Ideas Have Genomes: Benchmarking Scientific Lineage Reasoning and Lineage-Grounded Idea Generation

Scientific ideation is the capacity to formulate novel and testable hypotheses from scientific evidence, and autonomous AI scientists depend on it. Existing evaluations largely assess it by asking models to generate ideas from a static, curated set of reference papers. That passive setup departs from the retrieval-and-reasoning workflow of modern AI scientists, and it becomes less discriminative as models improve. We introduce AgentIdeaBench, a multidisciplinary benchmark that evaluates scientific ideation under two matched settings, static observation and active exploration. We report matched Static-Active evaluations for 33 LLMs across 40 densely scored subfields spanning five disciplines, using a multidimensional, literature-verified scoring framework whose critics assess originality against retrieved prior art. Active exploration reveals considerably more capability headroom, and that headroom is unevenly distributed across models. Performance scales about twice as fast as under static observation, and the exploration gain is capability-gated, favoring the strongest models over the weakest. The gain reflects better grounding, improving feasibility, clarity, and specificity while leaving measured originality unchanged under our critics. We further explore Scientific World Modeling, a generation-time loop that refines a draft hypothesis through structured thought experiments. It benefits mid-capability models, and its impact diminishes among frontier models that appear to have internalized such reasoning patterns already. AgentIdeaBench gives future work on scientific ideation a measurement basis suited to the agent era.

Generating novel, feasible, and high-quality research ideas is an important yet challenging task in scientific discovery. Recent Large Language Model (LLM)-based methods often ground idea generation with retrieved literature, but the retrieved evidence is usually provided as flat text, such as titles, abstracts, or summaries. Such flat contexts may contain redundant or weakly relevant information, while making cross-paper relations among problems, methods, mechanisms, and findings difficult to identify and trace. To address this challenge, we propose Graph2Idea, a knowledge graph-guided framework for retrieval-augmented scientific idea generation.Graph2Idea first retrieves papers according to the input topic, transforms them into structured knowledge triples, and dynamically constructs a target-centered knowledge graph to make literature relations explicit. It then extracts compact graph-derived contexts that retain target-relevant relational evidence while reducing noisy textual input. Based on these contexts, a two-stage generation process first identifies promising research directions and then guides the LLM to synthesize candidate ideas from graph-grounded evidence. Experiments on a scientific idea generation benchmark show that Graph2Idea outperforms representative baselines under the automatic evaluation protocol. Compared with the strongest baseline scores, it improves Novelty from 0.45 to 0.52, Quality from 0.24 to 0.29, and Feasibility from 0.22 to 0.28. These results suggest that graph-structured evidence helps LLMs generate research ideas through more explicit, compact, and traceable recombination of prior scientific knowledge.

Scientific ideation unfolds over multiple stages, including literature search, paper reading, tool use, claim checking, cross-paper synthesis, brainstorming, rejection of weak directions, and iterative writing. Yet most existing resources capture isolated components or final artifacts rather than the process connecting them. We introduce IdeaTrail, a dataset of 1,170 multi-turn trajectories for scientific ideation and proposal generation. Each trajectory follows a research process from evidence gathering to either idea selection or proposal construction, jointly recording tool use, acquired evidence, intermediate artifacts, and reasoning. IdeaTrail is synthesized from human-selected research papers and proposal artifacts through a Generator--Advisor loop. The Generator produces the visible sequence of actions, observations, and artifact edits, while the Advisor uses the full generation context to check grounding, causal order, naturalness, and leakage from hidden targets. This reverse-to-forward design keeps trajectories aligned with real scientific artifacts while retaining the uncertainty, evidence use, and staged convergence characteristic of research practice. IdeaTrail provides both reusable process supervision and a general recipe for constructing scientific-research-agent data.