Large-scale dataset of automatically classified rhetorical sections in scientific papers

Structured abstracts are important for biomedical literature processing, by facilitating information retrieval, text mining, and knowledge synthesis. However, a vast portion of abstracts indexed in PubMed remain unstructured, presenting a significant bottleneck for downstream text-processing workflows and applications. To resolve this limitation, we introduce Structured PubMed, a comprehensive corpus of section-labeled biomedical abstracts compiled from the complete PubMed database, encompassing over 23.2 million research-article records. The corpus is divided into two distinct subsets: a collection of 5.9 million author-structured abstracts parsed from official XML files, and an automatically labeled collection of 17.2 million originally unstructured abstracts structured via a verbatim-extraction Large Language Model pipeline. Every record is harmonized under a unified five-section schema and mapped to its original PubMed identifier, publication type, and publication date. This dataset can be utilized to train sentence-classification models, benchmark text-segmentation architectures, and perform large-scale, section-specific information extraction at an unprecedented PubMed-wide scale.

Scientific reasoning remains challenging for open-source models, largely due to the lack of high-quality scientific reasoning data. Existing datasets are often dominated by factual recall or formulaic problem solving, with limited emphasis on mechanism understanding, evidence-grounded reasoning, and hypothesis evaluation. To address this, we introduce SPARK (Scientific Paper Abstracted Reasoning sKeleton), a paper-oriented synthesis framework built on Sci-Base, a large-scale corpus of research papers spanning 10 scientific disciplines. Instead of directly converting papers into question-answer pairs, SPARK treats the claim-evidence-derivation structure of a paper as the fundamental unit of reasoning synthesis. Specifically, SPARK (1) distills each paper into a compact reasoning skeleton capturing its central claims and supporting evidence, enabling self-contained question generation, and (2) synthesizes reasoning tasks from four scientific perspectives: mechanistic reasoning, hypothesis falsification, quantitative derivation, and boundary calibration. A final consistency verification stage further removes unsupported or contradictory outputs. Using this framework, we construct Spark-234K, a scientific reasoning dataset with substantially higher difficulty and diversity than existing resources. Experiments show that Spark-234K consistently outperforms existing scientific reasoning datasets while achieving stronger performance with significantly fewer training samples.

The relentless expansion of scientific literature presents significant challenges for navigation and knowledge discovery. Within Research Information Retrieval, established tasks such as text summarization and classification remain crucial for enabling researchers and practitioners to effectively navigate this vast landscape, so that efforts have increasingly been focused on developing advanced research information systems. These systems aim not only to provide standard keyword-based search functionalities but also to incorporate capabilities for automatic content categorization within knowledge-intensive organizations across academia and industry. This study systematically evaluates the performance of off-the-shelf Large Language Models (LLMs) in analyzing scientific texts according to a given classification scheme. We utilized the hierarchical ORKG taxonomy as a classification framework, employing the FORC dataset as ground truth. We investigated the effectiveness of advanced prompt engineering strategies, namely In-Context Learning (ICL) and Prompt Chaining, and experimentally explored the influence of the LLMs' temperature hyperparameter on classification accuracy. Our experiments demonstrate that Prompt Chaining yields superior classification accuracy compared to pure ICL, particularly when applied to the nested structure of the ORKG taxonomy. LLMs with prompt chaining outperform the state-of-the-art models for domain (1st level) prediction and show even better performance for subject (2nd level) prediction compared to the older BERT model. However, LLMs are not yet able to perform well in classifying the topic (3rd level) of research areas based on this specific hierarchical taxonomy, as they only reach about 50% accuracy even with prompt chaining.