Shuang Gu

Yankai Jiang, Wenjie Lou, Lilong Wang et al.

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.

Haoran Sun, Yankai Jiang, Zhenyu Tang et al.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.