Mao Su

Junxian Li, Di Zhang, Xunzhi Wang et al. · mit

Large Language Models (LLMs) have achieved remarkable success and have been applied across various scientific fields, including chemistry. However, many chemical tasks require the processing of visual information, which cannot be successfully handled by existing chemical LLMs. This brings a growing need for models capable of integrating multimodal information in the chemical domain. In this paper, we introduce \textbf{ChemVLM}, an open-source chemical multimodal large language model specifically designed for chemical applications. ChemVLM is trained on a carefully curated bilingual multimodal dataset that enhances its ability to understand both textual and visual chemical information, including molecular structures, reactions, and chemistry examination questions. We develop three datasets for comprehensive evaluation, tailored to Chemical Optical Character Recognition (OCR), Multimodal Chemical Reasoning (MMCR), and Multimodal Molecule Understanding tasks. We benchmark ChemVLM against a range of open-source and proprietary multimodal large language models on various tasks. Experimental results demonstrate that ChemVLM achieves competitive performance across all evaluated tasks. Our model can be found at https://huggingface.co/AI4Chem/ChemVLM-26B.

Yang Zhong, Hongyu Yu, Mao Su et al.

Using the message-passing mechanism in machine learning (ML) instead of self-consistent iterations to directly build the mapping from structures to electronic Hamiltonian matrices will greatly improve the efficiency of density functional theory (DFT) calculations. In this work, we proposed a general analytic Hamiltonian representation in an E(3) equivariant framework, which can fit the ab initio Hamiltonian of molecules and solids by a complete data-driven method and are equivariant under rotation, space inversion, and time reversal operations. Our model reached state-of-the-art precision in the benchmark test and accurately predicted the electronic Hamiltonian matrices and related properties of various periodic and aperiodic systems, showing high transferability and generalization ability. This framework provides a general transferable model that can be used to accelerate the electronic structure calculations on different large systems with the same network weights trained on small structures.

Wanghan Xu, Yuhao Zhou, Yifan Zhou et al.

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

Linfeng Zhang, Taoyong Cui, Dongzhan Zhou et al.

Long-range electrostatic and polarization interactions play a central role in molecular and condensed-phase systems, yet remain fundamentally incompatible with locality-based machine-learning interatomic potentials. Although modern SO(3)-equivariant neural potentials achieve high accuracy for short-range chemistry, they cannot represent the anisotropic, slowly decaying multipolar correlations governing realistic materials, while existing long-range extensions either break SO(3) equivariance or fail to maintain energy-force consistency. Here we introduce EquiEwald, a unified neural interatomic potential that embeds an Ewald-inspired reciprocal-space formulation within an irreducible SO(3)-equivariant framework. By performing equivariant message passing in reciprocal space through learned equivariant k-space filters and an equivariant inverse transform, EquiEwald captures anisotropic, tensorial long-range correlations without sacrificing physical consistency. Across periodic and aperiodic benchmarks, EquiEwald captures long-range electrostatic behavior consistent with ab initio reference data and consistently improves energy and force accuracy, data efficiency, and long-range extrapolation. These results establish EquiEwald as a physically principled paradigm for long-range-capable machine-learning interatomic potentials.

Zeyu Xia, Jinzhe Ma, Congjie Zheng et al.

Large Language Models (LLMs) have emerged as powerful tools for accelerating scientific discovery, yet their static knowledge and hallucination issues hinder autonomous research applications. Recent advances integrate LLMs into agentic frameworks, enabling retrieval, reasoning, and tool use for complex scientific workflows. Here, we present a domain-specialized agent designed for reliable automation of first-principles materials computations. By embedding domain expertise, the agent ensures physically coherent multi-step workflows and consistently selects convergent, well-posed parameters, thereby enabling reliable end-to-end computational execution. A new benchmark of diverse computational tasks demonstrates that our system significantly outperforms standalone LLMs in both accuracy and robustness. This work establishes a verifiable foundation for autonomous computational experimentation and represents a key step toward fully automated scientific discovery.

Zhongyao Wang, Taoyong Cui, Jiawen Zou et al.

Uncertainty quantification (UQ) is critical for assessing the reliability of machine learning interatomic potentials (MLIPs) in molecular dynamics (MD) simulations, identifying extrapolation regimes and enabling uncertainty-aware workflows such as active learning for training dataset construction. Existing UQ approaches for MLIPs are often limited by high computational cost or suboptimal performance. Evidential deep learning (EDL) provides a theoretically grounded single-model alternative that determines both aleatoric and epistemic uncertainty in a single forward pass. However, extending evidential formulations from scalar targets to vector-valued quantities such as atomic forces introduces substantial challenges, particularly in maintaining statistical self-consistency under rotational transformations. To address this, we propose \textit{Equivariant Evidential Deep Learning for Interatomic Potentials} ($\text{e}^2$IP), a backbone-agnostic framework that models atomic forces and their uncertainty jointly by representing uncertainty as a full $3\times3$ symmetric positive definite covariance tensor that transforms equivariantly under rotations. Experiments on diverse molecular benchmarks show that $\text{e}^2$IP provides a stronger accuracy-efficiency-reliability balance than the non-equivariant evidential baseline and the widely used ensemble method. It also achieves better data efficiency through the fully equivariant architecture while retaining single-model inference efficiency.

Weida Wang, Dongchen Huang, Jiatong Li et al.

We introduce CMPhysBench, designed to assess the proficiency of Large Language Models (LLMs) in Condensed Matter Physics, as a novel Benchmark. CMPhysBench is composed of more than 520 graduate-level meticulously curated questions covering both representative subfields and foundational theoretical frameworks of condensed matter physics, such as magnetism, superconductivity, strongly correlated systems, etc. To ensure a deep understanding of the problem-solving process,we focus exclusively on calculation problems, requiring LLMs to independently generate comprehensive solutions. Meanwhile, leveraging tree-based representations of expressions, we introduce the Scalable Expression Edit Distance (SEED) score, which provides fine-grained (non-binary) partial credit and yields a more accurate assessment of similarity between prediction and ground-truth. Our results show that even the best models, Grok-4, reach only 36 average SEED score and 28% accuracy on CMPhysBench, underscoring a significant capability gap, especially for this practical and frontier domain relative to traditional physics. The code anddataset are publicly available at https://github.com/CMPhysBench/CMPhysBench.

Yifeng Guan, Chuyi Liu, Dongzhan Zhou et al.

Discovering interpretable physical laws from high-dimensional data is a fundamental challenge in scientific research. Traditional methods, such as symbolic regression, often produce complex, unphysical formulas when searching a vast space of possible forms. We introduce a framework that guides the search process by leveraging the embedded scientific knowledge of large language models, enabling efficient identification of physical laws in the data. We validate our approach by modeling key properties of perovskite materials. Our method mitigates the combinatorial explosion commonly encountered in traditional symbolic regression, reducing the effective search space by a factor of approximately $10^5$. A set of novel formulas for bulk modulus, band gap, and oxygen evolution reaction activity are identified, which not only provide meaningful physical insights but also outperform previous formulas in accuracy and simplicity.

Di Zhang, Wei Liu, Qian Tan et al.

Large language models (LLMs) have made impressive progress in chemistry applications. However, the community lacks an LLM specifically designed for chemistry. The main challenges are two-fold: firstly, most chemical data and scientific knowledge are stored in structured databases, which limits the model's ability to sustain coherent dialogue when used directly. Secondly, there is an absence of objective and fair benchmark that encompass most chemistry tasks. Here, we introduce ChemLLM, a comprehensive framework that features the first LLM dedicated to chemistry. It also includes ChemData, a dataset specifically designed for instruction tuning, and ChemBench, a robust benchmark covering nine essential chemistry tasks. ChemLLM is adept at performing various tasks across chemical disciplines with fluid dialogue interaction. Notably, ChemLLM achieves results comparable to GPT-4 on the core chemical tasks and demonstrates competitive performance with LLMs of similar size in general scenarios. ChemLLM paves a new path for exploration in chemical studies, and our method of incorporating structured chemical knowledge into dialogue systems sets a new standard for developing LLMs in various scientific fields. Codes, Datasets, and Model weights are publicly accessible at https://hf.co/AI4Chem

Ruifeng Li, Dongzhan Zhou, Ancheng Shen et al.

Artificial intelligence (AI) technology has demonstrated remarkable potential in drug dis-covery, where pharmacokinetics plays a crucial role in determining the dosage, safety, and efficacy of new drugs. A major challenge for AI-driven drug discovery (AIDD) is the scarcity of high-quality data, which often requires extensive wet-lab work. A typical example of this is pharmacokinetic experiments. In this work, we develop a physical formula enhanced mul-ti-task learning (PEMAL) method that predicts four key parameters of pharmacokinetics simultaneously. By incorporating physical formulas into the multi-task framework, PEMAL facilitates effective knowledge sharing and target alignment among the pharmacokinetic parameters, thereby enhancing the accuracy of prediction. Our experiments reveal that PEMAL significantly lowers the data demand, compared to typical Graph Neural Networks. Moreover, we demonstrate that PEMAL enhances the robustness to noise, an advantage that conventional Neural Networks do not possess. Another advantage of PEMAL is its high flexibility, which can be potentially applied to other multi-task machine learning scenarios. Overall, our work illustrates the benefits and potential of using PEMAL in AIDD and other scenarios with data scarcity and noise.

Hongwei Liu, Junnan Liu, Shudong Liu et al.

The rapid advancement of Large Language Models (LLMs) has led to performance saturation on many established benchmarks, questioning their ability to distinguish frontier models. Concurrently, existing high-difficulty benchmarks often suffer from narrow disciplinary focus, oversimplified answer formats, and vulnerability to data contamination, creating a fidelity gap with real-world scientific inquiry. To address these challenges, we introduce ATLAS (AGI-Oriented Testbed for Logical Application in Science), a large-scale, high-difficulty, and cross-disciplinary evaluation suite composed of approximately 800 original problems. Developed by domain experts (PhD-level and above), ATLAS spans seven core scientific fields: mathematics, physics, chemistry, biology, computer science, earth science, and materials science. Its key features include: (1) High Originality and Contamination Resistance, with all questions newly created or substantially adapted to prevent test data leakage; (2) Cross-Disciplinary Focus, designed to assess models' ability to integrate knowledge and reason across scientific domains; (3) High-Fidelity Answers, prioritizing complex, open-ended answers involving multi-step reasoning and LaTeX-formatted expressions over simple multiple-choice questions; and (4) Rigorous Quality Control, employing a multi-stage process of expert peer review and adversarial testing to ensure question difficulty, scientific value, and correctness. We also propose a robust evaluation paradigm using a panel of LLM judges for automated, nuanced assessment of complex answers. Preliminary results on leading models demonstrate ATLAS's effectiveness in differentiating their advanced scientific reasoning capabilities. We plan to develop ATLAS into a long-term, open, community-driven platform to provide a reliable "ruler" for progress toward Artificial General Intelligence.

Dong Han, Zhehong Ai, Pengxiang Cai et al.

Bayesian optimization (BO) is a powerful tool for scientific discovery in chemistry, yet its efficiency is often hampered by the sparse experimental data and vast search space. Here, we introduce ChemBOMAS: a large language model (LLM)-enhanced multi-agent system that accelerates BO through synergistic data- and knowledge-driven strategies. Firstly, the data-driven strategy involves an 8B-scale LLM regressor fine-tuned on a mere 1% labeled samples for pseudo-data generation, robustly initializing the optimization process. Secondly, the knowledge-driven strategy employs a hybrid Retrieval-Augmented Generation approach to guide LLM in dividing the search space while mitigating LLM hallucinations. An Upper Confidence Bound algorithm then identifies high-potential subspaces within this established partition. Across the LLM-refined subspaces and supported by LLM-generated data, BO achieves the improvement of effectiveness and efficiency. Comprehensive evaluations across multiple scientific benchmarks demonstrate that ChemBOMAS set a new state-of-the-art, accelerating optimization efficiency by up to 5-fold compared to baseline methods.

Taoyong Cui, Zhongyao Wang, Dongzhan Zhou et al.

Machine learning interatomic potentials (MLIPs) enable efficient molecular dynamics (MD) simulations with ab initio accuracy and have been applied across various domains in physical science. However, their performance often relies on large-scale labeled training data. While existing pretraining strategies can improve model performance, they often suffer from a mismatch between the objectives of pretraining and downstream tasks or rely on extensive labeled datasets and increasingly complex architectures to achieve broad generalization. To address these challenges, we propose Iterative Pretraining for Interatomic Potentials (IPIP), a framework designed to iteratively improve the predictive performance of MLIP models. IPIP incorporates a forgetting mechanism to prevent iterative training from converging to suboptimal local minima. Unlike general-purpose foundation models, which frequently underperform on specialized tasks due to a trade-off between generality and system-specific accuracy, IPIP achieves higher accuracy and efficiency using lightweight architectures. Compared to general-purpose force fields, this approach achieves over 80% reduction in prediction error and up to 4x speedup in the challenging Mo-S-O system, enabling fast and accurate simulations.