Towards Automatic Evolution Tree Generation from Citation Graphs

Existing research infrastructure is fundamentally document-centric, providing citation links between papers but lacking explicit representations of methodological evolution. In particular, it does not capture the structured relationships that explain how and why research methods emerge, adapt, and build upon one another. With the rise of AI-driven research agents as a new class of consumers of scientific knowledge, this limitation becomes increasingly consequential, as such agents cannot reliably reconstruct method evolution topologies from unstructured text. We introduce Intern-Atlas, a methodological evolution graph that automatically identifies method-level entities, infers lineage relationships among methodologies, and captures the bottlenecks that drive transitions between successive innovations. Built from 1,030,314 papers spanning AI conferences, journals, and arXiv preprints, the resulting graph comprises 9,410,201 semantically typed edges, each grounded in verbatim source evidence, forming a queryable causal network of methodological development. To operationalize this structure, we further propose a self-guided temporal tree search algorithm for constructing evolution chains that trace the progression of methods over time. We evaluate the quality of the resulting graph against expert-curated ground-truth evolution chains and observe strong alignment. In addition, we demonstrate that Intern-Atlas enables downstream applications in idea evaluation and automated idea generation. We position methodological evolution graphs as a foundational data layer for the emerging automated scientific discovery.

Effective research ideation requires moving beyond a static understanding of prior work to trace how research problems and solutions evolve across the literature. Existing methods either treat papers as unstructured context or model scholarly evolution as isolated citation chains, overlooking interactions among research trajectories. We propose Tree-of-Ideas (ToI), a two-stage framework. EvoTrace reconstructs branching scholarly trajectories from citations, tracking evolving methods, resolved problems, and gaps. EvoAgent then reasons across trajectories to identify convergent problems and complementary solutions, generating grounded research ideas. Across six AI research topics, ToI achieves the highest score among automatic methods (6.27 vs. 5.36 for the strongest baseline on a 10-point scale), with strong Novelty (6.36) and Groundedness (7.00). Also, its score approaches that of human-paper references (6.29), demonstrating the value of cross-path evolutionary reasoning.

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.