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An Agentic Framework Using Rules and LLMs for Embedding and Annotating Descriptive Document Layouts: A Plant Science Use Case

A new agentic framework combining rule-based parsers and large language models (LLMs) extracted 55,737 botanical trait annotations across 4,961 species from three regional datasets, averaging 9.1 traits per species. The system, proposed in an arXiv preprint (2608.14587v1), used OCR, segmentation, and LLM-based enrichment, which improved coverage for 75% of traits and increased total annotations by 59%, demonstrating robust scalability for plant science data extraction.

read1 min views5 publishedAug 18, 2026

arXiv:2608.14587v1 Announce Type: new Abstract: Background: Recent advances in information retrieval (IR) leverage both dense and sparse representations, large language models (LLMs), and specialized retrieval models to improve ranking accuracy, relevance, and cross-lingual performance. Complementary techniques such as passage indexing, document layout analysis, and semantic knowledge representation further enhance retrieval effectiveness by capturing fine-grained contextual and structural information. Emerging agentic LLM frameworks extend these capabilities by enabling planning, iterative reasoning, tool use, and multi-agent collaboration, thereby broadening applications across diverse domains. These frameworks also emphasize rigorous evaluation, ethical considerations, and trustworthiness, ensuring responsible deployment in real-world settings. We propose a modular, agent-based pipeline for botanical trait extraction. Optical character recognition (OCR) converts PDFs into machine-readable text, while segmentation and indexing organize content by genus and species. Rule-based parsers extract structured botanical traits, and ensembles of large language models (LLMs) expand trait vocabularies and resolve ambiguities. This approach ensures accurate species recognition, scalable annotation, and explainable integration of textual botanical descriptions, enabling robust and interpretable data extraction across large botanical corpora. Results: Using three regional botanical datasets, our system extracted 55,737 trait annotations across 4,961 species, averaging 9.1 traits per species. Integration of LLM-based enrichment improved coverage for 75% of traits, increasing total annotations by 59%. While the choice of OCR engine had a minor effect on species recognition, overall annotation counts remained stable, demonstrating the robustness, scalability, and reliability of the pipeline for large-scale botanical trait extraction.

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