Tree-of-Ideas: Automated Research Ideation via Cross-Trajectory Reasoning over Scholarly Evolution

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.

Large language models have made research ideation increasingly accessible, yet effective idea development requires more than generating candidate directions. Researchers must ground a problem in current literature, identify meaningful bottlenecks, differentiate from existing solutions, and evaluate risks before committing to implementation. We present ResearchStudio-Idea as a reusable skill suite for this first mile of research ideation. The suite includes Paper-Search, a standalone multi-source literature search skill; Scoop-Check, a standalone prior-art collision checker for novelty claims; and IdeaSpark, the end-to-end skill that composes evidence grounding, pattern-guided generation, collision retrieval, audit, and idea-card rendering into one workflow. IdeaSpark is constructed from a corpus of 1,947 machine learning conference papers collected from ICLR, ICML, and NeurIPS between 2021 and 2025, including Oral papers, a separately tracked high-citation subset, and rejected submissions. Analysis of these outcomes reveals 31 recurring ideation sub-patterns, consolidated into 15 reusable ideation patterns. Each pattern is operationalized as a structured card containing research contexts, bottleneck types, differentiation strategies, supporting precedents, and common failure modes. Given a research problem and an evidence bundle, IdeaSpark evaluates evidence readiness, reconstructs the surrounding research context, identifies unresolved bottlenecks, selects relevant patterns, instantiates one candidate direction, retrieves potentially conflicting prior work, and performs outcome-informed auditing. This workflow transforms reusable ideation patterns into traceable research proposals. Blind automated-judge evaluations show that IdeaSpark consistently produces stronger research proposals than no-skill and generic-skill baselines while maintaining competitive novelty.

Research idea generation is the innovation-driving step of automated scientific research. Recently, large language models (LLMs) have shown potential for automating idea generation at scale. However, existing methods mainly condition LLMs on eliciting idea generation through static retrieval of relevant literature or complex prompt engineering, without discarding the structural relations among references. We propose Graphs of Research (GoR), a supervised fine-tuning method that extracts a 2-hop reference neighborhood for each seed paper, derives the relations among those references from citation position, frequency, predecessor links, and publication time, and organizes them into a paper-evolution directed acyclic graph (DAG). We construct an automated extraction pipeline that draws data from five major ML/NLP venues, comprising 498/50/50 train/validation/test seed papers and approximately 7,600 cited references. Qwen2.5-7B-Instruct-1M is fine-tuned on a structured-text prompt that includes the citation graph, edge signals, reference information, and task definition to predict the idea for the seed paper. Across head-to-head LLM-judge tournaments against gpt-4o-driven baselines, GoR-SFT achieves SOTA, demonstrating the effectiveness of citation-evolution graphs as supervision signal for LLM-based idea generation. We hope that this reduces the barrier for citation evolution graphs as a supervision, accelerating automated scientific innovation.