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Full-Text Articles in Bioinformatics
Language Models For Rare Disease Information Extraction: Empirical Insights And Model Comparisons, Shashank Gupta
Language Models For Rare Disease Information Extraction: Empirical Insights And Model Comparisons, Shashank Gupta
Theses and Dissertations--Computer Science
End-to-end relation extraction (E2ERE) is a crucial task in natural language processing (NLP) that involves identifying and classifying semantic relationships between entities in text. This thesis compares three paradigms for end-to-end relation extraction (E2ERE) in biomedicine, focusing on rare diseases with discontinuous and nested entities. We evaluate Named Entity Recognition (NER) to Relation Extraction (RE) pipelines, sequence-to-sequence models, and generative pre-trained transformer (GPT) models using the RareDis information extraction dataset. Our findings indicate that pipeline models are the most effective, followed closely by sequence-to-sequence models. GPT models, despite having eight times as many parameters, perform worse than sequence-to-sequence models and …