# Automated Generation of Research Workflows from Academic Papers: A Full-text Mining Framework

arXiv: https://arxiv.org/abs/2509.12955 · HTML: https://mlsanity.com/paper/2509.12955/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 47 references that are in the map.
- First posted on arXiv 16 Sep 2025.

## Builds on (most cited first, 17 of 17)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Scaling Instruction-Finetuned Language Models](https://mlsanity.com/paper/2210.11416/) (2022)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [PEGASUS: Pre-training with Extracted Gap-sentences for Abstractive Summarization](https://mlsanity.com/paper/1912.08777/) (2019)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [DialoGPT: Large-Scale Generative Pre-training for Conversational Response Generation](https://mlsanity.com/paper/1911.00536/) (2019)
- [Data Boost: Text Data Augmentation Through Reinforcement Learning Guided Conditional Generation](https://mlsanity.com/paper/2012.02952/) (2020)
- [MVP: Multi-task Supervised Pre-training for Natural Language Generation](https://mlsanity.com/paper/2206.12131/) (2022)
- [Annotating and Extracting Synthesis Process of All-Solid-State Batteries from Scientific Literature](https://mlsanity.com/paper/2002.07339/) (2020)
- [Prompt-Learning for Short Text Classification](https://mlsanity.com/paper/2202.11345/) (2022)
- [PcMSP: A Dataset for Scientific Action Graphs Extraction from Polycrystalline Materials Synthesis Procedure Text](https://mlsanity.com/paper/2210.12401/) (2022)
- [Automatic Recognition and Classification of Future Work Sentences from Academic Articles in a Specific Domain](https://mlsanity.com/paper/2212.13860/) (2022)

## Abstract (arXiv)

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: https://github.com/ZH-heng/research_workflow.