Paper

Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

A unified multimodal model that turns native scientific structures into addressable tokens, then reasons over them in autoregressive, inspectable traces.

arXiv ↗Jul 8, 2026Code ↗

  • nlp
  • llm
  • multimodal
  • scientific reasoning
  • foundation models
  • molecular property prediction
Full pipeline diagram showing SciReasoner architecture, tokenization, and multi-modal scientific inputs/outputs
Full pipeline diagram showing SciReasoner architecture, tokenization, and multi-modal scientific inputs/outputs

What it is

A multimodal scientific foundation model that reasons directly over protein, molecule, and crystal structures using structure-aware tokens and inspectable traces. Instead of treating structures as text or using opaque task-specific predictors, it tokenizes native 3D/topological structure into evidence units and generates predictions with structure-linked reasoning across proteins, molecules, and crystals.

Key results

  • 67 of 86 benchmarks reach state of the art
  • Low-homology protein GO CC Fmax improves 0.42→0.55 vs ESM2
  • Single-step retrosynthesis accuracy rises 0.63→0.72

Shows that making native structure explicit reasoning evidence improves both accuracy and interpretability across scientific domains.

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