Trial2Vec: Zero-Shot Clinical Trial Document Similarity Search using Self-Supervision

Zifeng Wang, Jimeng Sun

Research output: Contribution to conferencePaperpeer-review

Abstract

Clinical trials are essential for drug development but are extremely expensive and time-consuming to conduct. It is beneficial to study similar historical trials when designing a clinical trial. However, lengthy trial documents and lack of labeled data make trial similarity search difficult. We propose a zero-shot clinical trial retrieval method, called Trial2Vec, which learns through self-supervision without the need for annotating similar clinical trials. Specifically, the meta-structure of trial documents (e.g., title, eligibility criteria, target disease) along with clinical knowledge (e.g., UMLS knowledge base) are leveraged to automatically generate contrastive samples. Besides, Trial2Vec encodes trial documents considering meta-structure thus producing compact embeddings aggregating multi-aspect information from the whole document. We show that our method yields medically interpretable embeddings by visualization and it gets 15% average improvement over the best baselines on precision/recall for trial retrieval, which is evaluated on our labeled 1600 trial pairs. In addition, we prove the pretrained embeddings benefit the downstream trial outcome prediction task over 240k trials.

Original languageEnglish (US)
Pages6406-6419
Number of pages14
StatePublished - 2022
Externally publishedYes
Event2022 Findings of the Association for Computational Linguistics: EMNLP 2022 - Abu Dhabi, United Arab Emirates
Duration: Dec 7 2022Dec 11 2022

Conference

Conference2022 Findings of the Association for Computational Linguistics: EMNLP 2022
Country/TerritoryUnited Arab Emirates
CityAbu Dhabi
Period12/7/2212/11/22

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Computer Science Applications
  • Information Systems

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