Deep Research of Deep Research: From Transformer to Agent, From AI to AI for Science

Modern science is reaching a critical inflection point. Instruments across disciplines, from particle physics and astronomy to genomics and climate modeling, now produce data of such scale, diversity, and interdependence that traditional analytical methods can no longer keep pace. This growing imbalance between data generation and data understanding signals the need for a new scientific paradigm. We propose that intelligent, human-supervised AI agents operating over deep-learning algorithms, represent the next evolution of the scientific method. Built upon large language models and multimodal learning, these agents can interpret scientific intent, design and execute analytical workflows, and ensure traceability through domain-specific languages that preserve human oversight and accountability. Particle physics, a historic incubator of computational innovation, offers the ideal testbed for this transition. At the Institute of High Energy Physics of the Chinese Academy of Sciences, the Dr. Sai system embodies this vision, a multi-agent reasoning framework deployed within collider research at the CEPC. This emerging approach does not replace human scientists but extends their cognitive reach, enabling discovery to scale with complexity and redefining how knowledge itself is produced in the age of intelligent machines. The significance of this paradigm transcends particle physics, offering a blueprint for all data-driven sciences facing the same complexity ceiling.

AI research agents now support large-scale AI-assisted scientific discovery. We examine whether AI-generated ideas broaden scientific exploration or primarily reinforce existing work. Using five agent frameworks and five large language models, we generate 219,655 ideas for different scientific fields. Across experiments, four consistent patterns emerge. First, AI-generated ideas are more concentrated than human-authored papers within the same research area. Second, they remain much closer to starting literature than later human follow-on work does. Third, AI-generated ideas align less with future human research. Last, AI-generated ideas are located in lower-impact regions of the historical scientific landscape. Overall, current AI research agents appear better suited to local elaboration than to broadening scientific exploration.

The application of Large Language Models (LLMs) in accelerating scientific discovery has garnered increasing attention, with a key focus on constructing research agents endowed with innovative capability, i.e., the ability to autonomously generate novel and significant research ideas. Existing approaches predominantly rely on sophisticated prompt engineering and lack a systematic training paradigm. To address this, we propose DeepInnovator, a training framework designed to trigger the innovative capability of LLMs. Our approach comprises two core components. (1) Standing on the shoulders of giants''. We construct an automated data extraction pipeline to extract and organize structured research knowledge from a vast corpus of unlabeled scientific literature. (2) Conjectures and refutations''. We introduce a ``Next Idea Prediction'' training paradigm, which models the generation of research ideas as an iterative process of continuously predicting, evaluating, and refining plausible and novel next idea. Both automatic and expert evaluations demonstrate that our DeepInnovator-14B significantly outperforms untrained baselines, achieving win rates of 80.53%-93.81%, and attains performance comparable to that of current leading LLMs. This work provides a scalable training pathway toward building research agents with genuine, originative innovative capability, and will open-source the dataset to foster community advancement. Source code and data are available at: https://github.com/HKUDS/DeepInnovator.