occupy sparse regions of the target space. Standard Graph Neural Networks (GNNs) commonly optimize for the average error, underperforming on these uncommon but critical cases, with existing oversampling methods often distorting molecular topology. In this paper, we introduce SPECTRA, a Spectral Target-Aware graph augmentation framework that generates realistic molecular graphs in the spectral domain. SPECTRA (i) reconstructs multi-attribute molecular graphs from SMILES; (ii) aligns molecule pairs via (Fused) Gromov-Wasserstein couplings to obtain node correspondences; (iii) interpolates Laplacian eigenvalues, eigenvectors and node features in a stable share-basis; and (iv) reconstructs edges to synthesize physically plausible intermediates with interpolated targets. A rarity-aware budgeting scheme, derived from a kernel density estimation of labels, concentrates augmentation where data are scarce. Coupled with a spectral GNN using edge-aware Chebyshev convolutions, SPECTRA densifies underrepresented regions without degrading global accuracy. On benchmarks, SPECTRA consistently improves error in relevant target ranges while maintaining competitive overall MAE, and yields interpretable synthetic molecules whose structure reflects the underlying spectral geometry. Our results demonstrate that spectral, geometry-aware augmentation is an effective and efficient strategy for imbalanced molecular property regression.

Machine learning has emerged as a new tool in chemistry to bypass expensive experiments or quantum-chemical calculations, for example, in high-throughput screening applications. However, many machine learning studies rely on small data sets, making it difficult to efficiently implement powerful deep learning architectures such as message passing neural networks. In this study, we benchmark common machine learning models for the prediction of molecular properties on small data sets, for which the best results are obtained with the message passing neural network PaiNN, as well as SOAP molecular descriptors concatenated to a set of simple molecular descriptors tailored to gradient boosting with regression trees. To further improve the predictive capabilities of PaiNN, we present a transfer learning strategy that uses large data sets to pre-train the respective models and allows to obtain more accurate models after fine-tuning on the original data sets. The pre-training labels are obtained from computationally cheap ab initio or semi-empirical models and corrected by simple linear regression on the target data set to obtain labels that are close to those of the original data. This strategy is tested on the Harvard Oxford Photovoltaics data set (HOPV, HOMO-LUMO-gaps), for which excellent results are obtained, and on the Freesolv data set (solvation energies), where this method is unsuccessful due to a complex underlying learning task and the dissimilar methods used to obtain pre-training and fine-tuning labels. Finally, we find that the final training results do not improve monotonically with the size of the pre-training data set, but pre-training with fewer data points can lead to more biased pre-trained models and higher accuracy after fine-tuning.

Predicting the properties of a molecule from its structure is a challenging task. Recently, deep learning methods have improved the state of the art for this task because of their ability to learn useful features from the given data. By treating molecule structure as graphs, where atoms and bonds are modeled as nodes and edges, graph neural networks (GNNs) have been widely used to predict molecular properties. However, the design and development of GNNs for a given data set rely on labor-intensive design and tuning of the network architectures. Neural architecture search (NAS) is a promising approach to discover high-performing neural network architectures automatically. To that end, we develop an NAS approach to automate the design and development of GNNs for molecular property prediction. Specifically, we focus on automated development of message-passing neural networks (MPNNs) to predict the molecular properties of small molecules in quantum mechanics and physical chemistry data sets from the MoleculeNet benchmark. We demonstrate the superiority of the automatically discovered MPNNs by comparing them with manually designed GNNs from the MoleculeNet benchmark. We study the relative importance of the choices in the MPNN search space, demonstrating that customizing the architecture is critical to enhancing performance in molecular property prediction and that the proposed approach can perform customization automatically with minimal manual effort.