Abstract
The active global SARS-CoV-2 pandemic caused more than 167 million cases and 3.4 million deaths worldwide. The development of completely new drugs for such a novel disease is a challenging, time intensive process and despite researchers around the world working on this task, no effective treatments have been developed yet. This emphasizes the importance of drug repurposing, where treatments are found among existing drugs that are meant for different diseases. A common approach to this is based on knowledge graphs, that condense relationships between entities like drugs, diseases and genes. Graph neural networks (GNNs) can then be used for the task at hand by predicting links in such knowledge graphs. Expanding on state-of-the-art GNN research, Doshi et al. recently developed the Dr-COVID model. We further extend their work using additional output interpretation strategies. The best aggregation strategy derives a top-100 ranking of candidate drugs, 32 of which currently being in COVID-19-related clinical trials. Moreover, we present an alternative application for the model, the generation of additional candidates based on a given pre-selection of drug candidates using collaborative filtering. In addition, we improved the implementation of the Dr-COVID model by significantly shortening the inference and pre-processing time by exploiting data-parallelism. As drug repurposing is a task that requires high computation and memory resources, we further accelerate the post-processing phase using a new emerging hardware—we propose a new approach to leverage the use of high-capacity Non-Volatile Memory for aggregate drug ranking.
Keywords
- Drug repurposing
- Knowledge graphs
- Link prediction
- Collaborative filtering
- Non-votile memory
- NVM
- MCAS
- Python
- PyMM
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Notes
- 1.
Our implementation of the experiments and the model can be found here: https://drive.google.com/file/d/1hYxMe3AFwcJ4UKsn8SPsZVPW3buXe0u4/view?usp=sharing.
- 2.
To precisely define the cosine similarity between two given drugs \(i,j\), let \(\hat{s}_{*i},\hat{s}_{*j}\) be their prediction scores along the disease dimension. Then their similarity is defined as \(\hat{s}_{*i}\cdot \hat{s}_{*j}\).
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Cohen, S. et al. (2022). Drug Repurposing Using Link Prediction on Knowledge Graphs with Applications to Non-volatile Memory. In: Benito, R.M., Cherifi, C., Cherifi, H., Moro, E., Rocha, L.M., Sales-Pardo, M. (eds) Complex Networks & Their Applications X. COMPLEX NETWORKS 2021. Studies in Computational Intelligence, vol 1016. Springer, Cham. https://doi.org/10.1007/978-3-030-93413-2_61
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