In recent years, pre-trained graph neural networks (GNNs) have been developed as general models which can be effectively fine-tuned for various potential downstream tasks in materials science, and have shown significant improvements in accuracy and data efficiency. The most widely used pre-training methods currently involve either supervised training to fit a general force field or self-supervised training by denoising atomic structures equilibrium. Both methods require datasets generated from quantum mechanical calculations, which quickly become intractable when scaling to larger datasets. Here we propose a novel pre-training objective which instead uses cheaply-computed structural fingerprints as targets while maintaining comparable performance across a range of different structural descriptors. Our experiments show this approach can act as a general strategy for pre-training GNNs with application towards large scale foundational models for atomistic data.

Geometric deep learning (GDL) has gained significant attention in various scientific fields, chiefly for its proficiency in modeling data with intricate geometric structures. Yet, very few works have delved into its capability of tackling the distribution shift problem, a prevalent challenge in many relevant applications. To bridge this gap, we propose GDL-DS, a comprehensive benchmark designed for evaluating the performance of GDL models in scenarios with distribution shifts. Our evaluation datasets cover diverse scientific domains from particle physics and materials science to biochemistry, and encapsulate a broad spectrum of distribution shifts including conditional, covariate, and concept shifts. Furthermore, we study three levels of information access from the out-of-distribution (OOD) testing data, including no OOD information, only OOD features without labels, and OOD features with a few labels. Overall, our benchmark results in 30 different experiment settings, and evaluates 3 GDL backbones and 11 learning algorithms in each setting. A thorough analysis of the evaluation results is provided, poised to illuminate insights for DGL researchers and domain practitioners who are to use DGL in their applications.

In the scope of "AI for Science", solving inverse problems is a longstanding challenge in materials and drug discovery, where the goal is to determine the hidden structures given a set of desirable properties. Deep generative models are recently proposed to solve inverse problems, but these currently use expensive forward operators and struggle in precisely localizing the exact solutions and fully exploring the parameter spaces without missing solutions. In this work, we propose a novel approach (called iPage) to accelerate the inverse learning process by leveraging probabilistic inference from deep invertible models and deterministic optimization via fast gradient descent. Given a target property, the learned invertible model provides a posterior over the parameter space; we identify these posterior samples as an intelligent prior initialization which enables us to narrow down the search space. We then perform gradient descent to calibrate the inverse solutions within a local region. Meanwhile, a space-filling sampling is imposed on the latent space to better explore and capture all possible solutions. We evaluate our approach on three benchmark tasks and two created datasets with real-world applications from quantum chemistry and additive manufacturing, and find our method achieves superior performance compared to several state-of-the-art baseline methods. The iPage code is available at https://github.com/jxzhangjhu/MatDesINNe.