Tao Chen

Haonan He, Yuchen Ren, Yining Tang et al.

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.

Yuchen Ren, Wenwei Han, Qianyuan Zhang et al.

As key elements within the central dogma, DNA, RNA, and proteins play crucial roles in maintaining life by guaranteeing accurate genetic expression and implementation. Although research on these molecules has profoundly impacted fields like medicine, agriculture, and industry, the diversity of machine learning approaches-from traditional statistical methods to deep learning models and large language models-poses challenges for researchers in choosing the most suitable models for specific tasks, especially for cross-omics and multi-omics tasks due to the lack of comprehensive benchmarks. To address this, we introduce the first comprehensive multi-omics benchmark COMET (Benchmark for Biological COmprehensive Multi-omics Evaluation Tasks and Language Models), designed to evaluate models across single-omics, cross-omics, and multi-omics tasks. First, we curate and develop a diverse collection of downstream tasks and datasets covering key structural and functional aspects in DNA, RNA, and proteins, including tasks that span multiple omics levels. Then, we evaluate existing foundational language models for DNA, RNA, and proteins, as well as the newly proposed multi-omics method, offering valuable insights into their performance in integrating and analyzing data from different biological modalities. This benchmark aims to define critical issues in multi-omics research and guide future directions, ultimately promoting advancements in understanding biological processes through integrated and different omics data analysis.

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.

Kun Chen, Tao Chen, Peng Ye et al.

Data assimilation is a vital component in modern global medium-range weather forecasting systems to obtain the best estimation of the atmospheric state by combining the short-term forecast and observations. Recently, AI-based data assimilation approaches have attracted increasing attention for their significant advantages over traditional techniques in terms of computational consumption. However, existing AI-based data assimilation methods can only handle observations with a specific resolution, lacking the compatibility and generalization ability to assimilate observations with other resolutions. Considering that complex real-world observations often have different resolutions, we propose the \textit{\textbf{Fourier Neural Processes}} (FNP) for \textit{arbitrary-resolution data assimilation} in this paper. Leveraging the efficiency of the designed modules and flexible structure of neural processes, FNP achieves state-of-the-art results in assimilating observations with varying resolutions, and also exhibits increasing advantages over the counterparts as the resolution and the amount of observations increase. Moreover, our FNP trained on a fixed resolution can directly handle the assimilation of observations with out-of-distribution resolutions and the observational information reconstruction task without additional fine-tuning, demonstrating its excellent generalization ability across data resolutions as well as across tasks.