The rapid advancement of scientific progress requires innovative tools that can accelerate knowledge discovery. Although recent AI methods, particularly large language models (LLMs), have shown promise in tasks such as hypothesis generation and experimental design, they fall short of replicating the collaborative nature of real-world scientific practices, where diverse experts work together in teams to tackle complex problems. To address the limitations, we propose an LLM-based multi-agent system, i.e., Virtual Scientists (VIRSCI), designed to mimic the teamwork inherent in scientific research. VIRSCI organizes a team of agents to collaboratively generate, evaluate, and refine research ideas. Through comprehensive experiments, we demonstrate that this multi-agent approach outperforms the state-of-the-art method in producing novel scientific ideas. We further investigate the collaboration mechanisms that contribute to its tendency to produce ideas with higher novelty, offering valuable insights to guide future research and illuminating pathways toward building a robust system for autonomous scientific discovery. The code is available at https://github.com/open-sciencelab/Virtual-Scientists.

Seed science is essential for modern agriculture, directly influencing crop yields and global food security. However, challenges such as interdisciplinary complexity and high costs with limited returns hinder progress, leading to a shortage of experts and insufficient technological support. While large language models (LLMs) have shown promise across various fields, their application in seed science remains limited due to the scarcity of digital resources, complex gene-trait relationships, and the lack of standardized benchmarks. To address this gap, we introduce SeedBench—the first multi-task benchmark specifically designed for seed science. Developed in collaboration with domain experts, SeedBench focuses on seed breeding and simulates key aspects of modern breeding processes. We conduct a comprehensive evaluation of 26 leading LLMs, encompassing proprietary, open-source, and domain-specific fine-tuned models. Our findings not only highlight the substantial gaps between the power of LLMs and the real-world seed science problems, but also make a foundational step for research on LLMs for seed design.

Large language models (LLMs) commonly struggle with specialized or emerging topics which are rarely seen in the training corpus. Graph-based retrieval-augmented generation (GraphRAG) addresses this by structuring domain knowledge as a graph for dynamic retrieval. However, existing pipelines involve complex engineering workflows, making it difficult to isolate the impact of individual components. It is also challenging to evaluate the retrieval effectiveness due to the overlap between the pretraining and evaluation datasets. In this work, we introduce ROGRAG, a Robustly Optimized GraphRAG framework. Specifically, we propose a multi-stage retrieval mechanism that integrates dual-level with logic form retrieval methods to improve retrieval robustness without increasing computational cost. To further refine the system, we incorporate various result verification methods and adopt an incremental database construction approach. Through extensive ablation experiments, we rigorously assess the effectiveness of each component. Our implementation includes comparative experiments on SeedBench, where Qwen2.5-7B-Instruct initially underperformed. ROGRAG significantly improves the score from 60.0% to 75.0% and outperforms mainstream methods. Experiments on domain-specific datasets reveal that dual-level retrieval enhances fuzzy matching, while logic form retrieval improves structured reasoning, highlighting the importance of multi-stage retrieval. ROGRAG is released as an open-source resource https://github.com/tpoisonooo/ROGRAG and supports installation with pip.

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.