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Probing Biomedical Embeddings from Language Models

2019/04/03 by Qiao Jin, Jin, Qiao, Bhuwan Dhingra +5 · 1 citation
Computer Science · #Computation and Language (cs.CL) #FOS: Computer and information sciences #Natural Language Processing Techniques #Text Readability and Simplification #Topic Modeling

paper · pdf · doi:10.48550/arxiv.1904.02181

openalex publication_date 2019/04/03 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

Contextualized word embeddings derived from pre-trained language models (LMs) show significant improvements on downstream NLP tasks. Pre-training on domain-specific corpora, such as biomedical articles, further improves their performance. In this paper, we conduct probing experiments to determine what additional information is carried intrinsically by the in-domain trained contextualized embeddings. For this we use the pre-trained LMs as fixed feature extractors and restrict the downstream task models to not have additional sequence modeling layers. We compare BERT, ELMo, BioBERT and BioELMo, a biomedical version of ELMo trained on 10M PubMed abstracts. Surprisingly, while fine-tuned BioBERT is better than BioELMo in biomedical NER and NLI tasks, as a fixed feature extractor BioELMo outperforms BioBERT in our probing tasks. We use visualization and nearest neighbor analysis to show that better encoding of entity-type and relational information leads to this superiority.

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