Santiago Miret

Alexandre Duval, Victor Schmidt, Alex Hernandez Garcia et al. · mila

Applications of machine learning techniques for materials modeling typically involve functions known to be equivariant or invariant to specific symmetries. While graph neural networks (GNNs) have proven successful in such tasks, they enforce symmetries via the model architecture, which often reduces their expressivity, scalability and comprehensibility. In this paper, we introduce (1) a flexible framework relying on stochastic frame-averaging (SFA) to make any model E(3)-equivariant or invariant through data transformations. (2) FAENet: a simple, fast and expressive GNN, optimized for SFA, that processes geometric information without any symmetrypreserving design constraints. We prove the validity of our method theoretically and empirically demonstrate its superior accuracy and computational scalability in materials modeling on the OC20 dataset (S2EF, IS2RE) as well as common molecular modeling tasks (QM9, QM7-X). A package implementation is available at https://faenet.readthedocs.io.

Kin Long Kelvin Lee, Carmelo Gonzales, Marcel Nassar et al. · deepmind

We propose MatSci ML, a novel benchmark for modeling MATerials SCIence using Machine Learning (MatSci ML) methods focused on solid-state materials with periodic crystal structures. Applying machine learning methods to solid-state materials is a nascent field with substantial fragmentation largely driven by the great variety of datasets used to develop machine learning models. This fragmentation makes comparing the performance and generalizability of different methods difficult, thereby hindering overall research progress in the field. Building on top of open-source datasets, including large-scale datasets like the OpenCatalyst, OQMD, NOMAD, the Carolina Materials Database, and Materials Project, the MatSci ML benchmark provides a diverse set of materials systems and properties data for model training and evaluation, including simulated energies, atomic forces, material bandgaps, as well as classification data for crystal symmetries via space groups. The diversity of properties in MatSci ML makes the implementation and evaluation of multi-task learning algorithms for solid-state materials possible, while the diversity of datasets facilitates the development of new, more generalized algorithms and methods across multiple datasets. In the multi-dataset learning setting, MatSci ML enables researchers to combine observations from multiple datasets to perform joint prediction of common properties, such as energy and forces. Using MatSci ML, we evaluate the performance of different graph neural networks and equivariant point cloud networks on several benchmark tasks spanning single task, multitask, and multi-data learning scenarios. Our open-source code is available at https://github.com/IntelLabs/matsciml.

Austin Cheng, Andy Cai, Santiago Miret et al.

We introduce Group SELFIES, a molecular string representation that leverages group tokens to represent functional groups or entire substructures while maintaining chemical robustness guarantees. Molecular string representations, such as SMILES and SELFIES, serve as the basis for molecular generation and optimization in chemical language models, deep generative models, and evolutionary methods. While SMILES and SELFIES leverage atomic representations, Group SELFIES builds on top of the chemical robustness guarantees of SELFIES by enabling group tokens, thereby creating additional flexibility to the representation. Moreover, the group tokens in Group SELFIES can take advantage of inductive biases of molecular fragments that capture meaningful chemical motifs. The advantages of capturing chemical motifs and flexibility are demonstrated in our experiments, which show that Group SELFIES improves distribution learning of common molecular datasets. Further experiments also show that random sampling of Group SELFIES strings improves the quality of generated molecules compared to regular SELFIES strings. Our open-source implementation of Group SELFIES is available online, which we hope will aid future research in molecular generation and optimization.

Moksh Jain, Sharath Chandra Raparthy, Alex Hernandez-Garcia et al. · mila

We study the problem of generating diverse candidates in the context of Multi-Objective Optimization. In many applications of machine learning such as drug discovery and material design, the goal is to generate candidates which simultaneously optimize a set of potentially conflicting objectives. Moreover, these objectives are often imperfect evaluations of some underlying property of interest, making it important to generate diverse candidates to have multiple options for expensive downstream evaluations. We propose Multi-Objective GFlowNets (MOGFNs), a novel method for generating diverse Pareto optimal solutions, based on GFlowNets. We introduce two variants of MOGFNs: MOGFN-PC, which models a family of independent sub-problems defined by a scalarization function, with reward-conditional GFlowNets, and MOGFN-AL, which solves a sequence of sub-problems defined by an acquisition function in an active learning loop. Our experiments on wide variety of synthetic and benchmark tasks demonstrate advantages of the proposed methods in terms of the Pareto performance and importantly, improved candidate diversity, which is the main contribution of this work.

Alexandre Duval, Victor Schmidt, Santiago Miret et al. · mila

Mitigating the climate crisis requires a rapid transition towards lower-carbon energy. Catalyst materials play a crucial role in the electrochemical reactions involved in numerous industrial processes key to this transition, such as renewable energy storage and electrofuel synthesis. To reduce the energy spent on such activities, we must quickly discover more efficient catalysts to drive electrochemical reactions. Machine learning (ML) holds the potential to efficiently model materials properties from large amounts of data, accelerating electrocatalyst design. The Open Catalyst Project OC20 dataset was constructed to that end. However, ML models trained on OC20 are still neither scalable nor accurate enough for practical applications. In this paper, we propose task-specific innovations applicable to most architectures, enhancing both computational efficiency and accuracy. This includes improvements in (1) the graph creation step, (2) atom representations, (3) the energy prediction head, and (4) the force prediction head. We describe these contributions, referred to as PhAST, and evaluate them thoroughly on multiple architectures. Overall, PhAST improves energy MAE by 4 to 42$\%$ while dividing compute time by 3 to 8$\times$ depending on the targeted task/model. PhAST also enables CPU training, leading to 40$\times$ speedups in highly parallelized settings. Python package: \url{https://phast.readthedocs.io}.

Santiago Miret, Kin Long Kelvin Lee, Carmelo Gonzales et al.

We present the Open MatSci ML Toolkit: a flexible, self-contained, and scalable Python-based framework to apply deep learning models and methods on scientific data with a specific focus on materials science and the OpenCatalyst Dataset. Our toolkit provides: 1. A scalable machine learning workflow for materials science leveraging PyTorch Lightning, which enables seamless scaling across different computation capabilities (laptop, server, cluster) and hardware platforms (CPU, GPU, XPU). 2. Deep Graph Library (DGL) support for rapid graph neural network prototyping and development. By publishing and sharing this toolkit with the research community via open-source release, we hope to: 1. Lower the entry barrier for new machine learning researchers and practitioners that want to get started with the OpenCatalyst dataset, which presently comprises the largest computational materials science dataset. 2. Enable the scientific community to apply advanced machine learning tools to high-impact scientific challenges, such as modeling of materials behavior for clean energy applications. We demonstrate the capabilities of our framework by enabling three new equivariant neural network models for multiple OpenCatalyst tasks and arrive at promising results for compute scaling and model performance.

Parishad BehnamGhader, Santiago Miret, Siva Reddy

Augmenting pretrained language models with retrievers has shown promise in effectively solving common NLP problems, such as language modeling and question answering. In this paper, we evaluate the strengths and weaknesses of popular retriever-augmented language models, namely kNN-LM, REALM, DPR + FiD, Contriever + ATLAS, and Contriever + Flan-T5, in reasoning over retrieved statements across different tasks. Our findings indicate that the simple similarity metric employed by retrievers is insufficient for retrieving all the necessary statements for reasoning. Additionally, the language models do not exhibit strong reasoning even when provided with only the required statements. Furthermore, when combined with imperfect retrievers, the performance of the language models becomes even worse, e.g., Flan-T5's performance drops by 28.6% when retrieving 5 statements using Contriever. While larger language models improve performance, there is still a substantial room for enhancement. Our further analysis indicates that multihop retrieve-and-read is promising for large language models like GPT-3.5, but does not generalize to other language models like Flan-T5-xxl.

Alexandra Volokhova, Michał Koziarski, Alex Hernández-García et al.

Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this paper we propose to use GFlowNet for sampling conformations of small molecules from the Boltzmann distribution, as determined by the molecule's energy. The proposed approach can be used in combination with energy estimation methods of different fidelity and discovers a diverse set of low-energy conformations for highly flexible drug-like molecules. We demonstrate that GFlowNet can reproduce molecular potential energy surfaces by sampling proportionally to the Boltzmann distribution.

Vaibhav Bihani, Utkarsh Pratiush, Sajid Mannan et al.

Equivariant graph neural networks force fields (EGraFFs) have shown great promise in modelling complex interactions in atomic systems by exploiting the graphs' inherent symmetries. Recent works have led to a surge in the development of novel architectures that incorporate equivariance-based inductive biases alongside architectural innovations like graph transformers and message passing to model atomic interactions. However, thorough evaluations of these deploying EGraFFs for the downstream task of real-world atomistic simulations, is lacking. To this end, here we perform a systematic benchmarking of 6 EGraFF algorithms (NequIP, Allegro, BOTNet, MACE, Equiformer, TorchMDNet), with the aim of understanding their capabilities and limitations for realistic atomistic simulations. In addition to our thorough evaluation and analysis on eight existing datasets based on the benchmarking literature, we release two new benchmark datasets, propose four new metrics, and three challenging tasks. The new datasets and tasks evaluate the performance of EGraFF to out-of-distribution data, in terms of different crystal structures, temperatures, and new molecules. Interestingly, evaluation of the EGraFF models based on dynamic simulations reveals that having a lower error on energy or force does not guarantee stable or reliable simulation or faithful replication of the atomic structures. Moreover, we find that no model clearly outperforms other models on all datasets and tasks. Importantly, we show that the performance of all the models on out-of-distribution datasets is unreliable, pointing to the need for the development of a foundation model for force fields that can be used in real-world simulations. In summary, this work establishes a rigorous framework for evaluating machine learning force fields in the context of atomic simulations and points to open research challenges within this domain.

Minghao Xu, Xinyu Yuan, Santiago Miret et al.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Yu Song, Santiago Miret, Huan Zhang et al.

We propose an instruction-based process for trustworthy data curation in materials science (MatSci-Instruct), which we then apply to finetune a LLaMa-based language model targeted for materials science (HoneyBee). MatSci-Instruct helps alleviate the scarcity of relevant, high-quality materials science textual data available in the open literature, and HoneyBee is the first billion-parameter language model specialized to materials science. In MatSci-Instruct we improve the trustworthiness of generated data by prompting multiple commercially available large language models for generation with an Instructor module (e.g. Chat-GPT) and verification from an independent Verifier module (e.g. Claude). Using MatSci-Instruct, we construct a dataset of multiple tasks and measure the quality of our dataset along multiple dimensions, including accuracy against known facts, relevance to materials science, as well as completeness and reasonableness of the data. Moreover, we iteratively generate more targeted instructions and instruction-data in a finetuning-evaluation-feedback loop leading to progressively better performance for our finetuned HoneyBee models. Our evaluation on the MatSci-NLP benchmark shows HoneyBee's outperformance of existing language models on materials science tasks and iterative improvement in successive stages of instruction-data refinement. We study the quality of HoneyBee's language modeling through automatic evaluation and analyze case studies to further understand the model's capabilities and limitations. Our code and relevant datasets are publicly available at \url{https://github.com/BangLab-UdeM-Mila/NLP4MatSci-HoneyBee}.

Mara Schilling-Wilhelmi, Martiño Ríos-García, Sherjeel Shabih et al.

The vast majority of materials science knowledge exists in unstructured natural language, yet structured data is crucial for innovative and systematic materials design. Traditionally, the field has relied on manual curation and partial automation for data extraction for specific use cases. The advent of large language models (LLMs) represents a significant shift, potentially enabling efficient extraction of structured, actionable data from unstructured text by non-experts. While applying LLMs to materials science data extraction presents unique challenges, domain knowledge offers opportunities to guide and validate LLM outputs. This review provides a comprehensive overview of LLM-based structured data extraction in materials science, synthesizing current knowledge and outlining future directions. We address the lack of standardized guidelines and present frameworks for leveraging the synergy between LLMs and materials science expertise. This work serves as a foundational resource for researchers aiming to harness LLMs for data-driven materials research. The insights presented here could significantly enhance how researchers across disciplines access and utilize scientific information, potentially accelerating the development of novel materials for critical societal needs.

Alvaro Carbonero, Alexandre Duval, Victor Schmidt et al.

The use of machine learning for material property prediction and discovery has traditionally centered on graph neural networks that incorporate the geometric configuration of all atoms. However, in practice not all this information may be readily available, e.g.~when evaluating the potentially unknown binding of adsorbates to catalyst. In this paper, we investigate whether it is possible to predict a system's relaxed energy in the OC20 dataset while ignoring the relative position of the adsorbate with respect to the electro-catalyst. We consider SchNet, DimeNet++ and FAENet as base architectures and measure the impact of four modifications on model performance: removing edges in the input graph, pooling independent representations, not sharing the backbone weights and using an attention mechanism to propagate non-geometric relative information. We find that while removing binding site information impairs accuracy as expected, modified models are able to predict relaxed energies with remarkably decent MAE. Our work suggests future research directions in accelerated materials discovery where information on reactant configurations can be reduced or altogether omitted.

Daniel Levy, Sékou-Oumar Kaba, Carmelo Gonzales et al.

We present a natural extension to E(n)-equivariant graph neural networks that uses multiple equivariant vectors per node. We formulate the extension and show that it improves performance across different physical systems benchmark tasks, with minimal differences in runtime or number of parameters. The proposed multichannel EGNN outperforms the standard singlechannel EGNN on N-body charged particle dynamics, molecular property predictions, and predicting the trajectories of solar system bodies. Given the additional benefits and minimal additional cost of multi-channel EGNN, we suggest that this extension may be of practical use to researchers working in machine learning for the physical sciences

Huan Zhang, Yu Song, Ziyu Hou et al.

The emergence of specialized large language models (LLMs) has shown promise in addressing complex tasks for materials science. Many LLMs, however, often struggle with distinct complexities of material science tasks, such as materials science computational tasks, and often rely heavily on outdated implicit knowledge, leading to inaccuracies and hallucinations. To address these challenges, we introduce HoneyComb, the first LLM-based agent system specifically designed for materials science. HoneyComb leverages a novel, high-quality materials science knowledge base (MatSciKB) and a sophisticated tool hub (ToolHub) to enhance its reasoning and computational capabilities tailored to materials science. MatSciKB is a curated, structured knowledge collection based on reliable literature, while ToolHub employs an Inductive Tool Construction method to generate, decompose, and refine API tools for materials science. Additionally, HoneyComb leverages a retriever module that adaptively selects the appropriate knowledge source or tools for specific tasks, thereby ensuring accuracy and relevance. Our results demonstrate that HoneyComb significantly outperforms baseline models across various tasks in materials science, effectively bridging the gap between current LLM capabilities and the specialized needs of this domain. Furthermore, our adaptable framework can be easily extended to other scientific domains, highlighting its potential for broad applicability in advancing scientific research and applications.

Emily Jin, Andrei Cristian Nica, Mikhail Galkin et al.

Accurately predicting experimentally-realizable 3D molecular crystal structures from their 2D chemical graphs is a long-standing open challenge in computational chemistry called crystal structure prediction (CSP). Efficiently solving this problem has implications ranging from pharmaceuticals to organic semiconductors, as crystal packing directly governs the physical and chemical properties of organic solids. In this paper, we introduce OXtal, a large-scale 100M parameter all-atom diffusion model that directly learns the conditional joint distribution over intramolecular conformations and periodic packing. To efficiently scale OXtal, we abandon explicit equivariant architectures imposing inductive bias arising from crystal symmetries in favor of data augmentation strategies. We further propose a novel crystallization-inspired lattice-free training scheme, Stoichiometric Stochastic Shell Sampling ($S^4$), that efficiently captures long-range interactions while sidestepping explicit lattice parametrization -- thus enabling more scalable architectural choices at all-atom resolution. By leveraging a large dataset of 600K experimentally validated crystal structures (including rigid and flexible molecules, co-crystals, and solvates), OXtal achieves orders-of-magnitude improvements over prior ab initio machine learning CSP methods, while remaining orders of magnitude cheaper than traditional quantum-chemical approaches. Specifically, OXtal recovers experimental structures with conformer $\text{RMSD}_1<0.5$ Å and attains over 80\% packing similarity rate, demonstrating its ability to model both thermodynamic and kinetic regularities of molecular crystallization.

Ali Jaberi, Yonatan Kurniawan, Robert Black et al.

This paper introduces AutoREC, an open-source Python package for developing reinforcement learning (RL) agents to automatically generate equivalent circuit models (ECMs) from electrochemical impedance spectroscopy (EIS) data. While ECMs are a standard framework for interpreting EIS data, traditional identification is typically based on manual trial-and-error, which requires domain experts and limits scalability, particularly in autonomous experimental pipelines such as self-driving laboratories. AutoREC addresses this challenge by formulating ECM construction as a sequential decision-making problem within a Markov Decision Process framework. It implements a Double Deep Q-Network with prioritized experience replay, along with a dedicated dead-loop mitigation strategy, to efficiently explore a complex action space for circuit generation. To demonstrate the capabilities of the platform, we trained an RL agent using AutoREC and evaluated its strengths and limitations across diverse datasets, while also discussing possible strategies to mitigate these limitations in future agent designs. The trained agent achieved a success rate exceeding $99.6\%$ on synthetic datasets and demonstrated strong generalization to unseen experimental EIS data from batteries, corrosion, oxygen evolution reaction, and CO$_2$ reduction systems. These results position AutoREC as a promising platform for adaptive and data-driven ECM generation, with potential for integration into automated electrochemical workflows.

Raj Ghugare, Santiago Miret, Adriana Hugessen et al.

Reinforcement learning (RL) over text representations can be effective for finding high-value policies that can search over graphs. However, RL requires careful structuring of the search space and algorithm design to be effective in this challenge. Through extensive experiments, we explore how different design choices for text grammar and algorithmic choices for training can affect an RL policy's ability to generate molecules with desired properties. We arrive at a new RL-based molecular design algorithm (ChemRLformer) and perform a thorough analysis using 25 molecule design tasks, including computationally complex protein docking simulations. From this analysis, we discover unique insights in this problem space and show that ChemRLformer achieves state-of-the-art performance while being more straightforward than prior work by demystifying which design choices are actually helpful for text-based molecule design.

Austin Cheng, Alston Lo, Santiago Miret et al.

Structure determination is necessary to identify unknown organic molecules, such as those in natural products, forensic samples, the interstellar medium, and laboratory syntheses. Rotational spectroscopy enables structure determination by providing accurate 3D information about small organic molecules via their moments of inertia. Using these moments, Kraitchman analysis determines isotopic substitution coordinates, which are the unsigned $|x|,|y|,|z|$ coordinates of all atoms with natural isotopic abundance, including carbon, nitrogen, and oxygen. While unsigned substitution coordinates can verify guesses of structures, the missing $+/-$ signs make it challenging to determine the actual structure from the substitution coordinates alone. To tackle this inverse problem, we develop KREED (Kraitchman REflection-Equivariant Diffusion), a generative diffusion model that infers a molecule's complete 3D structure from its molecular formula, moments of inertia, and unsigned substitution coordinates of heavy atoms. KREED's top-1 predictions identify the correct 3D structure with >98% accuracy on the QM9 and GEOM datasets when provided with substitution coordinates of all heavy atoms with natural isotopic abundance. When substitution coordinates are restricted to only a subset of carbons, accuracy is retained at 91% on QM9 and 32% on GEOM. On a test set of experimentally measured substitution coordinates gathered from the literature, KREED predicts the correct all-atom 3D structure in 25 of 33 cases, demonstrating experimental applicability for context-free 3D structure determination with rotational spectroscopy.

Pablo Martínez Crespo, Stefano Ribes, Martin Rahm et al.

Atomic properties such as partial charges or multipoles encode chemically meaningful information that can inform downstream molecular property prediction, but their evaluation as machine learning targets has been complicated by the absence of a principled out-of-distribution evaluation protocol at the atomic level. In this work, we propose a held-out evaluation protocol that clusters atomic environments by SOAP descriptors and computes metrics accounting only for cluster labels unseen during training. Following this procedure, we use 5$\times$5 cross-validation and Tukey's HSD to run a statistically rigorous comparison of E(3)-equivariant against non-equivariant, rotationally augmented models for predicting electron populations and multipoles of H, C, N, and O atoms. Building on our results, we introduce the Quantum Topological Neural Network (QT-Net), a rotationally augmented, non-equivariant graph neural network. We show that QT-Net can be used to infer properties of atoms in molecules from QM9 outside our training set, and that these inferred properties can yield improvement when used as input features for downstream molecular property prediction. To further validate the framework, molecular dipole moments computed from QT-Net's per-atom outputs recover the ground-truth values reported in QM9. We release all code and data, including a JAX implementation of QT-Net, to support the broader use of learned QTA properties as inductive biases for atomic-scale molecular machine learning.

Prashant Govindarajan, Mathieu Reymond, Antoine Clavaud et al.

In silico design and optimization of new materials primarily relies on high-accuracy atomic simulators that perform density functional theory (DFT) calculations. While recent works showcase the strong potential of machine learning to accelerate the material design process, they mostly consist of generative approaches that do not use direct DFT signals as feedback to improve training and generation mainly due to DFT's high computational cost. To aid the adoption of direct DFT signals in the materials design loop through online reinforcement learning (RL), we propose CrystalGym, an open-source RL environment for crystalline material discovery. Using CrystalGym, we benchmark common value- and policy-based reinforcement learning algorithms for designing various crystals conditioned on target properties. Concretely, we optimize for challenging properties like the band gap, bulk modulus, and density, which are directly calculated from DFT in the environment. While none of the algorithms we benchmark solve all CrystalGym tasks, our extensive experiments and ablations show different sample efficiencies and ease of convergence to optimality for different algorithms and environment settings. Additionally, we include a case study on the scope of fine-tuning large language models with reinforcement learning for improving DFT-based rewards. Our goal is for CrystalGym to serve as a test bed for reinforcement learning researchers and material scientists to address these real-world design problems with practical applications. We therefore introduce a novel class of challenges for reinforcement learning methods dealing with time-consuming reward signals, paving the way for future interdisciplinary research for machine learning motivated by real-world applications.

Yu Song, Santiago Miret, Bang Liu

We present MatSci-NLP, a natural language benchmark for evaluating the performance of natural language processing (NLP) models on materials science text. We construct the benchmark from publicly available materials science text data to encompass seven different NLP tasks, including conventional NLP tasks like named entity recognition and relation classification, as well as NLP tasks specific to materials science, such as synthesis action retrieval which relates to creating synthesis procedures for materials. We study various BERT-based models pretrained on different scientific text corpora on MatSci-NLP to understand the impact of pretraining strategies on understanding materials science text. Given the scarcity of high-quality annotated data in the materials science domain, we perform our fine-tuning experiments with limited training data to encourage the generalize across MatSci-NLP tasks. Our experiments in this low-resource training setting show that language models pretrained on scientific text outperform BERT trained on general text. MatBERT, a model pretrained specifically on materials science journals, generally performs best for most tasks. Moreover, we propose a unified text-to-schema for multitask learning on \benchmark and compare its performance with traditional fine-tuning methods. In our analysis of different training methods, we find that our proposed text-to-schema methods inspired by question-answering consistently outperform single and multitask NLP fine-tuning methods. The code and datasets are publicly available at \url{https://github.com/BangLab-UdeM-Mila/NLP4MatSci-ACL23}.

Alexandre Duval, Simon V. Mathis, Chaitanya K. Joshi et al. · cambridge

Recent advances in computational modelling of atomic systems, spanning molecules, proteins, and materials, represent them as geometric graphs with atoms embedded as nodes in 3D Euclidean space. In these graphs, the geometric attributes transform according to the inherent physical symmetries of 3D atomic systems, including rotations and translations in Euclidean space, as well as node permutations. In recent years, Geometric Graph Neural Networks have emerged as the preferred machine learning architecture powering applications ranging from protein structure prediction to molecular simulations and material generation. Their specificity lies in the inductive biases they leverage - such as physical symmetries and chemical properties - to learn informative representations of these geometric graphs. In this opinionated paper, we provide a comprehensive and self-contained overview of the field of Geometric GNNs for 3D atomic systems. We cover fundamental background material and introduce a pedagogical taxonomy of Geometric GNN architectures: (1) invariant networks, (2) equivariant networks in Cartesian basis, (3) equivariant networks in spherical basis, and (4) unconstrained networks. Additionally, we outline key datasets and application areas and suggest future research directions. The objective of this work is to present a structured perspective on the field, making it accessible to newcomers and aiding practitioners in gaining an intuition for its mathematical abstractions.

Santiago Miret, N M Anoop Krishnan

Large Language Models (LLMs) create exciting possibilities for powerful language processing tools to accelerate research in materials science. While LLMs have great potential to accelerate materials understanding and discovery, they currently fall short in being practical materials science tools. In this position paper, we show relevant failure cases of LLMs in materials science that reveal current limitations of LLMs related to comprehending and reasoning over complex, interconnected materials science knowledge. Given those shortcomings, we outline a framework for developing Materials Science LLMs (MatSci-LLMs) that are grounded in materials science knowledge and hypothesis generation followed by hypothesis testing. The path to attaining performant MatSci-LLMs rests in large part on building high-quality, multi-modal datasets sourced from scientific literature where various information extraction challenges persist. As such, we describe key materials science information extraction challenges which need to be overcome in order to build large-scale, multi-modal datasets that capture valuable materials science knowledge. Finally, we outline a roadmap for applying future MatSci-LLMs for real-world materials discovery via: 1. Automated Knowledge Base Generation; 2. Automated In-Silico Material Design; and 3. MatSci-LLM Integrated Self-Driving Materials Laboratories.

Daniel Levy, Siba Smarak Panigrahi, Sékou-Oumar Kaba et al. · deepmind

Generating novel crystalline materials has the potential to lead to advancements in fields such as electronics, energy storage, and catalysis. The defining characteristic of crystals is their symmetry, which plays a central role in determining their physical properties. However, existing crystal generation methods either fail to generate materials that display the symmetries of real-world crystals, or simply replicate the symmetry information from examples in a database. To address this limitation, we propose SymmCD, a novel diffusion-based generative model that explicitly incorporates crystallographic symmetry into the generative process. We decompose crystals into two components and learn their joint distribution through diffusion: 1) the asymmetric unit, the smallest subset of the crystal which can generate the whole crystal through symmetry transformations, and; 2) the symmetry transformations needed to be applied to each atom in the asymmetric unit. We also use a novel and interpretable representation for these transformations, enabling generalization across different crystallographic symmetry groups. We showcase the competitive performance of SymmCD on a subset of the Materials Project, obtaining diverse and valid crystals with realistic symmetries and predicted properties.

Qianggang Ding, Santiago Miret, Bang Liu

Material discovery is a critical research area with profound implications for various industries. In this work, we introduce MatExpert, a novel framework that leverages Large Language Models (LLMs) and contrastive learning to accelerate the discovery and design of new solid-state materials. Inspired by the workflow of human materials design experts, our approach integrates three key stages: retrieval, transition, and generation. First, in the retrieval stage, MatExpert identifies an existing material that closely matches the desired criteria. Second, in the transition stage, MatExpert outlines the necessary modifications to transform this material formulation to meet specific requirements outlined by the initial user query. Third, in the generation state, MatExpert performs detailed computations and structural generation to create new materials based on the provided information. Our experimental results demonstrate that MatExpert outperforms state-of-the-art methods in material generation tasks, achieving superior performance across various metrics including validity, distribution, and stability. As such, MatExpert represents a meaningful advancement in computational material discovery using langauge-based generative models.

Vaibhav Mishra, Somaditya Singh, Dhruv Ahlawat et al.

Materials discovery and development are critical for addressing global challenges. Yet, the exponential growth in materials science literature comprising vast amounts of textual data has created significant bottlenecks in knowledge extraction, synthesis, and scientific reasoning. Large Language Models (LLMs) offer unprecedented opportunities to accelerate materials research through automated analysis and prediction. Still, their effective deployment requires domain-specific adaptation for understanding and solving domain-relevant tasks. Here, we present LLaMat, a family of foundational models for materials science developed through continued pretraining of LLaMA models on an extensive corpus of materials literature and crystallographic data. Through systematic evaluation, we demonstrate that LLaMat excels in materials-specific NLP and structured information extraction while maintaining general linguistic capabilities. The specialized LLaMat-CIF variant demonstrates unprecedented capabilities in crystal structure generation, predicting stable crystals with high coverage across the periodic table. Intriguingly, despite LLaMA-3's superior performance in comparison to LLaMA-2, we observe that LLaMat-2 demonstrates unexpectedly enhanced domain-specific performance across diverse materials science tasks, including structured information extraction from text and tables, more particularly in crystal structure generation, a potential adaptation rigidity in overtrained LLMs. Altogether, the present work demonstrates the effectiveness of domain adaptation towards developing practically deployable LLM copilots for materials research. Beyond materials science, our findings reveal important considerations for domain adaptation of LLMs, such as model selection, training methodology, and domain-specific performance, which may influence the development of specialized scientific AI systems.

Adrian Mirza, Nawaf Alampara, Sreekanth Kunchapu et al.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. However, we possess only a limited systematic understanding of the chemical capabilities of LLMs, which would be required to improve models and mitigate potential harm. Here, we introduce "ChemBench," an automated framework for evaluating the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of chemists. We curated more than 2,700 question-answer pairs, evaluated leading open- and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. However, the models struggle with some basic tasks and provide overconfident predictions. These findings reveal LLMs' impressive chemical capabilities while emphasizing the need for further research to improve their safety and usefulness. They also suggest adapting chemistry education and show the value of benchmarking frameworks for evaluating LLMs in specific domains.

Austin Cheng, Alston Lo, Kin Long Kelvin Lee et al.

Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of predicting a molecule's all-atom 3D structure given only its molecular formula and moments of inertia, motivated by the ability of rotational spectroscopy to measure these moments. While existing generative models can conditionally sample 3D structures with approximately correct moments, this soft conditioning fails to leverage the many digits of precision afforded by experimental rotational spectroscopy. To address this, we first show that the space of $n$-atom point clouds with a fixed set of moments of inertia is embedded in the Stiefel manifold $\mathrm{St}(n, 4)$. We then propose Stiefel Flow Matching as a generative model for elucidating 3D structure under exact moment constraints. Additionally, we learn simpler and shorter flows by finding approximate solutions for equivariant optimal transport on the Stiefel manifold. Empirically, enforcing exact moment constraints allows Stiefel Flow Matching to achieve higher success rates and faster sampling than Euclidean diffusion models, even on high-dimensional manifolds corresponding to large molecules in the GEOM dataset.

Santiago Miret, Kin Long Kelvin Lee, Carmelo Gonzales et al.

Universal Machine Learning Interactomic Potentials (MLIPs) enable accelerated simulations for materials discovery. However, current research efforts fail to impactfully utilize MLIPs due to: 1. Overreliance on Density Functional Theory (DFT) for MLIP training data creation; 2. MLIPs' inability to reliably and accurately perform large-scale molecular dynamics (MD) simulations for diverse materials; 3. Limited understanding of MLIPs' underlying capabilities. To address these shortcomings, we aargue that MLIP research efforts should prioritize: 1. Employing more accurate simulation methods for large-scale MLIP training data creation (e.g. Coupled Cluster Theory) that cover a wide range of materials design spaces; 2. Creating MLIP metrology tools that leverage large-scale benchmarking, visualization, and interpretability analyses to provide a deeper understanding of MLIPs' inner workings; 3. Developing computationally efficient MLIPs to execute MD simulations that accurately model a broad set of materials properties. Together, these interdisciplinary research directions can help further the real-world application of MLIPs to accurately model complex materials at device scale.

Sajid Mannan, Vaibhav Bihani, Carmelo Gonzales et al.

Universal machine learning force fields (UMLFFs) promise to revolutionize materials science by enabling rapid atomistic simulations across the periodic table. However, their evaluation has been limited to computational benchmarks that may not reflect real-world performance. Here, we present UniFFBench, a comprehensive framework for evaluating UMLFFs against experimental measurements of ~1,500 carefully curated mineral structures spanning diverse chemical environments, bonding types, structural complexity, and elastic properties. Our systematic evaluation of six state-of-the-art UMLFFs reveals a substantial reality gap: models achieving impressive performance on computational benchmarks often fail when confronted with experimental complexity. Even the best-performing models exhibit higher density prediction error than the threshold required for practical applications. Most strikingly, we observe disconnects between simulation stability and mechanical property accuracy, with prediction errors correlating with training data representation rather than the modeling method. These findings demonstrate that while current computational benchmarks provide valuable controlled comparisons, they may overestimate model reliability when extrapolated to experimentally complex chemical spaces. Altogether, UniFFBench establishes essential experimental validation standards and reveals systematic limitations that must be addressed to achieve truly universal force field capabilities.

Michael Przystupa, Hongyao Tang, Martin Jagersand et al.

Morphology-aware policy learning is a means of enhancing policy sample efficiency by aggregating data from multiple agents. These types of policies have previously been shown to help generalize over dynamic, kinematic, and limb configuration variations between agent morphologies. Unfortunately, these policies still have sub-optimal zero-shot performance compared to end-to-end finetuning on morphologies at deployment. This limitation has ramifications in practical applications such as robotics because further data collection to perform end-to-end finetuning can be computationally expensive. In this work, we investigate combining morphology-aware pretraining with parameter efficient finetuning (PEFT) techniques to help reduce the learnable parameters necessary to specialize a morphology-aware policy to a target embodiment. We compare directly tuning sub-sets of model weights, input learnable adapters, and prefix tuning techniques for online finetuning. Our analysis reveals that PEFT techniques in conjunction with policy pre-training generally help reduce the number of samples to necessary to improve a policy compared to training models end-to-end from scratch. We further find that tuning as few as less than 1% of total parameters will improve policy performance compared the zero-shot performance of the base pretrained a policy.

Rafael Rosales, Santiago Miret

Effectively leveraging diversity has been shown to improve performance for various machine learning models, including large language models (LLMs). However, determining the most effective way of using diversity remains a challenge. In this work, we compare two diversity approaches for answering binary questions using LLMs: model diversity, which relies on multiple models answering the same question, and question interpretation diversity, which relies on using the same model to answer the same question framed in different ways. For both cases, we apply majority voting as the ensemble consensus heuristic to determine the final answer. Our experiments on boolq, strategyqa, and pubmedqa show that question interpretation diversity consistently leads to better ensemble accuracy compared to model diversity. Furthermore, our analysis of GPT and LLaMa shows that model diversity typically produces results between the best and the worst ensemble members without clear improvement.

Nawaf Alampara, Santiago Miret, Kevin Maik Jablonka

Predicting properties from coordinate-category data -- sets of vectors paired with categorical information -- is fundamental to computational science. In materials science, this challenge manifests as predicting properties like formation energies or elastic moduli from crystal structures comprising atomic positions (vectors) and element types (categorical information). While large language models (LLMs) have increasingly been applied to such tasks, with researchers encoding structural data as text, optimal strategies for achieving reliable predictions remain elusive. Here, we report fundamental limitations in LLM's ability to learn from coordinate information in coordinate-category data. Through systematic experiments using synthetic datasets with tunable coordinate and category contributions, combined with a comprehensive benchmarking framework (MatText) spanning multiple representations and model scales, we find that LLMs consistently fail to capture coordinate information while excelling at category patterns. This geometric blindness persists regardless of model size (up to 70B parameters), dataset scale (up to 2M structures), or text representation strategy. Our findings suggest immediate practical implications: for materials property prediction tasks dominated by structural effects, specialized geometric architectures consistently outperform LLMs by significant margins, as evidenced by a clear "GNN-LM wall" in performance benchmarks. Based on our analysis, we provide concrete guidelines for architecture selection in scientific machine learning, while highlighting the critical importance of understanding model inductive biases when tackling scientific prediction problems.

Santiago Miret, Vui Seng Chua, Mattias Marder et al.

Mixed-precision quantization is a powerful tool to enable memory and compute savings of neural network workloads by deploying different sets of bit-width precisions on separate compute operations. In this work, we present a flexible and scalable framework for automated mixed-precision quantization that concurrently optimizes task performance, memory compression, and compute savings through multi-objective evolutionary computing. Our framework centers on Neuroevolution-Enhanced Multi-Objective Optimization (NEMO), a novel search method, which combines established search methods with the representational power of neural networks. Within NEMO, the population is divided into structurally distinct sub-populations, or species, which jointly create the Pareto frontier of solutions for the multi-objective problem. At each generation, species perform separate mutation and crossover operations, and are re-sized in proportion to the goodness of their contribution to the Pareto frontier. In our experiments, we define a graph-based representation to describe the underlying workload, enabling us to deploy graph neural networks trained by NEMO via neuroevolution, to find Pareto optimal configurations for MobileNet-V2, ResNet50 and ResNeXt-101-32x8d. Compared to the state-of-the-art, we achieve competitive results on memory compression and superior results for compute compression. Further analysis reveals that the graph representation and the species-based approach employed by NEMO are critical to finding optimal solutions.

Hassam Sheikh, Shauharda Khadka, Santiago Miret et al.

Learning effective policies for sparse objectives is a key challenge in Deep Reinforcement Learning (RL). A common approach is to design task-related dense rewards to improve task learnability. While such rewards are easily interpreted, they rely on heuristics and domain expertise. Alternate approaches that train neural networks to discover dense surrogate rewards avoid heuristics, but are high-dimensional, black-box solutions offering little interpretability. In this paper, we present a method that discovers dense rewards in the form of low-dimensional symbolic trees - thus making them more tractable for analysis. The trees use simple functional operators to map an agent's observations to a scalar reward, which then supervises the policy gradient learning of a neural network policy. We test our method on continuous action spaces in Mujoco and discrete action spaces in Atari and Pygame environments. We show that the discovered dense rewards are an effective signal for an RL policy to solve the benchmark tasks. Notably, we significantly outperform a widely used, contemporary neural-network based reward-discovery algorithm in all environments considered.

Santiago Miret, Somdeb Majumdar, Carroll Wainwright

As reinforcement learning agents become increasingly integrated into complex, real-world environments, designing for safety becomes a critical consideration. We specifically focus on researching scenarios where agents can cause undesired side effects while executing a policy on a primary task. Since one can define multiple tasks for a given environment dynamics, there are two important challenges. First, we need to abstract the concept of safety that applies broadly to that environment independent of the specific task being executed. Second, we need a mechanism for the abstracted notion of safety to modulate the actions of agents executing different policies to minimize their side-effects. In this work, we propose Safety Aware Reinforcement Learning (SARL) - a framework where a virtual safe agent modulates the actions of a main reward-based agent to minimize side effects. The safe agent learns a task-independent notion of safety for a given environment. The main agent is then trained with a regularization loss given by the distance between the native action probabilities of the two agents. Since the safe agent effectively abstracts a task-independent notion of safety via its action probabilities, it can be ported to modulate multiple policies solving different tasks within the given environment without further training. We contrast this with solutions that rely on task-specific regularization metrics and test our framework on the SafeLife Suite, based on Conway's Game of Life, comprising a number of complex tasks in dynamic environments. We show that our solution is able to match the performance of solutions that rely on task-specific side-effect penalties on both the primary and safety objectives while additionally providing the benefit of generalizability and portability.

Shauharda Khadka, Estelle Aflalo, Mattias Marder et al.

For deep neural network accelerators, memory movement is both energetically expensive and can bound computation. Therefore, optimal mapping of tensors to memory hierarchies is critical to performance. The growing complexity of neural networks calls for automated memory mapping instead of manual heuristic approaches; yet the search space of neural network computational graphs have previously been prohibitively large. We introduce Evolutionary Graph Reinforcement Learning (EGRL), a method designed for large search spaces, that combines graph neural networks, reinforcement learning, and evolutionary search. A set of fast, stateless policies guide the evolutionary search to improve its sample-efficiency. We train and validate our approach directly on the Intel NNP-I chip for inference. EGRL outperforms policy-gradient, evolutionary search and dynamic programming baselines on BERT, ResNet-101 and ResNet-50. We additionally achieve 28-78\% speed-up compared to the native NNP-I compiler on all three workloads.

Shauharda Khadka, Somdeb Majumdar, Santiago Miret et al.

Many cooperative multiagent reinforcement learning environments provide agents with a sparse team-based reward, as well as a dense agent-specific reward that incentivizes learning basic skills. Training policies solely on the team-based reward is often difficult due to its sparsity. Furthermore, relying solely on the agent-specific reward is sub-optimal because it usually does not capture the team coordination objective. A common approach is to use reward shaping to construct a proxy reward by combining the individual rewards. However, this requires manual tuning for each environment. We introduce Multiagent Evolutionary Reinforcement Learning (MERL), a split-level training platform that handles the two objectives separately through two optimization processes. An evolutionary algorithm maximizes the sparse team-based objective through neuroevolution on a population of teams. Concurrently, a gradient-based optimizer trains policies to only maximize the dense agent-specific rewards. The gradient-based policies are periodically added to the evolutionary population as a way of information transfer between the two optimization processes. This enables the evolutionary algorithm to use skills learned via the agent-specific rewards toward optimizing the global objective. Results demonstrate that MERL significantly outperforms state-of-the-art methods, such as MADDPG, on a number of difficult coordination benchmarks.

Shauharda Khadka, Somdeb Majumdar, Tarek Nassar et al.

Deep reinforcement learning algorithms have been successfully applied to a range of challenging control tasks. However, these methods typically struggle with achieving effective exploration and are extremely sensitive to the choice of hyperparameters. One reason is that most approaches use a noisy version of their operating policy to explore - thereby limiting the range of exploration. In this paper, we introduce Collaborative Evolutionary Reinforcement Learning (CERL), a scalable framework that comprises a portfolio of policies that simultaneously explore and exploit diverse regions of the solution space. A collection of learners - typically proven algorithms like TD3 - optimize over varying time-horizons leading to this diverse portfolio. All learners contribute to and use a shared replay buffer to achieve greater sample efficiency. Computational resources are dynamically distributed to favor the best learners as a form of online algorithm selection. Neuroevolution binds this entire process to generate a single emergent learner that exceeds the capabilities of any individual learner. Experiments in a range of continuous control benchmarks demonstrate that the emergent learner significantly outperforms its composite learners while remaining overall more sample-efficient - notably solving the Mujoco Humanoid benchmark where all of its composite learners (TD3) fail entirely in isolation.