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Nate Gruver, Anuroop Sriram, Andrea Madotto, Andrew Gordon Wilson, C. Lawrence Zitnick, Zachary Ulissi

We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.

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Nima Shoghi, Adeesh Kolluru, John R. Kitchin, Zachary W. Ulissi, C. Lawrence Zitnick, Brandon M. Wood

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of $\sim$120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

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Saro Passaro, C. Lawrence Zitnick

Graph neural networks that model 3D data, such as point clouds or atoms, are typically desired to be $SO(3)$ equivariant, i.e., equivariant to 3D rotations. Unfortunately equivariant convolutions, which are a fundamental operation for equivariant networks, increase significantly in computational complexity as higher-order tensors are used. In this paper, we address this issue by reducing the $SO(3)$ convolutions or tensor products to mathematically equivalent convolutions in $SO(2)$ . This is accomplished by aligning the node embeddings' primary axis with the edge vectors, which sparsifies the tensor product and reduces the computational complexity from $O(L^6)$ to $O(L^3)$, where $L$ is the degree of the representation. We demonstrate the potential implications of this improvement by proposing the Equivariant Spherical Channel Network (eSCN), a graph neural network utilizing our novel approach to equivariant convolutions, which achieves state-of-the-art results on the large-scale OC-20 dataset.

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Janice Lan, Aini Palizhati, Muhammed Shuaibi, Brandon M. Wood, Brook Wander, Abhishek Das, Matt Uyttendaele, C. Lawrence Zitnick, Zachary W. Ulissi

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the minimum binding energy - the adsorption energy - for an adsorbate and a catalyst surface of interest. Traditionally, the identification of low energy adsorbate-surface configurations relies on heuristic methods and researcher intuition. As the desire to perform high-throughput screening increases, it becomes challenging to use heuristics and intuition alone. In this paper, we demonstrate machine learning potentials can be leveraged to identify low energy adsorbate-surface configurations more accurately and efficiently. Our algorithm provides a spectrum of trade-offs between accuracy and efficiency, with one balanced option finding the lowest energy configuration, within a 0.1 eV threshold, 86.63% of the time, while achieving a 1387x speedup in computation. To standardize benchmarking, we introduce the Open Catalyst Dense dataset containing nearly 1,000 diverse surfaces and 87,045 unique configurations.

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C. Lawrence Zitnick, Abhishek Das, Adeesh Kolluru, Janice Lan, Muhammed Shuaibi, Anuroop Sriram, Zachary Ulissi, Brandon Wood

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst 2020 dataset in both energy and force prediction for numerous tasks and metrics.

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Richard Tran, Janice Lan, Muhammed Shuaibi, Siddharth Goyal, Brandon M. Wood, Abhishek Das, Javier Heras-Domingo, Adeesh Kolluru, Ammar Rizvi, Nima Shoghi, Anuroop Sriram, Zachary Ulissi, C. Lawrence Zitnick

Computational catalysis and machine learning communities have made considerable progress in developing machine learning models for catalyst discovery and design. Yet, a general machine learning potential that spans the chemical space of catalysis is still out of reach. A significant hurdle is obtaining access to training data across a wide range of materials. One important class of materials where data is lacking are oxides, which inhibits models from studying the Oxygen Evolution Reaction and oxide electrocatalysis more generally. To address this we developed the Open Catalyst 2022(OC22) dataset, consisting of 62,521 Density Functional Theory (DFT) relaxations (~9,884,504 single point calculations) across a range of oxide materials, coverages, and adsorbates (*H, *O, *N, *C, *OOH, *OH, *OH2, *O2, *CO). We define generalized tasks to predict the total system energy that are applicable across catalysis, develop baseline performance of several graph neural networks (SchNet, DimeNet++, ForceNet, SpinConv, PaiNN, GemNet-dT, GemNet-OC), and provide pre-defined dataset splits to establish clear benchmarks for future efforts. For all tasks, we study whether combining datasets leads to better results, even if they contain different materials or adsorbates. Specifically, we jointly train models on Open Catalyst 2020 (OC20) Dataset and OC22, or fine-tune pretrained OC20 models on OC22. In the most general task, GemNet-OC sees a ~32% improvement in energy predictions through fine-tuning and a ~9% improvement in force predictions via joint training. Surprisingly, joint training on both the OC20 and much smaller OC22 datasets also improves total energy predictions on OC20 by ~19%. The dataset and baseline models are open sourced, and a public leaderboard will follow to encourage continued community developments on the total energy tasks and data.

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Johannes Gasteiger, Muhammed Shuaibi, Anuroop Sriram, Stephan Günnemann, Zachary Ulissi, C. Lawrence Zitnick, Abhishek Das

The predominant method of demonstrating progress of atomic graph neural networks are benchmarks on small and limited datasets. The implicit hypothesis behind this approach is that progress on these narrow datasets generalize to the large diversity of chemistry. This generalizability would be very helpful for research, but currently remains untested. In this work we test this assumption by identifying four aspects of complexity in which many datasets are lacking: 1. Chemical diversity (number of different elements), 2. system size (number of atoms per sample), 3. dataset size (number of data samples), and 4. domain shift (similarity of the training and test set). We introduce multiple subsets of the large Open Catalyst 2020 (OC20) dataset to independently investigate each of these aspects. We then perform 21 ablation studies and sensitivity analyses on 9 datasets testing both previously proposed and new model enhancements. We find that some improvements are consistent between datasets, but many are not and some even have opposite effects. Based on this analysis, we identify a smaller dataset that correlates well with the full OC20 dataset, and propose the GemNet-OC model, which outperforms the previous state-of-the-art on OC20 by 16%, while reducing training time by a factor of 10. Overall, our findings challenge the common belief that graph neural networks work equally well independent of dataset size and diversity, and suggest that caution must be exercised when making generalizations based on narrow datasets.

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Anuroop Sriram, Abhishek Das, Brandon M. Wood, Siddharth Goyal, C. Lawrence Zitnick

Recent progress in Graph Neural Networks (GNNs) for modeling atomic simulations has the potential to revolutionize catalyst discovery, which is a key step in making progress towards the energy breakthroughs needed to combat climate change. However, the GNNs that have proven most effective for this task are memory intensive as they model higher-order interactions in the graphs such as those between triplets or quadruplets of atoms, making it challenging to scale these models. In this paper, we introduce Graph Parallelism, a method to distribute input graphs across multiple GPUs, enabling us to train very large GNNs with hundreds of millions or billions of parameters. We empirically evaluate our method by scaling up the number of parameters of the recently proposed DimeNet++ and GemNet models by over an order of magnitude. On the large-scale Open Catalyst 2020 (OC20) dataset, these graph-parallelized models lead to relative improvements of 1) 15% on the force MAE metric for the S2EF task and 2) 21% on the AFbT metric for the IS2RS task, establishing new state-of-the-art results.

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Drew A. Hudson, C. Lawrence Zitnick

We introduce the GANformer2 model, an iterative object-oriented transformer, explored for the task of generative modeling. The network incorporates strong and explicit structural priors, to reflect the compositional nature of visual scenes, and synthesizes images through a sequential process. It operates in two stages: a fast and lightweight planning phase, where we draft a high-level scene layout, followed by an attention-based execution phase, where the layout is being refined, evolving into a rich and detailed picture. Our model moves away from conventional black-box GAN architectures that feature a flat and monolithic latent space towards a transparent design that encourages efficiency, controllability and interpretability. We demonstrate GANformer2's strengths and qualities through a careful evaluation over a range of datasets, from multi-object CLEVR scenes to the challenging COCO images, showing it successfully achieves state-of-the-art performance in terms of visual quality, diversity and consistency. Further experiments demonstrate the model's disentanglement and provide a deeper insight into its generative process, as it proceeds step-by-step from a rough initial sketch, to a detailed layout that accounts for objects' depths and dependencies, and up to the final high-resolution depiction of vibrant and intricate real-world scenes. See https://github.com/dorarad/gansformer for model implementation.

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Muhammed Shuaibi, Adeesh Kolluru, Abhishek Das, Aditya Grover, Anuroop Sriram, Zachary Ulissi, C. Lawrence Zitnick

Progress towards the energy breakthroughs needed to combat climate change can be significantly accelerated through the efficient simulation of atomic systems. Simulation techniques based on first principles, such as Density Functional Theory (DFT), are limited in their practical use due to their high computational expense. Machine learning approaches have the potential to approximate DFT in a computationally efficient manner, which could dramatically increase the impact of computational simulations on real-world problems. Approximating DFT poses several challenges. These include accurately modeling the subtle changes in the relative positions and angles between atoms, and enforcing constraints such as rotation invariance or energy conservation. We introduce a novel approach to modeling angular information between sets of neighboring atoms in a graph neural network. Rotation invariance is achieved for the network's edge messages through the use of a per-edge local coordinate frame and a novel spin convolution over the remaining degree of freedom. Two model variants are proposed for the applications of structure relaxation and molecular dynamics. State-of-the-art results are demonstrated on the large-scale Open Catalyst 2020 dataset. Comparisons are also performed on the MD17 and QM9 datasets.

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