Jinouwen Zhang

Chen Tang, Yizhou Wang, Jianyu Wu et al.

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

Encheng Su, Jianyu Wu, Chen Tang et al.

As large language models (LLMs) transition from general knowledge retrieval to complex scientific discovery, their evaluation standards must also incorporate the rigorous norms of scientific inquiry. Existing benchmarks exhibit a critical blind spot: general instruction-following metrics focus on superficial formatting, while domain-specific scientific benchmarks assess only final-answer correctness, often rewarding models that arrive at the right result with the wrong reasons. To address this gap, we introduce scientific instruction following: the capability to solve problems while strictly adhering to the constraints that establish scientific validity. Specifically, we introduce SciIF, a multi-discipline benchmark that evaluates this capability by pairing university-level problems with a fixed catalog of constraints across three pillars: scientific conditions (e.g., boundary checks and assumptions), semantic stability (e.g., unit and symbol conventions), and specific processes(e.g., required numerical methods). Uniquely, SciIF emphasizes auditability, requiring models to provide explicit evidence of constraint satisfaction rather than implicit compliance. By measuring both solution correctness and multi-constraint adherence, SciIF enables finegrained diagnosis of compositional reasoning failures, ensuring that LLMs can function as reliable agents within the strict logical frameworks of science.