Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer

Constructing transferable descriptors for conformation representation of molecular and biological systems finds numerous applications in drug discovery, learning-based molecular dynamics, and protein mechanism analysis. Geometric graph neural networks (Geom-GNNs) with all-atom information have transformed atomistic simulations by serving as a general learnable geometric descriptors for downstream tasks including prediction of interatomic potential and molecular properties. However, common practices involve supervising Geom-GNNs on specific downstream tasks, which suffer from the lack of high-quality data and inaccurate labels leading to poor generalization and performance degradation on out-of-distribution (OOD) scenarios. In this work, we explored the possibility of using pre-trained Geom-GNNs as transferable and highly effective geometric descriptors for improved generalization. To explore their representation power, we studied the scaling behaviors of Geom-GNNs under self-supervised pre-training, supervised and unsupervised learning setups. We find that the expressive power of different architectures can differ on the pre-training task. Interestingly, Geom-GNNs do not follow the power-law scaling on the pre-training task, and universally lack predictable scaling behavior on the supervised tasks with quantum chemical labels important for screening and design of novel molecules. More importantly, we demonstrate how all-atom graph embedding can be organically combined with other neural architectures to enhance the expressive power. Meanwhile, the low-dimensional projection of the latent space shows excellent agreement with conventional geometrical descriptors.

Faithful Low-Resource Data-to-Text Generation through Cycle Training

Methods to generate text from structured data have advanced significantly in recent years, primarily due to fine-tuning of pre-trained language models on large datasets. However, such models can fail to produce output faithful to the input data, particularly on out-of-domain data. Sufficient annotated data is often not available for specific domains, leading us to seek an unsupervised approach to improve the faithfulness of output text. Since the problem is fundamentally one of consistency between the representations of the structured data and text, we evaluate the effectiveness of cycle training in this work. Cycle training uses two models which are inverses of each other: one that generates text from structured data, and one which generates the structured data from natural language text. We show that cycle training, when initialized with a small amount of supervised data (100 samples in our case), achieves nearly the same performance as fully supervised approaches for the data-to-text generation task on the WebNLG, E2E, WTQ, and WSQL datasets. We perform extensive empirical analysis with automated evaluation metrics and a newly designed human evaluation schema to reveal different cycle training strategies' effectiveness of reducing various types of generation errors. Our code is publicly available at https://github.com/Edillower/CycleNLG.