arXiv subjects

Yuqiang Li

Publications and source records attributed to Yuqiang Li.

At least 73 records · Page 4Linked to original sources

arXiv2026

CH3CCH as a thermometer in warm molecular gas

Kinetic temperature is a fundamental parameter in molecular clouds. Symmetric top molecules, such as NH$_3$ and CH$_3$CCH, are often used as thermometers. However, at high temperatures, NH$_3$(2,2) can be collisionally excited to NH$_3$(2,1) and rapidly decay to NH$_3$(1,1), which can lead to an underestimation of the kinetic temperature when using rotation temperatures derived from NH$_3$(1,1) and NH$_3$(2,2). In contrast, CH$_3$CCH is a symmetric top molecule with lower critical densities of its rotational levels than those of NH$_3$, which can be thermalized close to the kinetic temperature at relatively low densities of about 10$^{4}$ cm$^{-3}$. To compare the rotation temperatures derived from NH$_3$(1,1)$\&$(2,2) and CH$_3$CCH rotational levels in warm molecular gas, we used observational data toward 55 massive star-forming regions obtained with Yebes 40m and TMRT 65m. Our results show that rotation temperatures derived from NH$_3$(1,1)$\&$(2,2) are systematically lower than those from CH$_3$CCH 5-4. This suggests that CH$_3$CCH rotational lines with the same $J$+1$\rightarrow$$J$ quantum number may be a more reliable thermometer than NH$_3$(1,1)$\&$(2,2) in warm molecular gas located in the surroundings of massive young stellar objects or, more generally, in massive star-forming regions.

astro-ph.GA↗

arXiv2026

Vib2Mol: from vibrational spectra to molecular structures-a unified deep learning framework

There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular structures with spectral information, is the core step in understanding the experimental results and to close the loop. However, current approaches usually divide the task into either database-dependent retrieval and database-independent generation and neglect the inherent complementarity between them. In this study, we proposed Vib2Mol, a unified deep learning framework designed to flexibly handle diverse spectrum-to-structure tasks according to the available prior knowledge by bridging the retrieval and generation. Empowered by our coarse-to-fine retrieval and generate-then-rerank strategies, Vib2Mol not only achieves state-of-the-art performance in analyzing theoretical Infrared and Raman spectra, but also outperform previous models on experimental data. Moreover, our model demonstrates promising capabilities in predicting reaction products and sequencing peptides, enabling vibrational spectroscopy a potential guide for autonomous scientific discovery workflows.

physics.chem-ph↗

arXiv2025

Leveraging Adaptive Group Negotiation for Heterogeneous Multi-Robot Collaboration with Large Language Models

Multi-robot collaboration tasks often require heterogeneous robots to work together over long horizons under spatial constraints and environmental uncertainties. Although Large Language Models (LLMs) excel at reasoning and planning, their potential for coordinated control has not been fully explored. Inspired by human teamwork, we present CLiMRS (Cooperative Large-Language-Model-Driven Heterogeneous Multi-Robot System), an adaptive group negotiation framework among LLMs for multi-robot collaboration. This framework pairs each robot with an LLM agent and dynamically forms subgroups through a general proposal planner. Within each subgroup, a subgroup manager leads perception-driven multi-LLM discussions to get commands for actions. Feedback is provided by both robot execution outcomes and environment changes. This grouping-planning-execution-feedback loop enables efficient planning and robust execution. To evaluate these capabilities, we introduce CLiMBench, a heterogeneous multi-robot benchmark of challenging assembly tasks. Our experiments show that CLiMRS surpasses the best baseline, achieving over 40% higher efficiency on complex tasks without sacrificing success on simpler ones. Overall, our results demonstrate that leveraging human-inspired group formation and negotiation principles significantly enhances the efficiency of heterogeneous multi-robot collaboration. Our code is available here: https://github.com/song-siqi/CLiMRS.

cs.RO↗

arXiv2025

MolAct: An Agentic RL Framework for Molecular Editing and Property Optimization

Molecular editing and optimization are multi-step problems that require iteratively improving properties while keeping molecules chemically valid and structurally similar. We frame both tasks as sequential, tool-guided decisions and introduce MolAct, an agentic reinforcement learning framework that employs a two-stage training paradigm: first building editing capability, then optimizing properties while reusing the learned editing behaviors. To the best of our knowledge, this is the first work to formalize molecular design as an Agentic Reinforcement Learning problem, where an LLM agent learns to interleave reasoning, tool-use, and molecular optimization. The framework enables agents to interact in multiple turns, invoking chemical tools for validity checking, property assessment, and similarity control, and leverages their feedback to refine subsequent edits. We instantiate the MolAct framework to train two model families: MolEditAgent for molecular editing tasks and MolOptAgent for molecular optimization tasks. In molecular editing, MolEditAgent-7B delivers 100, 95, and 98 valid add, delete, and substitute edits, outperforming strong closed "thinking" baselines such as DeepSeek-R1; MolEditAgent-3B approaches the performance of much larger open "thinking" models like Qwen3-32B-think. In molecular optimization, MolOptAgent-7B (trained on MolEditAgent-7B) surpasses the best closed "thinking" baseline (e.g., Claude 3.7) on LogP and remains competitive on solubility, while maintaining balanced performance across other objectives. These results highlight that treating molecular design as a multi-step, tool-augmented process is key to reliable and interpretable improvements.

cs.AI↗

arXiv2025

Probing Scientific General Intelligence of LLMs with Scientist-Aligned Workflows

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.

cs.AI↗

arXiv2025

ATLAS: A High-Difficulty, Multidisciplinary Benchmark for Frontier Scientific Reasoning

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.

cs.CL↗

arXiv2025

A High-Precision Dynamical Model of Callisto: Incorporating Rotation Effects within Multi-Layer Internal Structure Models

China is planing to launch the Tianwen-4 mission around the year 2030, with its aim being the exploration of Jupiter and its moon, Callisto. Within the realm of deep space exploration, the accuracy of ephemerides is of great importance. Current ephemerides employ a simplified rotation model for Callisto, which this study addresses by proposing a novel dynamical model. This model enhancesthe existing orbital dynamics by integrating Callisto's rotational motions influenced by gravitational torques from the Sun, Jupiter, and other Galilean moons within an inertial frame, capturing the intricate coupling between Callisto's orbital and rotational dynamics. The study establishes a full dynamical model by deriving analytical expressions for this coupling and developing an adjustment model for data fitting using precise orbit determination methods. Furthermore, the influence of tidal effects on Callisto's motion is investigated, considering its multi-layered internal structure. Results demonstrate that the difference between the newly established full model and the model in current ephemerides is on the order of tens of meters. When calculating the impact of different internal structures of Callisto on its orbit, the influence of three-layered and two-layered structures is on the order of meters, suggesting that the development of a high-precision dynamical model requires additional constraints on the internal structure of Callisto. This research provides a novel alternative for a new generation of precise numerical ephemerides for Callisto. Additionally, these findings provide a testing platform for the data from the Tianwen-4 mission.

astro-ph.EP↗

arXiv2025

ChemBOMAS: Accelerated BO in Chemistry with LLM-Enhanced Multi-Agent System

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.

cs.LG↗

arXiv2025

MOOSE-Chem: Large Language Models for Rediscovering Unseen Chemistry Scientific Hypotheses

Scientific discovery plays a pivotal role in advancing human society, and recent progress in large language models (LLMs) suggests their potential to accelerate this process. However, it remains unclear whether LLMs can autonomously generate novel and valid hypotheses in chemistry. In this work, we investigate whether LLMs can discover high-quality chemistry hypotheses given only a research background-comprising a question and/or a survey-without restriction on the domain of the question. We begin with the observation that hypothesis discovery is a seemingly intractable task. To address this, we propose a formal mathematical decomposition grounded in a fundamental assumption: that most chemistry hypotheses can be composed from a research background and a set of inspirations. This decomposition leads to three practical subtasks-retrieving inspirations, composing hypotheses with inspirations, and ranking hypotheses - which together constitute a sufficient set of subtasks for the overall scientific discovery task. We further develop an agentic LLM framework, MOOSE-Chem, that is a direct implementation of this mathematical decomposition. To evaluate this framework, we construct a benchmark of 51 high-impact chemistry papers published and online after January 2024, each manually annotated by PhD chemists with background, inspirations, and hypothesis. The framework is able to rediscover many hypotheses with high similarity to the groundtruth, successfully capturing the core innovations-while ensuring no data contamination since it uses an LLM with knowledge cutoff date prior to 2024. Finally, based on LLM's surprisingly high accuracy on inspiration retrieval, a task with inherently out-of-distribution nature, we propose a bold assumption: that LLMs may already encode latent scientific knowledge associations not yet recognized by humans.

cs.CL↗

arXiv2025

ChemVLM: Exploring the Power of Multimodal Large Language Models in Chemistry Area

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.

cs.LG↗

arXiv2025

MOOSE-Chem3: Toward Experiment-Guided Hypothesis Ranking via Simulated Experimental Feedback

Hypothesis ranking is vital for automated scientific discovery, especially in cost-intensive, throughput-limited natural science domains. Current methods focus on pre-experiment ranking, relying solely on language model reasoning without empirical feedback. We introduce experiment-guided ranking, which prioritizes hypotheses based on feedback from prior tests. Due to the impracticality of real experiments, we propose a simulator grounded in domain-specific concepts that models hypothesis performance as a function of similarity to a hidden ground truth, perturbed by noise. Validated against 124 hypotheses with experimentally reported outcomes, the simulator approximates real results with consistent trend alignment. Although deviations exist, they mimic wet-lab noise, promoting more robust ranking strategies. We frame experiment-guided ranking as a sequential decision-making problem and propose an in-context reinforcement learning (ICRL) framework. Our LLM-based policy decomposes hypotheses into functional elements, clusters them by mechanistic roles, and prioritizes recombinations based on feedback. Experiments show our approach significantly outperforms pre-experiment baselines and strong ablations. Our toolkit, comprising the simulator and ICRL framework, enables systematic research on experiment-guided ranking, with the policy serving as a strong proof of concept.

cs.CL↗

arXiv2025

Chem-R: Learning to Reason as a Chemist

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 32% on molecular tasks and 48% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery. The code and model are available at https://github.com/davidweidawang/Chem-R.

cs.CE↗

arXiv2025

Widespread Hot Molecular Gas Heated by Shear-induced Turbulence in the Galactic Center

We observed NH3 metastable inversion lines from (3, 3) to (18, 18) toward G0.66-0.13 in the Galactic center with the Shanghai Tianma 65m radio telescope and Yebes 40 m telescope. Highly-excited lines of NH3 (17, 17), (18, 18) were detected in emission for the first time in the interstellar medium, with upper energy levels up to 3100 K. Mapping observations reveal widespread hot molecular gas traced by NH3 (13, 13) toward G0.66-0.13. The rotation temperatures of hot gas traced by NH3 exceed 400 K, which amounts to five percent of the total NH3 in the Galactic Center. Hot gas (>400 K) and warm gas (100-140 K) are found in distinct clumps, with the hot gas located at the interfacing regions between different warm clouds. The theory of intermittency in turbulence reproduces the complex temperature structure in the central molecular zone, especially the hot gas observed here. The results presented here demonstrate that turbulence heating dominates the heating of the molecular gas in the Central Molecular Zone, while the turbulence is induced by the shear-motion of molecular clouds under the gravitational potential of the nuclear star clusters and the supermassive black hole. Our results suggest that shear-induced turbulence heating could be a widespread factor influencing galactic evolution.

astro-ph.GA↗

arXiv2025

QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry

Quantitative chemistry is central to modern chemical research, yet the ability of large language models (LLMs) to perform its rigorous, step-by-step calculations remains underexplored. To fill this blank, we propose QCBench, a Quantitative Chemistry oriented benchmark comprising 350 computational chemistry problems across 7 chemistry subfields, which contains analytical chemistry, bio/organic chemistry, general chemistry, inorganic chemistry, physical chemistry, polymer chemistry and quantum chemistry. To systematically evaluate the mathematical reasoning abilities of large language models (LLMs), they are categorized into three tiers: easy, medium, and difficult. Each problem, rooted in realistic chemical scenarios, is structured to prevent heuristic shortcuts and demand explicit numerical reasoning. QCBench enables fine-grained diagnosis of computational weaknesses, reveals model-specific limitations across difficulty levels, and lays the groundwork for future improvements such as domain-adaptive fine-tuning or multi-modal integration. Evaluations on 24 LLMs demonstrate a consistent performance degradation with increasing task complexity, highlighting the current gap between language fluency and scientific computation accuracy. Code for QCBench is available at https://github.com/jiaqingxie/QCBench.

cs.AI↗

arXiv2025

Sequential Diffusion Language Models

Diffusion language models (DLMs) have strong theoretical efficiency but are limited by fixed-length decoding and incompatibility with key-value (KV) caches. Block diffusion mitigates these issues, yet still enforces a fixed block size and requires expensive training. We introduce Next Sequence Prediction (NSP), which unifies next-token and next-block prediction, enabling the model to adaptively determine the generation length at each step. When the length is fixed to 1, NSP reduces to standard next-token prediction. Building on NSP, we propose Sequential Diffusion Language Model (SDLM), which can retrofit pre-trained autoregressive language models (ALMs) at minimal cost. Specifically, SDLM performs diffusion inference within fixed-size mask blocks, but dynamically decodes consecutive subsequences based on model confidence, thereby preserving KV-cache compatibility and improving robustness to varying uncertainty and semantics across the sequence. Experiments show that SDLM matches or surpasses strong autoregressive baselines using only 3.5M training samples, while achieving 2.1 higher throughput than Qwen-2.5. Notably, the SDLM-32B model delivers even more pronounced efficiency gains, demonstrating the strong scalability potential of our modeling paradigm. Project page and codes: https://github.com/OpenGVLab/SDLM

cs.CL↗

arXiv2025

Reasoning BO: Enhancing Bayesian Optimization with Long-Context Reasoning Power of LLMs

Many real-world scientific and industrial applications require the optimization of expensive black-box functions. Bayesian Optimization (BO) provides an effective framework for such problems. However, traditional BO methods are prone to get trapped in local optima and often lack interpretable insights. To address this issue, this paper designs Reasoning BO, a novel framework that leverages reasoning models to guide the sampling process in BO while incorporating multi-agent systems and knowledge graphs for online knowledge accumulation. By integrating the reasoning and contextual understanding capabilities of Large Language Models (LLMs), we can provide strong guidance to enhance the BO process. As the optimization progresses, Reasoning BO provides real-time sampling recommendations along with critical insights grounded in plausible scientific theories, aiding in the discovery of superior solutions within the search space. We systematically evaluate our approach across 10 diverse tasks encompassing synthetic mathematical functions and complex real-world applications. The framework demonstrates its capability to progressively refine sampling strategies through real-time insights and hypothesis evolution, effectively identifying higher-performing regions of the search space for focused exploration. This process highlights the powerful reasoning and context-learning abilities of LLMs in optimization scenarios. For example, in the Direct Arylation task, our method increased the yield to 60.7%, whereas traditional BO achieved only a 25.2% yield. Furthermore, our investigation reveals that smaller LLMs, when fine-tuned through reinforcement learning, can attain comparable performance to their larger counterparts.

cs.AI↗

arXiv2025

SpectrumWorld: Artificial Intelligence Foundation for Spectroscopy

Deep learning holds immense promise for spectroscopy, yet research and evaluation in this emerging field often lack standardized formulations. To address this issue, we introduce SpectrumLab, a pioneering unified platform designed to systematize and accelerate deep learning research in spectroscopy. SpectrumLab integrates three core components: a comprehensive Python library featuring essential data processing and evaluation tools, along with leaderboards; an innovative SpectrumAnnotator module that generates high-quality benchmarks from limited seed data; and SpectrumBench, a multi-layered benchmark suite covering 14 spectroscopic tasks and over 10 spectrum types, featuring spectra curated from over 1.2 million distinct chemical substances. Thorough empirical studies on SpectrumBench with 18 cutting-edge multimodal LLMs reveal critical limitations of current approaches. We hope SpectrumLab will serve as a crucial foundation for future advancements in deep learning-driven spectroscopy.

cs.LG↗

arXiv2025

Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

q-bio.BM↗