MatExpert: Decomposing Materials Discovery by Mimicking Human Experts

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.

Deconstructing equivariant representations in molecular systems

Recent equivariant models have shown significant progress in not just chemical property prediction, but as surrogates for dynamical simulations of molecules and materials. Many of the top performing models in this category are built within the framework of tensor products, which preserves equivariance by restricting interactions and transformations to those that are allowed by symmetry selection rules. Despite being a core part of the modeling process, there has not yet been much attention into understanding what information persists in these equivariant representations, and their general behavior outside of benchmark metrics. In this work, we report on a set of experiments using a simple equivariant graph convolution model on the QM9 dataset, focusing on correlating quantitative performance with the resulting molecular graph embeddings. Our key finding is that, for a scalar prediction task, many of the irreducible representations are simply ignored during training -- specifically those pertaining to vector ($l=1$) and tensor quantities ($l=2$) -- an issue that does not necessarily make itself evident in the test metric. We empirically show that removing some unused orders of spherical harmonics improves model performance, correlating with improved latent space structure. We provide a number of recommendations for future experiments to try and improve efficiency and utilization of equivariant features based on these observations.

HoneyComb: A Flexible LLM-Based Agent System for Materials Science

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.

From Text to Insight: Large Language Models for Materials Science Data Extraction

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.

MatText: Do Language Models Need More than Text & Scale for Materials Modeling?

Effectively representing materials as text has the potential to leverage the vast advancements of large language models (LLMs) for discovering new materials. While LLMs have shown remarkable success in various domains, their application to materials science remains underexplored. A fundamental challenge is the lack of understanding of how to best utilize text-based representations for materials modeling. This challenge is further compounded by the absence of a comprehensive benchmark to rigorously evaluate the capabilities and limitations of these text representations in capturing the complexity of material systems. To address this gap, we propose MatText, a suite of benchmarking tools and datasets designed to systematically evaluate the performance of language models in modeling materials. MatText encompasses nine distinct text-based representations for material systems, including several novel representations. Each representation incorporates unique inductive biases that capture relevant information and integrate prior physical knowledge about materials. Additionally, MatText provides essential tools for training and benchmarking the performance of language models in the context of materials science. These tools include standardized dataset splits for each representation, probes for evaluating sensitivity to geometric factors, and tools for seamlessly converting crystal structures into text. Using MatText, we conduct an extensive analysis of the capabilities of language models in modeling materials. Our findings reveal that current language models consistently struggle to capture the geometric information crucial for materials modeling across all representations. Instead, these models tend to leverage local information, which is emphasized in some of our novel representations. Our analysis underscores MatText's ability to reveal shortcomings of text-based methods for materials design.

Are large language models superhuman chemists?

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. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Are LLMs Ready for Real-World Materials Discovery?

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.

A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems

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.

Towards equilibrium molecular conformation generation with GFlowNets

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.

Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance

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.