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

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.

Hidden in Plain Sight: Visual-to-Symbolic Analytical Solution Inference from Field Visualizations

Recovering analytical solutions of physical fields from visual observations is a fundamental yet underexplored capability for AI-assisted scientific reasoning. We study visual-to-symbolic analytical solution inference (ViSA) for two-dimensional linear steady-state fields: given field visualizations (and first-order derivatives) plus minimal auxiliary metadata, the model must output a single executable SymPy expression with fully instantiated numeric constants. We introduce ViSA-R2 and align it with a self-verifying, solution-centric chain-of-thought pipeline that follows a physicist-like pathway: structural pattern recognition solution-family (ansatz) hypothesis parameter derivation consistency verification. We also release ViSA-Bench, a VLM-ready synthetic benchmark covering 30 linear steady-state scenarios with verifiable analytical/symbolic annotations, and evaluate predictions by numerical accuracy, expression-structure similarity, and character-level accuracy. Using an 8B open-weight Qwen3-VL backbone, ViSA-R2 outperforms strong open-source baselines and the evaluated closed-source frontier VLMs under a standardized protocol.

SciIF: Benchmarking Scientific Instruction Following Towards Rigorous Scientific Intelligence

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.

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Mimicking the Physicist's Eye:A VLM-centric Approach for Physics Formula Discovery

Automated discovery of physical laws from observational data in the real world is a grand challenge in AI. Current methods, relying on symbolic regression or LLMs, are limited to uni-modal data and overlook the rich, visual phenomenological representations of motion that are indispensable to physicists. This "sensory deprivation" severely weakens their ability to interpret the inherent spatio-temporal patterns within dynamic phenomena. To address this gap, we propose VIPER-R1, a multimodal model that performs Visual Induction for Physics-based Equation Reasoning to discover fundamental symbolic formulas. It integrates visual perception, trajectory data, and symbolic reasoning to emulate the scientific discovery process. The model is trained via a curriculum of Motion Structure Induction (MSI), using supervised fine-tuning to interpret kinematic phase portraits and to construct hypotheses guided by a Causal Chain of Thought (C-CoT), followed by Reward-Guided Symbolic Calibration (RGSC) to refine the formula structure with reinforcement learning. During inference, the trained VIPER-R1 acts as an agent: it first posits a high-confidence symbolic ansatz, then proactively invokes an external symbolic regression tool to perform Symbolic Residual Realignment (SR^2). This final step, analogous to a physicist's perturbation analysis, reconciles the theoretical model with empirical data. To support this research, we introduce PhysSymbol, a new 5,000-instance multimodal corpus. Experiments show that VIPER-R1 consistently outperforms state-of-the-art VLM baselines in accuracy and interpretability, enabling more precise discovery of physical laws. Project page: https://jiaaqiliu.github.io/VIPER-R1/

Examining the Source of Defects from a Mechanical Perspective for 3D Anomaly Detection

In this paper, we go beyond identifying anomalies only in structural terms and think about better anomaly detection motivated by anomaly causes. Most anomalies are regarded as the result of unpredictable defective forces from internal and external sources, and their opposite forces are sought to correct the anomalies. We introduced a Mechanics Complementary framework for 3D anomaly detection (MC4AD) to generate internal and external Corrective forces for each point. A Diverse Anomaly-Generation (DA-Gen) module is first proposed to simulate various anomalies. Then, we present a Corrective Force Prediction Network (CFP-Net) with complementary representations for point-level representation to simulate the different contributions of internal and external corrective forces. A combined loss was proposed, including a new symmetric loss and an overall loss, to constrain the corrective forces properly. As a highlight, we consider 3D anomaly detection in industry more comprehensively, creating a hierarchical quality control strategy based on a three-way decision and contributing a dataset named Anomaly-IntraVariance with intraclass variance to evaluate the model. On the proposed and existing five datasets, we obtained nine state-of-the-art performers with the minimum parameters and the fastest inference speed. The source is available at https://github.com/hzzzzzhappy/MC4AD