Data - Predicting Clinical Trial Outcomes Using Drug Bioactivities

Citation Author(s):
Vidhya
Murali
Submitted by:
Prashanth Athri
Last updated:
Mon, 12/27/2021 - 10:58
DOI:
10.21227/4wv9-q902
License:
0
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Abstract 

The ability to estimate the probability of a drug to receive approval in clinical trials provides natural advantages to optimizing pharmaceutical research workflows. Success rates of a clinical trials have deep implications to costs, duration of development, and under pressure due to stringent regulatory approval processes. We propose a machine learning approach that can predict the outcome of trial with reliable accuracies, using biological activities, physico-chemical properties of the compounds, target related features and NLP-based compound representation. Biological activities have never been used as a predictive feature. We have extracted the drug-disease pair from clinical trials and mapped target[s] to that pair using multiple data sources. Empirical results demonstrate that ensemble learning outperforms independently trained, small-data ML models. We report results and inferences derived from a Random forest classifier with an average accuracy of 93\%, and F1 score of 0.96 for the 'Pass' class. 'Pass' refers to one of the two classes (Pass/ Fail) of all clinical trials and the model performed well in predicting the 'Pass' category. An analysis of the features demonstrates that bioactivity plays an important role in predicting the outcome of a clinical trial. A significant effort has gone into production of the dataset that, for the first time, integrates clinical trial information with protein targets. All code to map these entities are available through this study, and all data are from publicly available sources. While our model identifies low-lying inferences when biological activities are included, the code to integrate biological activity and target information provides researchers with access to deep curated and proprietary clinical trial databases the ability to get deeper insights, better statistical significance, and capabilities to better predict trial failures.

Instructions: 

The data uploaded contains

  • Integrated data (Neo4j) as zip file.  The unzipped file shall be copied  to data folder of Neo4j (e.g. neo4j-community-4.1.3/data/databases
  • Subset of labelled data (as .xlsx file)  curated from multiple databases for the development of machine learning models

Comments

I would like to use these data for teaching purposes.

Submitted by Mihiretu kebede on Mon, 01/24/2022 - 06:02