Siamese foundation models for crystal structure prediction

Predicting crystal structures from chemical compositions is a fundamental challenge in materials discovery, complicated by complex 3D geometries that distinguish it from fields like protein folding. Here, we present Diffusion-based crystAl Omni (DAO), a pretrain-finetune framework for crystal structure prediction integrating two Siamese foundation models: a structure generator and an energy predictor. The generator is pretrained via a two-stage pipeline on a vast dataset of stable and unstable structures, leveraging the predictor to relax unstable configurations and guide the generative sampling. Across two well-known benchmarks, pretraining significantly enhances performance across multiple backbone architectures. Ablation studies confirm that the synergy between the generator and predictor mutually benefits both components. We further validate DAO on three real-world superconductors (Cr₆Os₂, Zr₁₆Rh₈O₄, and Zr₁₆Pd₈O₄) typically inaccessible to conventional computation. For Cr₆Os₂, DAO achieves a 100% match rate with experimental references and an atomic-position error of 0.0012 under 20-shot generation, performing over 2000 × faster per iteration than DFT-based structure predictors. These compelling results collectively highlight the potential of our approach for advancing materials science research.