Computational conceptual history of scientific concepts: From early digital methods to LLMs

Large language models (LLMs) encode rich concept-like information, but represent it implicitly through distributed statistical associations rather than as explicit, structured, compositional concepts. Consequently, concept-level structure is typically \emph{found} rather than \emph{designed}: it is recovered after training through probing or dictionary learning, with no architectural guarantee of stability, compositionality, controllability, or alignment with human conceptual organization. We organize concept-aware interventions along two dimensions: whether concept structure is internally induced or externally grounded, and the stage of the pipeline where it is introduced. This taxonomy reveals three broad patterns: inference-time approaches remain comparatively underexplored, related ideas have developed largely in isolation across pipeline stages, and externally grounded methods span the entire pipeline despite often being described under different terminology. Together, these observations motivate moving beyond recovering concept-like structure from trained models toward designing LLMs with explicit conceptual representations.

This discussion paper reflects on how quantitative approaches to historical linguistics interact with dataset properties. Drawing on two worked examples, we examine English data using quad-based concept modelling of Early Modern English discourse in EEBO-TCP (c. 1470s-1690s; 765M words) alongside SynFlow analysis of scientific writing in Royal Society Corpus 6.0.4 (1750-1799; drawn from a 78.6M-token open corpus). Through parallel comparison, the paper explores how each approach operationalises concepts, the data assumptions they entail, and the diachronic interpretations they support. We argue that comparative methodological reflection clarifies the limits of purely lexical, frequency-based approaches and highlights how dataset structure shapes the kinds of semantic change that quantitative methods can reliably detect.

Large Language Models (LLMs) are increasingly used to guide research methodology, yet their default methodological tendencies under minimal prompting remain unclear. Here, we prompt GPT-5.1, Gemini 3 Pro, and DeepSeek-V3.2 with an LLM-extracted research question from each of 1,000 recent arXiv computer-science papers and compare the resulting methodology suggestions against a paper-derived experimental inventory. Since we provide only the research question, the differences we measure reflect initial suggestions and not how optimal those suggestions are. We extract structured method features from both sources, map them into a shared taxonomy, and quantify divergence across multiple taxonomy dimensions including model provider, dataset task type, and evaluation metric type. The strongest imbalance appears in provider choice, with Jensen-Shannon divergence about 3-5x larger than any other taxonomy dimension. Other/Academic single-occurrence models are underrepresented by 23-24 percentage points, while reused academic/community models are slightly overrepresented (4-6pp). LLMs also suggest a much narrower range of methods overall: the effective number of model entities contracts from 1,232 to 59-96, and inter-LLM rank correlations (0.55-0.68) generally exceed LLM-to-paper correlations (0.33-0.56), so the distortions are largely shared across models. Popularity baselines, BM25 retrieval calibration, and paper-level similarity tests confirm that the outputs are query-specific responses, but filtered through a narrower set of options. Researchers who rely on LLM suggestions without cross-checking therefore risk narrowing their methodological search space toward a more concentrated default.