Multi-Perspective Semantic Information Retrieval in the Biomedical Domain

TL;DR

This paper introduces a multi-perspective BERT-based approach for semantic information retrieval in the biomedical domain, addressing domain-specific challenges and demonstrating practical applications in clinical and biomedical literature search.

Contribution

It presents a novel multi-perspective sentence relevance methodology using BERT for biomedical IR and provides a live system and challenge proposal for clinical tasks.

Findings

Effective retrieval of biomedical literature using the proposed method.

Improved relevance ranking in clinical query scenarios.

Practical deployment of a biomedical IR system.

Abstract

Information Retrieval (IR) is the task of obtaining pieces of data (such as documents) that are relevant to a particular query or need from a large repository of information. IR is a valuable component of several downstream Natural Language Processing (NLP) tasks. Practically, IR is at the heart of many widely-used technologies like search engines. While probabilistic ranking functions like the Okapi BM25 function have been utilized in IR systems since the 1970's, modern neural approaches pose certain advantages compared to their classical counterparts. In particular, the release of BERT (Bidirectional Encoder Representations from Transformers) has had a significant impact in the NLP community by demonstrating how the use of a Masked Language Model trained on a large corpus of data can improve a variety of downstream NLP tasks, including sentence classification and passage re-ranking. IR Systems are also important in the biomedical and clinical domains. Given the increasing amount of scientific literature across biomedical domain, the ability find answers to specific clinical queries from a repository of millions of articles is a matter of practical value to medical professionals. Moreover, there are domain-specific challenges present, including handling clinical jargon and evaluating the similarity or relatedness of various medical symptoms when determining the relevance between a query and a sentence. This work presents contributions to several aspects of the Biomedical Semantic Information Retrieval domain. First, it introduces Multi-Perspective Sentence Relevance, a novel methodology of utilizing BERT-based models for contextual IR. The system is evaluated using the BioASQ Biomedical IR Challenge. Finally, practical contributions in the form of a live IR system for medics and a proposed challenge on the Living Systematic Review clinical task are provided.