Chemistry Foundation Models (CFMs) that leverage Graph Neural Networks (GNNs) operating on 3D molecular graph structures are becoming indispensable tools for computational chemists and materials scientists. These models facilitate the understanding of matter and the discovery of new molecules and materials. In contrast to GNNs operating on large homogeneous graphs, GNNs used by CFMs process a large number of geometric graphs of varying sizes, requiring different optimization strategies than those developed for large homogeneous GNNs. This paper presents optimizations for two critical phases of CFM training: data distribution and model training, targeting MACE - a state-of-the-art CFM. We address the challenge of load balancing in data distribution by formulating it as a multi-objective bin packing problem. We propose an iterative algorithm that provides a highly effective, fast, and practical solution, ensuring efficient data distribution. For the training phase, we identify symmetric tensor contraction as the key computational kernel in MACE and optimize this kernel to improve the overall performance. Our combined approach of balanced data distribution and kernel optimization significantly enhances the training process of MACE. Experimental results demonstrate a substantial speedup, reducing per-epoch execution time for training from 12 to 2 minutes on 740 GPUs with a 2.6M sample dataset.

Fast and accurate generation of molecular conformers is desired for downstream computational chemistry and drug discovery tasks. Currently, training and sampling state-of-the-art diffusion or flow-based models for conformer generation require significant computational resources. In this work, we build upon flow-matching and propose two mechanisms for accelerating training and inference of generative models for 3D molecular conformer generation. For fast training, we introduce the SO(3)-*Averaged Flow* training objective, which leads to faster convergence to better generation quality compared to conditional optimal transport flow or Kabsch-aligned flow. We demonstrate that models trained using SO(3)-*Averaged Flow* can reach state-of-the-art conformer generation quality. For fast inference, we show that the reflow and distillation methods of flow-based models enable few-steps or even one-step molecular conformer generation with high quality. The training techniques proposed in this work show a path towards highly efficient molecular conformer generation with flow-based models.

Pruning methods can considerably reduce the size of artificial neural networks without harming their performance and in some cases they can even uncover sub-networks that, when trained in isolation, match or surpass the test accuracy of their dense counterparts. Here, we characterize the inductive bias that pruning imprints in such "winning lottery tickets": focusing on visual tasks, we analyze the architecture resulting from iterative magnitude pruning of a simple fully connected network. We show that the surviving node connectivity is local in input space, and organized in patterns reminiscent of the ones found in convolutional networks. We investigate the role played by data and tasks in shaping the architecture of the pruned sub-network. We find that pruning performances, and the ability to sift out the noise and make local features emerge, improve by increasing the size of the training set, and the semantic value of the data. We also study different pruning procedures, and find that iterative magnitude pruning is particularly effective in distilling meaningful connectivity out of features present in the original task. Our results suggest the possibility to automatically discover new and efficient architectural inductive biases in other datasets and tasks.

Neural networks have been shown to perform incredibly well in classification tasks over structured high-dimensional datasets. However, the learning dynamics of such networks is still poorly understood. In this paper we study in detail the training dynamics of a simple type of neural network: a single hidden layer trained to perform a classification task. We show that in a suitable mean-field limit this case maps to a single-node learning problem with a time-dependent dataset determined self-consistently from the average nodes population. We specialize our theory to the prototypical case of a linearly separable dataset and a linear hinge loss, for which the dynamics can be explicitly solved in the infinite dataset limit. This allow us to address in a simple setting several phenomena appearing in modern networks such as slowing down of training dynamics, crossover between feature and lazy learning, and overfitting. Finally, we asses the limitations of mean-field theory by studying the case of large but finite number of nodes and of training samples.