Text Mining to Identify and Extract Novel Disease Treatments From Unstructured Datasets

TL;DR

This paper presents a pipeline that extracts potential drug-disease treatment pairs from unstructured spoken text, using language models and validation against medical knowledge graphs, demonstrating promising results in identifying novel treatments.

Contribution

The study introduces a modular, adaptable pipeline leveraging pre-trained language models and validation tools to identify potential disease treatments from unstructured spoken text sources.

Findings

30.4% of proposed pairs found in ROBOKOP database

Successfully identified Omeprazole as a treatment for heartburn

Pipeline is adaptable to various unstructured text sources

Abstract

Objective: We aim to learn potential novel cures for diseases from unstructured text sources. More specifically, we seek to extract drug-disease pairs of potential cures to diseases by a simple reasoning over the structure of spoken text. Materials and Methods: We use Google Cloud to transcribe podcast episodes of an NPR radio show. We then build a pipeline for systematically pre-processing the text to ensure quality input to the core classification model, which feeds to a series of post-processing steps for obtaining filtered results. Our classification model itself uses a language model pre-trained on PubMed text. The modular nature of our pipeline allows for ease of future developments in this area by substituting higher quality components at each stage of the pipeline. As a validation measure, we use ROBOKOP, an engine over a medical knowledge graph with only validated pathways, as a ground truth source for checking the existence of the proposed pairs. For the proposed pairs not found in ROBOKOP, we provide further verification using Chemotext. Results: We found 30.4% of our proposed pairs in the ROBOKOP database. For example, our model successfully identified that Omeprazole can help treat heartburn.We discuss the significance of this result, showing some examples of the proposed pairs. Discussion and Conclusion: The agreement of our results with the existing knowledge source indicates a step in the right direction. Given the plug-and-play nature of our framework, it is easy to add, remove, or modify parts to improve the model as necessary. We discuss the results showing some examples, and note that this is a potentially new line of research that has further scope to be explored. Although our approach was originally oriented on radio podcast transcripts, it is input-agnostic and could be applied to any source of textual data and to any problem of interest.