SCP: Accelerating Discovery with a Global Web of Autonomous Scientific Agents

We introduce SCP: the Science Context Protocol, an open-source standard designed to accelerate discovery by enabling a global network of autonomous scientific agents. SCP is built on two foundational pillars: (1) Unified Resource Integration: At its core, SCP provides a universal specification for describing and invoking scientific resources, spanning software tools, models, datasets, and physical instruments. This protocol-level standardization enables AI agents and applications to discover, call, and compose capabilities seamlessly across disparate platforms and institutional boundaries. (2) Orchestrated Experiment Lifecycle Management: SCP complements the protocol with a secure service architecture, which comprises a centralized SCP Hub and federated SCP Servers. This architecture manages the complete experiment lifecycle (registration, planning, execution, monitoring, and archival), enforces fine-grained authentication and authorization, and orchestrates traceable, end-to-end workflows that bridge computational and physical laboratories. Based on SCP, we have constructed a scientific discovery platform that offers researchers and agents a large-scale ecosystem of more than 1,600 tool resources. Across diverse use cases, SCP facilitates secure, large-scale collaboration between heterogeneous AI systems and human researchers while significantly reducing integration overhead and enhancing reproducibility. By standardizing scientific context and tool orchestration at the protocol level, SCP establishes essential infrastructure for scalable, multi-institution, agent-driven science.

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.

SynWeather: Weather Observation Data Synthesis across Multiple Regions and Variables via a General Diffusion Transformer

With the advancement of meteorological instruments, abundant data has become available. Current approaches are typically focus on single-variable, single-region tasks and primarily rely on deterministic modeling. This limits unified synthesis across variables and regions, overlooks cross-variable complementarity and often leads to over-smoothed results. To address above challenges, we introduce SynWeather, the first dataset designed for Unified Multi-region and Multi-variable Weather Observation Data Synthesis. SynWeather covers four representative regions: the Continental United States, Europe, East Asia, and Tropical Cyclone regions, as well as provides high-resolution observations of key weather variables, including Composite Radar Reflectivity, Hourly Precipitation, Visible Light, and Microwave Brightness Temperature. In addition, we introduce SynWeatherDiff, a general and probabilistic weather synthesis model built upon the Diffusion Transformer framework to address the over-smoothed problem. Experiments on the SynWeather dataset demonstrate the effectiveness of our network compared with both task-specific and general models.

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.

EarthLink: A Self-Evolving AI Agent for Climate Science

Modern Earth science is at an inflection point. The vast, fragmented, and complex nature of Earth system data, coupled with increasingly sophisticated analytical demands, creates a significant bottleneck for rapid scientific discovery. Here we introduce EarthLink, the first AI agent designed as an interactive copilot for Earth scientists. It automates the end-to-end research workflow, from planning and code generation to multi-scenario analysis. Unlike static diagnostic tools, EarthLink can learn from user interaction, continuously refining its capabilities through a dynamic feedback loop. We validated its performance on a number of core scientific tasks of climate change, ranging from model-observation comparisons to the diagnosis of complex phenomena. In a multi-expert evaluation, EarthLink produced scientifically sound analyses and demonstrated an analytical competency that was rated as comparable to specific aspects of a human junior researcher's workflow. Additionally, its transparent, auditable workflows and natural language interface empower scientists to shift from laborious manual execution to strategic oversight and hypothesis generation. EarthLink marks a pivotal step towards an efficient, trustworthy, and collaborative paradigm for Earth system research in an era of accelerating global change. The system is accessible at our website https://earthlink.intern-ai.org.cn.

ReconMOST: Multi-Layer Sea Temperature Reconstruction with Observations-Guided Diffusion

Accurate reconstruction of ocean is essential for reflecting global climate dynamics and supporting marine meteorological research. Conventional methods face challenges due to sparse data, algorithmic complexity, and high computational costs, while increasing usage of machine learning (ML) method remains limited to reconstruction problems at the sea surface and local regions, struggling with issues like cloud occlusion. To address these limitations, this paper proposes ReconMOST, a data-driven guided diffusion model framework for multi-layer sea temperature reconstruction. Specifically, we first pre-train an unconditional diffusion model using a large collection of historical numerical simulation data, enabling the model to attain physically consistent distribution patterns of ocean temperature fields. During the generation phase, sparse yet high-accuracy in-situ observational data are utilized as guidance points for the reverse diffusion process, generating accurate reconstruction results. Importantly, in regions lacking direct observational data, the physically consistent spatial distribution patterns learned during pre-training enable implicitly guided and physically plausible reconstructions. Our method extends ML-based SST reconstruction to a global, multi-layer setting, handling over 92.5% missing data while maintaining reconstruction accuracy, spatial resolution, and superior generalization capability. We pre-train our model on CMIP6 numerical simulation data and conduct guided reconstruction experiments on CMIP6 and EN4 analysis data. The results of mean squared error (MSE) values achieve 0.049 on guidance, 0.680 on reconstruction, and 0.633 on total, respectively, demonstrating the effectiveness and robustness of the proposed framework. Our source code is available at https://github.com/norsheep/ReconMOST.

Scientists' First Exam: Probing Cognitive Abilities of MLLM via Perception, Understanding, and Reasoning

Scientific discoveries increasingly rely on complex multimodal reasoning based on information-intensive scientific data and domain-specific expertise. Empowered by expert-level scientific benchmarks, scientific Multimodal Large Language Models (MLLMs) hold the potential to significantly enhance this discovery process in realistic workflows. However, current scientific benchmarks mostly focus on evaluating the knowledge understanding capabilities of MLLMs, leading to an inadequate assessment of their perception and reasoning abilities. To address this gap, we present the Scientists' First Exam (SFE) benchmark, designed to evaluate the scientific cognitive capacities of MLLMs through three interconnected levels: scientific signal perception, scientific attribute understanding, scientific comparative reasoning. Specifically, SFE comprises 830 expert-verified VQA pairs across three question types, spanning 66 multimodal tasks across five high-value disciplines. Extensive experiments reveal that current state-of-the-art GPT-o3 and InternVL-3 achieve only 34.08% and 26.52% on SFE, highlighting significant room for MLLMs to improve in scientific realms. We hope the insights obtained in SFE will facilitate further developments in AI-enhanced scientific discoveries.

OmniEarth-Bench: Towards Holistic Evaluation of Earth's Six Spheres and Cross-Spheres Interactions with Multimodal Observational Earth Data

Existing benchmarks for Earth science multimodal learning exhibit critical limitations in systematic coverage of geosystem components and cross-sphere interactions, often constrained to isolated subsystems (only in Human-activities sphere or atmosphere) with limited evaluation dimensions (less than 16 tasks). To address these gaps, we introduce OmniEarth-Bench, the first comprehensive multimodal benchmark spanning all six Earth science spheres (atmosphere, lithosphere, Oceansphere, cryosphere, biosphere and Human-activities sphere) and cross-spheres with one hundred expert-curated evaluation dimensions. Leveraging observational data from satellite sensors and in-situ measurements, OmniEarth-Bench integrates 29,779 annotations across four tiers: perception, general reasoning, scientific knowledge reasoning and chain-of-thought (CoT) reasoning. This involves the efforts of 2-5 experts per sphere to establish authoritative evaluation dimensions and curate relevant observational datasets, 40 crowd-sourcing annotators to assist experts for annotations, and finally, OmniEarth-Bench is validated via hybrid expert-crowd workflows to reduce label ambiguity. Experiments on 9 state-of-the-art MLLMs reveal that even the most advanced models struggle with our benchmarks, where none of them reach 35\% accuracy. Especially, in some cross-spheres tasks, the performance of leading models like GPT-4o drops to 0.0\%. OmniEarth-Bench sets a new standard for geosystem-aware AI, advancing both scientific discovery and practical applications in environmental monitoring and disaster prediction. The dataset, source code, and trained models were released.

Align-DA: Align Score-based Atmospheric Data Assimilation with Multiple Preferences

Data assimilation (DA) aims to estimate the full state of a dynamical system by combining partial and noisy observations with a prior model forecast, commonly referred to as the background. In atmospheric applications, this problem is fundamentally ill-posed due to the sparsity of observations relative to the high-dimensional state space. Traditional methods address this challenge by simplifying background priors to regularize the solution, which are empirical and require continual tuning for application. Inspired by alignment techniques in text-to-image diffusion models, we propose Align-DA, which formulates DA as a generative process and uses reward signals to guide background priors, replacing manual tuning with data-driven alignment. Specifically, we train a score-based model in the latent space to approximate the background-conditioned prior, and align it using three complementary reward signals for DA: (1) assimilation accuracy, (2) forecast skill initialized from the assimilated state, and (3) physical adherence of the analysis fields. Experiments with multiple reward signals demonstrate consistent improvements in analysis quality across different evaluation metrics and observation-guidance strategies. These results show that preference alignment, implemented as a soft constraint, can automatically adapt complex background priors tailored to DA, offering a promising new direction for advancing the field.

MSEarth: A Benchmark for Multimodal Scientific Comprehension of Earth Science

The rapid advancement of multimodal large language models (MLLMs) has unlocked new opportunities to tackle complex scientific challenges. Despite this progress, their application in addressing earth science problems, especially at the graduate level, remains underexplored. A significant barrier is the absence of benchmarks that capture the depth and contextual complexity of geoscientific reasoning. Current benchmarks often rely on synthetic datasets or simplistic figure-caption pairs, which do not adequately reflect the intricate reasoning and domain-specific insights required for real-world scientific applications. To address these gaps, we introduce MSEarth, a multimodal scientific benchmark curated from high-quality, open-access scientific publications. MSEarth encompasses the five major spheres of Earth science: atmosphere, cryosphere, hydrosphere, lithosphere, and biosphere, featuring over 7K figures with refined captions. These captions are crafted from the original figure captions and enriched with discussions and reasoning from the papers, ensuring the benchmark captures the nuanced reasoning and knowledge-intensive content essential for advanced scientific tasks. MSEarth supports a variety of tasks, including scientific figure captioning, multiple choice questions, and open-ended reasoning challenges. By bridging the gap in graduate-level benchmarks, MSEarth provides a scalable and high-fidelity resource to enhance the development and evaluation of MLLMs in scientific reasoning. The benchmark is publicly available to foster further research and innovation in this field. Resources related to this benchmark can be found at https://huggingface.co/MSEarth and https://github.com/xiangyu-mm/MSEarth.