A practical guide to machine learning interatomic potentials -- Status and future

The rapid development and large body of literature on machine learning interatomic potentials (MLIPs) can make it difficult to know how to proceed for researchers who are not experts but wish to use these tools. The spirit of this review is to help such researchers by serving as a practical, accessible guide to the state-of-the-art in MLIPs. This review paper covers a broad range of topics related to MLIPs, including (i) central aspects of how and why MLIPs are enablers of many exciting advancements in molecular modeling, (ii) the main underpinnings of different types of MLIPs, including their basic structure and formalism, (iii) the potentially transformative impact of universal MLIPs for both organic and inorganic systems, including an overview of the most recent advances, capabilities, downsides, and potential applications of this nascent class of MLIPs, (iv) a practical guide for estimating and understanding the execution speed of MLIPs, including guidance for users based on hardware availability, type of MLIP used, and prospective simulation size and time, (v) a manual for what MLIP a user should choose for a given application by considering hardware resources, speed requirements, energy and force accuracy requirements, as well as guidance for choosing pre-trained potentials or fitting a new potential from scratch, (vi) discussion around MLIP infrastructure, including sources of training data, pre-trained potentials, and hardware resources for training, (vii) summary of some key limitations of present MLIPs and current approaches to mitigate such limitations, including methods of including long-range interactions, handling magnetic systems, and treatment of excited states, and finally (viii) we finish with some more speculative thoughts on what the future holds for the development and application of MLIPs over the next 3-10+ years.

All-atom Diffusion Transformers: Unified generative modelling of molecules and materials

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems - such as molecules and materials - the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on QM9 and MP20 datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, exceeding state-of-the-art results from molecule and crystal-specific models. ADiT uses standard Transformers for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer

Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction

Machine learning interatomic potentials (MLIPs) have become increasingly effective at approximating quantum mechanical calculations at a fraction of the computational cost. However, lower errors on held out test sets do not always translate to improved results on downstream physical property prediction tasks. In this paper, we propose testing MLIPs on their practical ability to conserve energy during molecular dynamic simulations. If passed, improved correlations are found between test errors and their performance on physical property prediction tasks. We identify choices which may lead to models failing this test, and use these observations to improve upon highly-expressive models. The resulting model, eSEN, provides state-of-the-art results on a range of physical property prediction tasks, including materials stability prediction, thermal conductivity prediction, and phonon calculations.

CeViT: Copula-Enhanced Vision Transformer in multi-task learning and bi-group image covariates with an application to myopia screening

We aim to assist image-based myopia screening by resolving two longstanding problems, "how to integrate the information of ocular images of a pair of eyes" and "how to incorporate the inherent dependence among high-myopia status and axial length for both eyes." The classification-regression task is modeled as a novel 4-dimensional muti-response regression, where discrete responses are allowed, that relates to two dependent 3rd-order tensors (3D ultrawide-field fundus images). We present a Vision Transformer-based bi-channel architecture, named CeViT, where the common features of a pair of eyes are extracted via a shared Transformer encoder, and the interocular asymmetries are modeled through separated multilayer perceptron heads. Statistically, we model the conditional dependence among mixture of discrete-continuous responses given the image covariates by a so-called copula loss. We establish a new theoretical framework regarding fine-tuning on CeViT based on latent representations, allowing the black-box fine-tuning procedure interpretable and guaranteeing higher relative efficiency of fine-tuning weight estimation in the asymptotic setting. We apply CeViT to an annotated ultrawide-field fundus image dataset collected by Shanghai Eye \& ENT Hospital, demonstrating that CeViT enhances the baseline model in both accuracy of classifying high-myopia and prediction of AL on both eyes.

Open Materials 2024 (OMat24) Inorganic Materials Dataset and Models

The ability to discover new materials with desirable properties is critical for numerous applications from helping mitigate climate change to advances in next generation computing hardware. AI has the potential to accelerate materials discovery and design by more effectively exploring the chemical space compared to other computational methods or by trial-and-error. While substantial progress has been made on AI for materials data, benchmarks, and models, a barrier that has emerged is the lack of publicly available training data and open pre-trained models. To address this, we present a Meta FAIR release of the Open Materials 2024 (OMat24) large-scale open dataset and an accompanying set of pre-trained models. OMat24 contains over 110 million density functional theory (DFT) calculations focused on structural and compositional diversity. Our EquiformerV2 models achieve state-of-the-art performance on the Matbench Discovery leaderboard and are capable of predicting ground-state stability and formation energies to an F1 score above 0.9 and an accuracy of 20 meV/atom, respectively. We explore the impact of model size, auxiliary denoising objectives, and fine-tuning on performance across a range of datasets including OMat24, MPtraj, and Alexandria. The open release of the OMat24 dataset and models enables the research community to build upon our efforts and drive further advancements in AI-assisted materials science.

High Performance Im2win and Direct Convolutions using Three Tensor Layouts on SIMD Architectures

Convolution is the core component within deep neural networks and it is computationally intensive and time consuming. Tensor data layouts significantly impact convolution operations in terms of memory access and computational efficiency. Yet, there is still a lack of comprehensive performance characterization on data layouts on SIMD architectures concerning convolution methods. This paper proposes three novel data layouts for im2win convolution: NHWC, CHWN, and CHWN8, and introduces a set of general optimization techniques for both direct and im2win convolutions. We compare the optimized im2win convolution with the direct convolution and PyTorch's im2col-based convolution across the aforementioned layouts on SIMD machines. The experiments demonstrated that the im2win convolution with the new NHWC layout achieved up to 355% performance speedup over NCHW layout. Our optimizations also significantly improve the performance of both im2win and direct convolutions. Our optimized im2win and direct convolutions achieved up to 95% and 94% of machine's theoretical peak performance, respectively.

Structural Constraint Integration in Generative Model for Discovery of Quantum Material Candidates

Billions of organic molecules are known, but only a tiny fraction of the functional inorganic materials have been discovered, a particularly relevant problem to the community searching for new quantum materials. Recent advancements in machine-learning-based generative models, particularly diffusion models, show great promise for generating new, stable materials. However, integrating geometric patterns into materials generation remains a challenge. Here, we introduce Structural Constraint Integration in the GENerative model (SCIGEN). Our approach can modify any trained generative diffusion model by strategic masking of the denoised structure with a diffused constrained structure prior to each diffusion step to steer the generation toward constrained outputs. Furthermore, we mathematically prove that SCIGEN effectively performs conditional sampling from the original distribution, which is crucial for generating stable constrained materials. We generate eight million compounds using Archimedean lattices as prototype constraints, with over 10% surviving a multi-staged stability pre-screening. High-throughput density functional theory (DFT) on 26,000 survived compounds shows that over 50% passed structural optimization at the DFT level. Since the properties of quantum materials are closely related to geometric patterns, our results indicate that SCIGEN provides a general framework for generating quantum materials candidates.

A Recipe for Charge Density Prediction

In density functional theory, charge density is the core attribute of atomic systems from which all chemical properties can be derived. Machine learning methods are promising in significantly accelerating charge density prediction, yet existing approaches either lack accuracy or scalability. We propose a recipe that can achieve both. In particular, we identify three key ingredients: (1) representing the charge density with atomic and virtual orbitals (spherical fields centered at atom/virtual coordinates); (2) using expressive and learnable orbital basis sets (basis function for the spherical fields); and (3) using high-capacity equivariant neural network architecture. Our method achieves state-of-the-art accuracy while being more than an order of magnitude faster than existing methods. Furthermore, our method enables flexible efficiency-accuracy trade-offs by adjusting the model/basis sizes.

MatterGen: a generative model for inorganic materials design

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.

Learning to See Physical Properties with Active Sensing Motor Policies

Knowledge of terrain's physical properties inferred from color images can aid in making efficient robotic locomotion plans. However, unlike image classification, it is unintuitive for humans to label image patches with physical properties. Without labeled data, building a vision system that takes as input the observed terrain and predicts physical properties remains challenging. We present a method that overcomes this challenge by self-supervised labeling of images captured by robots during real-world traversal with physical property estimators trained in simulation. To ensure accurate labeling, we introduce Active Sensing Motor Policies (ASMP), which are trained to explore locomotion behaviors that increase the accuracy of estimating physical parameters. For instance, the quadruped robot learns to swipe its foot against the ground to estimate the friction coefficient accurately. We show that the visual system trained with a small amount of real-world traversal data accurately predicts physical parameters. The trained system is robust and works even with overhead images captured by a drone despite being trained on data collected by cameras attached to a quadruped robot walking on the ground.