Interactive Visual Explanations for Deep Drug Repurposing

Faced with skyrocketing costs for developing new drugs from scratch, repurposing existing drugs for new uses is an enticing alternative that con-siderably reduces safety risks and development costs. However, successful drug repurposing has been mainly based on serendipitous discoveries. Here, we present a tool that combines a graph transformer network with interactive visual explanations to assist scientists in generating, exploring, and understanding drug repurposing predictions. Leveraging semantic attention in our graph transformer network, our tool introduces a novel way to visualize meta path explanations that provide biomedical context for interpretation. Our results show that the tool generates accurate drug predictions and provides interpretable predictions.

[1]  A. Vlahou,et al.  Drug repurposing in oncology. , 2020, The Lancet. Oncology.

[2]  My T. Thai,et al.  PGM-Explainer: Probabilistic Graphical Model Explanations for Graph Neural Networks , 2020, NeurIPS.

[3]  Nicola De Cao,et al.  Interpreting Graph Neural Networks for NLP With Differentiable Edge Masking , 2020, ICLR.

[4]  A. Barabasi,et al.  Network medicine framework for identifying drug-repurposing opportunities for COVID-19 , 2020, Proceedings of the National Academy of Sciences.

[5]  Hayato Akimoto,et al.  Antidiabetic Drugs for the Risk of Alzheimer Disease in Patients With Type 2 DM Using FAERS , 2020, American journal of Alzheimer's disease and other dementias.

[6]  Qiang Huang,et al.  GraphLIME: Local Interpretable Model Explanations for Graph Neural Networks , 2020, IEEE Transactions on Knowledge and Data Engineering.

[7]  Andrew R. Leach,et al.  Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens , 2020, bioRxiv.

[8]  A. Lin,et al.  Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials , 2019, Science Translational Medicine.

[9]  Sung-il Cho,et al.  Association of Anticholinergic Use with Incidence of Alzheimer’s Disease: Population-based Cohort Study , 2019, Scientific Reports.

[10]  J. Leskovec,et al.  GNNExplainer: Generating Explanations for Graph Neural Networks , 2019, NeurIPS.

[11]  P. Sanseau,et al.  Drug repurposing: progress, challenges and recommendations , 2018, Nature Reviews Drug Discovery.

[12]  Bo Wang,et al.  Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities , 2018, Inf. Fusion.

[13]  Pietro Liò,et al.  Graph Attention Networks , 2017, ICLR.

[14]  R. Vernooij,et al.  Effect of the treatment of Type 2 diabetes mellitus on the development of cognitive impairment and dementia. , 2017, The Cochrane database of systematic reviews.

[15]  K. Ono,et al.  Anti-Parkinsonian agents have anti-amyloidogenic activity for Alzheimer's β-amyloid fibrils in vitro , 2006, Neurochemistry International.

[16]  T. Ashburn,et al.  Drug repositioning: identifying and developing new uses for existing drugs , 2004, Nature Reviews Drug Discovery.

[17]  K. Ashe,et al.  Ibuprofen Suppresses Plaque Pathology and Inflammation in a Mouse Model for Alzheimer's Disease , 2000, The Journal of Neuroscience.

[18]  H. Pinedo,et al.  Mechanism of action of antitumor drug etoposide: a review. , 1988, Journal of the National Cancer Institute.

[19]  Marinka Zitnik,et al.  Representation Learning for Networks in Biology and Medicine: Advancements, Challenges, and Opportunities , 2021, ArXiv.

[20]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .

[21]  NEW TRICKS FOR OLD DRUGS , 1982 .