Lei Bai

Shuizhou Chen, Lang Yu, Kedu Jin et al.

Virtual cell models aim to enable in silico experimentation by predicting how cells respond to genetic, chemical, or cytokine perturbations from single-cell measurements. In practice, however, large-scale perturbation prediction remains constrained by three coupled bottlenecks: inefficient training and inference pipelines, unstable modeling in high-dimensional sparse expression space, and evaluation protocols that overemphasize reconstruction-like accuracy while underestimating biological fidelity. In this work we present a specialized large-scale foundation model SCALE for virtual cell perturbation prediction that addresses the above limitations jointly. First, we build a BioNeMo-based training and inference framework that substantially improves data throughput, distributed scalability, and deployment efficiency, yielding 12.51* speedup on pretrain and 1.29* on inference over the prior SOTA pipeline under matched system settings. Second, we formulate perturbation prediction as conditional transport and implement it with a set-aware flow architecture that couples LLaMA-based cellular encoding with endpoint-oriented supervision. This design yields more stable training and stronger recovery of perturbation effects. Third, we evaluate the model on Tahoe-100M using a rigorous cell-level protocol centered on biologically meaningful metrics rather than reconstruction alone. On this benchmark, our model improves PDCorr by 12.02% and DE Overlap by 10.66% over STATE. Together, these results suggest that advancing virtual cells requires not only better generative objectives, but also the co-design of scalable infrastructure, stable transport modeling, and biologically faithful evaluation.

Xiaoyu Zhan, Wenxuan Huang, Hao Sun et al.

Recent advances in Multimodal Large Language Models (MLLMs) have significantly improved 2D visual understanding, prompting interest in their application to complex 3D reasoning tasks. However, it remains unclear whether these models can effectively capture the detailed spatial information required for robust real-world performance, especially cross-view consistency, a key requirement for accurate 3D reasoning. Considering this issue, we introduce Viewpoint Learning, a task designed to evaluate and improve the spatial reasoning capabilities of MLLMs. We present the Viewpoint-100K dataset, consisting of 100K object-centric image pairs with diverse viewpoints and corresponding question-answer pairs. Our approach employs a two-stage fine-tuning strategy: first, foundational knowledge is injected to the baseline MLLM via Supervised Fine-Tuning (SFT) on Viewpoint-100K, resulting in significant improvements across multiple tasks; second, generalization is enhanced through Reinforcement Learning using the Group Relative Policy Optimization (GRPO) algorithm on a broader set of questions. Additionally, we introduce a hybrid cold-start initialization method designed to simultaneously learn viewpoint representations and maintain coherent reasoning thinking. Experimental results show that our approach significantly activates the spatial reasoning ability of MLLM, improving performance on both in-domain and out-of-domain reasoning tasks. Our findings highlight the value of developing foundational spatial skills in MLLMs, supporting future progress in robotics, autonomous systems, and 3D scene understanding.

Yuanyi Song, Pumeng Lyu, Ben Fei et al.

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.

Wanghan Xu, Xiangyu Zhao, Yuhao Zhou et al.

Advancements in Large Language Models (LLMs) drive interest in scientific applications, necessitating specialized benchmarks such as Earth science. Existing benchmarks either present a general science focus devoid of Earth science specificity or cover isolated subdomains, lacking holistic evaluation. Furthermore, current benchmarks typically neglect the assessment of LLMs' capabilities in open-ended scientific exploration. In this paper, we present a comprehensive and professional benchmark for the Earth sciences, designed to evaluate the capabilities of LLMs in scientific exploration within this domain, spanning from fundamental to advanced levels. Leveraging a corpus of 100,000 research papers, we first construct two Question Answering (QA) datasets: Earth-Iron, which offers extensive question coverage for broad assessment, and Earth-Silver, which features a higher level of difficulty to evaluate professional depth. These datasets encompass five Earth spheres, 114 disciplines, and 11 task categories, assessing foundational knowledge crucial for scientific exploration. Most notably, we introduce Earth-Gold with new metrics, a dataset comprising open-ended multi-turn dialogues specifically designed to evaluate the advanced capabilities of LLMs in scientific exploration, including methodology induction, limitation analysis, and concept proposal. Extensive experiments reveal limitations in 11 leading LLMs across different domains and tasks, highlighting considerable room for improvement in their scientific exploration capabilities. The benchmark is available on https://huggingface.co/ai-earth .

Xiangyu Zhao, Wanghan Xu, Bo Liu et al.

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 289K 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.

Xiaoyu Yue, Zidong Wang, Zeyu Lu et al.

Conventional class-guided diffusion models generally succeed in generating images with correct semantic content, but often struggle with texture details. This limitation stems from the usage of class priors, which only provide coarse and limited conditional information. To address this issue, we propose Diffusion on Diffusion (DoD), an innovative multi-stage generation framework that first extracts visual priors from previously generated samples, then provides rich guidance for the diffusion model leveraging visual priors from the early stages of diffusion sampling. Specifically, we introduce a latent embedding module that employs a compression-reconstruction approach to discard redundant detail information from the conditional samples in each stage, retaining only the semantic information for guidance. We evaluate DoD on the popular ImageNet-$256 \times 256$ dataset, reducing 7$\times$ training cost compared to SiT and DiT with even better performance in terms of the FID-50K score. Our largest model DoD-XL achieves an FID-50K score of 1.83 with only 1 million training steps, which surpasses other state-of-the-art methods without bells and whistles during inference.

Peilin Feng, Zhutao Lv, Junyan Ye et al.

Earth observation (EO) is essential for understanding the evolving states of the Earth system. Although recent MLLMs have advanced EO research, they still lack the capability to tackle complex tasks that require multi-step reasoning and the use of domain-specific tools. Agent-based methods offer a promising direction, but current attempts remain in their infancy, confined to RGB perception, shallow reasoning, and lacking systematic evaluation protocols. To overcome these limitations, we introduce Earth-Agent, the first agentic framework that unifies RGB and spectral EO data within an MCP-based tool ecosystem, enabling cross-modal, multi-step, and quantitative spatiotemporal reasoning beyond pretrained MLLMs. Earth-Agent supports complex scientific tasks such as geophysical parameter retrieval and quantitative spatiotemporal analysis by dynamically invoking expert tools and models across modalities. To support comprehensive evaluation, we further propose Earth-Bench, a benchmark of 248 expert-curated tasks with 13,729 images, spanning spectrum, products and RGB modalities, and equipped with a dual-level evaluation protocol that assesses both reasoning trajectories and final outcomes. We conduct comprehensive experiments varying different LLM backbones, comparisons with general agent frameworks, and comparisons with MLLMs on remote sensing benchmarks, demonstrating both the effectiveness and potential of Earth-Agent. Earth-Agent establishes a new paradigm for EO analysis, moving the field toward scientifically grounded, next-generation applications of LLMs in Earth observation.

Xiaoyu Yue, Zidong Wang, Yuqing Wang et al.

Recent studies have demonstrated the importance of high-quality visual representations in image generation and have highlighted the limitations of generative models in image understanding. As a generative paradigm originally designed for natural language, autoregressive models face similar challenges. In this work, we present the first systematic investigation into the mechanisms of applying the next-token prediction paradigm to the visual domain. We identify three key properties that hinder the learning of high-level visual semantics: local and conditional dependence, inter-step semantic inconsistency, and spatial invariance deficiency. We show that these issues can be effectively addressed by introducing self-supervised objectives during training, leading to a novel training framework, Self-guided Training for AutoRegressive models (ST-AR). Without relying on pre-trained representation models, ST-AR significantly enhances the image understanding ability of autoregressive models and leads to improved generation quality. Specifically, ST-AR brings approximately 42% FID improvement for LlamaGen-L and 49% FID improvement for LlamaGen-XL, while maintaining the same sampling strategy.

Zijie Guo, Jiong Wang, Fenghua Ling et al.

Scientific progress in Earth science depends on integrating data across the planet's interconnected spheres. However, the accelerating volume and fragmentation of multi-sphere knowledge and data have surpassed human analytical capacity. This creates a major bottleneck for discovery, especially in climate science. To address this challenge, we introduce EarthLink, the first self-evolving AI agent system designed as an interactive "copilot" for Earth scientists. Through natural language interaction, EarthLink automates the entire research workflow by integrating planning, code execution, data analysis, and physical reasoning into a unified process that directly addresses this limitation. Beyond efficiency, it exhibits human-like cross-disciplinary analytical ability and achieves proficiency comparable to a junior researcher in expert evaluations on core large-scale climate tasks, including model-observation comparison and climate change understanding. When tasked with an open scientific problem, specifically the discovery of precursors of the Atlantic Niño, EarthLink autonomously developed a research strategy, identified sources of predictability, verified its hypotheses with available data, and proposed a physically consistent mechanism. These emerging capabilities enable a new human-AI research paradigm. Scientists can focus on value and result judgments, while AI systems handle complex data analysis and knowledge integration. This accelerates the pace and breadth of discovery in Earth sciences. The system is accessible at our website https://earthlink.intern-ai.org.cn.