Structured Fine-Tuning of Contextual Embeddings for Effective Biomedical Retrieval

Abstract

Biomedical literature retrieval has greatly benefited from recent advances in neural language modeling. In particular, fine-tuning pretrained contextual language models has shown impressive results in recent biomedical retrieval evaluation campaigns. Nevertheless, current approaches neglect the inherent structure available from biomedical abstracts, which are (often explicitly) organised into semantically coherent sections such as background, methods, results, and conclusions. In this paper, we investigate the suitability of leveraging biomedical abstract sections for fine-tuning pretrained contextual language models at a finer granularity. Our results on two TREC biomedical test collections demonstrate the effectiveness of the proposed structured fine-tuning regime in contrast to a standard fine-tuning that does not leverage structure. Through an ablation study, we show that models fine-tuned on individual sections are able to capture potentially useful word contexts that may be otherwise ignored by structure-agnostic models.