AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use

Machine learning-based interatomic potentials and force fields depend critically on accurate atomic structures, yet such data are scarce due to the limited availability of experimentally resolved crystals. Although atomic-resolution electron microscopy offers a potential source of structural data, converting these images into simulation-ready formats remains labor-intensive and error-prone, creating a bottleneck for model training and validation. We introduce AutoMat, an end-to-end, agent-assisted pipeline that automatically transforms scanning transmission electron microscopy (STEM) images into atomic crystal structures and predicts their physical properties. AutoMat combines pattern-adaptive denoising, physics-guided template retrieval, symmetry-aware atomic reconstruction, fast relaxation and property prediction via MatterSim, and coordinated orchestration across all stages. We propose the first dedicated STEM2Mat-Bench for this task and evaluate performance using lattice RMSD, formation energy MAE, and structure-matching success rate. By orchestrating external tool calls, AutoMat enables a text-only LLM to outperform vision-language models in this domain, achieving closed-loop reasoning throughout the pipeline. In large-scale experiments over 450 structure samples, AutoMat substantially outperforms existing multimodal large language models and tools. These results validate both AutoMat and STEM2Mat-Bench, marking a key step toward bridging microscopy and atomistic simulation in materials science.The code and dataset are publicly available at https://github.com/yyt-2378/AutoMat and https://huggingface.co/datasets/yaotianvector/STEM2Mat.

Integrating Chemistry Knowledge in Large Language Models via Prompt Engineering

This paper presents a study on the integration of domain-specific knowledge in prompt engineering to enhance the performance of large language models (LLMs) in scientific domains. A benchmark dataset is curated to encapsulate the intricate physical-chemical properties of small molecules, their drugability for pharmacology, alongside the functional attributes of enzymes and crystal materials, underscoring the relevance and applicability across biological and chemical domains.The proposed domain-knowledge embedded prompt engineering method outperforms traditional prompt engineering strategies on various metrics, including capability, accuracy, F1 score, and hallucination drop. The effectiveness of the method is demonstrated through case studies on complex materials including the MacMillan catalyst, paclitaxel, and lithium cobalt oxide. The results suggest that domain-knowledge prompts can guide LLMs to generate more accurate and relevant responses, highlighting the potential of LLMs as powerful tools for scientific discovery and innovation when equipped with domain-specific prompts. The study also discusses limitations and future directions for domain-specific prompt engineering development.