SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-Learning

Zifeng Wang, Cao Xiao, Jimeng Sun

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Clinical trials are essential to drug development but time-consuming, costly, and prone to failure. Accurate trial outcome prediction based on historical trial data promises better trial investment decisions and more trial success. Existing trial outcome prediction models were not designed to model the relations among similar trials, capture the progression of features and designs of similar trials, or address the skewness of trial data which causes inferior performance for less common trials.To fill the gap and provide accurate trial outcome prediction, we propose Sequential Predictive mOdeling of clinical Trial outcome (SPOT) that first identifies trial topics to cluster the multisourced trial data into relevant trial topics. It then generates trial embeddings and organizes them by topic and time to create clinical trial sequences. With the consideration of each trial sequence as a task, it uses a meta-learning strategy to achieve a point where the model can rapidly adapt to new tasks with minimal updates. In particular, the topic discovery module enables a deeper understanding of the underlying structure of the data, while sequential learning captures the evolution of trial designs and outcomes. This results in predictions that are not only more accurate but also more interpretable, taking into account the temporal patterns and unique characteristics of each trial topic. We demonstrate that SPOT wins over the prior methods by a significant margin on trial outcome benchmark data: with a 21.5% lift on phase I, an 8.9% lift on phase II, and a 5.5% lift on phase III trials in the metric of the area under precision-recall curve (PR-AUC). Code is available at https://github.com/RyanWangZf/PyTrial.

Original languageEnglish (US)
Title of host publicationACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
PublisherAssociation for Computing Machinery
ISBN (Electronic)9798400701269
DOIs
StatePublished - Sep 3 2023
Event14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2023 - Houston, United States
Duration: Sep 3 2023Sep 6 2023

Publication series

NameACM-BCB 2023 - 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Conference

Conference14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2023
Country/TerritoryUnited States
CityHouston
Period9/3/239/6/23

ASJC Scopus subject areas

  • Computer Science Applications
  • Software
  • Biomedical Engineering
  • Health Informatics

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