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  • https://doi.org/10.7490/f1000research.1119583.1Copy DOI Icon

Transforming unstructured biomedical texts with large language models

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Abstract

Creating biological knowledge bases and ontologies relies on time-consuming curation. Newly-emerging approaches driven by artificial intelligence and natural language processing can assist curators in populating these knowledge bases, but current approaches rely on extensive training data and are unable to populate arbitrarily complex nested knowledge schemas. We have developed Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a schema. Given a user-defined schema and an input text, SPIRES recursively queries GPT-3+ to obtain responses matching the schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. SPIRES may be applied to varied tasks, including extraction of cellular signaling pathways, disease treatments, drug mechanisms, and chemical to disease causation graphs. This approach offers easy customization, flexibility, and the ability to perform new tasks in the absence of any additional training data. SPIRES supports a strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM.

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