ArticleBMC bioinformatics2023
Comparing methods for drug-gene interaction prediction on the biomedical literature knowledge graph: performance versus explainability.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- An inductive learning-based method for predicting drug-gene interactions using a multi-relational drug-disease-gene graph.Journal of pharmaceutical analysis · 2025Article
- PubMed knowledge graph 2.0: Connecting papers, patents, and clinical trials in biomedical science.Scientific data · 2025Article
- Knowledge graphs in psychiatric research: Potential applications and future perspectives.Acta psychiatrica Scandinavica · 2025Review
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Authors and funding
2 authors.
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Abstract
This paper applies different link prediction methods on a knowledge graph generated from biomedical literature, with the aim to compare their ability to identify unknown drug-gene interactions and explain their predictions. Identifying novel drug-target interactions is a crucial step in drug discovery and repurposing. One approach to this problem is to predict missing links between drug and gene nodes, in a graph that contains relevant biomedical knowledge. Such a knowledge graph can be extracted from biomedical literature, using text mining tools. In this work, we compare state-of-the-art graph embedding approaches and contextual path analysis on the interaction prediction task. The comparison reveals a trade-off between predictive accuracy and explainability of predictions. Focusing on explainability, we train a decision tree on model predictions and show how it can aid the understanding of the prediction process. We further test the methods on a drug repurposing task and validate the predicted interactions against external databases, with very encouraging results.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.