Automated generation of research workflows from academic papers: a full-text mining framework

Abstract

The automated generation of research workflows is essential for improving the reproducibility of research and accelerating the paradigm of “AI for Science”. However, existing methods typically extract merely fragmented procedural components and thus fail to capture complete research workflows. To address this gap, we propose an end-to-end framework that generates comprehensive, structured research workflows by mining full-text academic papers. As a case study in the Natural Language Processing (NLP) domain, our paragraph-centric approach first employs Positive-Unlabeled (PU) Learning with SciBERT to identify workflow-descriptive paragraphs, achieving an F₁-score of 0.9772. Subsequently, we utilize Flan-T5 with prompt learning to generate workflow phrases from these paragraphs, yielding ROUGE-1, ROUGE-2, and ROUGE-L scores of 0.4543, 0.2877, and 0.4427, respectively. These phrases are then systematically categorized into data preparation, data processing, and data analysis stages using ChatGPT with few-shot learning, achieving a classification precision of 0.958. By mapping categorized phrases to their document locations in the documents, we finally generate readable visual flowcharts of the entire research workflows. This approach facilitates the analysis of workflows derived from an NLP corpus and reveals key methodological shifts over the past two decades, including the increasing emphasis on data analysis and the transition from feature engineering to ablation studies. Our work offers a validated technical framework for automated workflow generation, along with a novel, process-oriented perspective for the empirical investigation of evolving scientific paradigms. Source code and data are available at: h ttps://github.com/ZH-heng/research_workflow.