Toward Auto-Research: Mining Falsifiable Research Ideas from Paper Knowledge Graphs with Categorical Structure

Abstract

Automated research-idea generation systems built on large language models (LLMs) share a structural weakness: they reduce ideation to free-text recombination, random paper pairing, or embedding-similarity retrieval. The three approaches fail in the same way: each treats a paper as a flat object, a string or a vector, and so quotients away the typed problem-method-metric-claim arrows a researcher actually uses when reasoning about a cross-domain analogy. We recover the missing structure with the minimal piece of category theory that a typed graph alone does not provide: composition, together with identity arrows, which makes it possible to ask whether a proposed analogy preserves relation chains. Concretely, each paper $p$ is modelled as a small category $C_p$ whose objects are extracted typed research entities and whose morphisms are the relations the paper asserts; a cross-paper bridge from $p$ to $q$ is then a partial functor candidate $F: C_p -> C_q$ that preserves object kinds and covered relation classes. We instantiate the model as a three-layer algorithm: categorical signature clustering, a functor-preservation gate, and a six-axis LLM plausibility judge. Evaluated on a corpus of tens of thousands of full-text-parsed papers under four ablation conditions, the categorical gate filters cross-domain candidates at roughly a 17:1 ratio while the quantitative-falsifier rate of accepted ideas stays above 83% throughout; every rejected candidate is retained with its per-axis rationale, so the gate doubles as a logging layer rather than a silent filter.