How Genentech extracted information for clinical trial analytics with Snorkel Flow

Unlocking the value of clinical trial protocol data

Scientists at Genentech and other life sciences companies write and perform thousands of Clinical Trial Protocols (CTPs) every year. These CTPs are complex documents that describe the plan for a clinical trial, including the objectives, the methodologies, and the population for the trial. There’s a lot of useful information in these CTPs that study design teams can reuse to reduce trial times and costs, increase recruitment of diverse patient populations and reduce the dropout rate of patients in a trial. If study teams have access to this data, their net outcome is a reduction in cost for drug development.

Unfortunately, this information is buried within thousands of dense documents. Genentech wanted to use machine learning to automate extracting certain data from CTPs. They tried various approaches, including off-the-shelf NLP libraries, unsupervised learning techniques, and domain-adapted language models but failed to yield meaningful business impact at scale. They realized that they needed to focus on iterating and improving on their training data to deliver better results.

To do this, Genentech needed a large team with the domain experience to annotate CTPs by hand. For Genentech, manual labeling wasn’t an option because it did not scale — they estimated that it would take 140 experts over a month to label a dataset of 340k CTPs needed to build their AI applications.

Genentech replaced months of manual data labeling using Snorkel Flow

Genentech started by using Snorkel Flow to build an AI application to extract 21 CMS Chronic Condition Entities from internal and external clinical trial protocols. Their application consisted of a named entity recognition NER model, an entity linking model, and a rules-based relationship extractor. Genentech leveraged programmatic labeling and a data-centric AI development approach to yield accurate inclusion-exclusion criteria that clinical scientists and study design teams used for analysis and data-informed protocol design.

The data science team at Genentech built their end-to-end application pipeline in a few weeks achieving 98% accuracy with the help of Snorkel’s guided error analysis.

Snorkel Flow made the [clinical trial analytics] pipeline development adrag and drop experience. Michael DAndrea, Principal Data Scientist, Genentech

Genentech also used Snorkel Flow to build an AI application that estimated participant burden from CTPs. Their AI application identified and extracted procedure names from Schedule of Assessment tables and classified them into one of 8 categories. Since their data was labeled programmatically by Snorkel Flow, they were able to quickly adapt to changes in their label schema. The output data was used to harmonize terminology for clinical trial protocols across the organization.

By deploying AI applications built with Snorkel Flow Genentech estimates that they can increase recruitment for diverse populations and reduce clinical trial times costs and patient dropout rates. The combination of these outcomes will help Genentech dramatically reduce drug development costs and increase the number of drugs in their development pipeline leading to more cures.

This work was presented at the Future of Data-centric AI event hosted by Snorkel AI. Dive deeper into how Genentech used Snorkel Flow to build clinical trial analysis pipelines in this article.