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Drug Repurposing using Data Integration in Deep Learning

Mohammadzadeh Vardin, Taha | 2025

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 58324 (19)
  4. University: Sharif University of Technology
  5. Department: Computer Engineering
  6. Advisor(s): Rabiee, Hamid Reza
  7. Abstract:
  8. Treatment of cancer has become one of the biggest challenges in the world today. Different treatments are used against cancer; drug-based treatments have shown better results. On the other hand, designing new drugs for cancer is costly and time-consuming. Some computational methods have been suggested to solve these challenges using drug repurposing, such as machine learning and deep learning. Despite the promise of classical machine-learning methods in repurposing cancer drugs and predicting responses, deep-learning methods performed better. This study aims to develop a deep-learning model that predicts cancer drug response based on multi-omics data, drug descriptors, and drug fingerprints and facilitates the repurposing of drugs based on those responses. To reduce multi-omics data's dimensionality, we use autoencoders. As a multi-task learning model, autoencoders are connected to MLPs. We extensively tested our model using three primary datasets, GDSC, CTRP, and CCLE, to determine its efficacy. In multiple experiments, our model consistently outperforms existing state-of-the-art methods. In comparison with state-of-the-art models, our model achieves an impressive AUPRC of 0.99. Furthermore, in a cross-dataset evaluation, where the model is trained on GDSC and tested on CCLE, it surpasses the performance of three previous works, achieving an AUPRC of 0.72. In conclusion, we presented a deep learning model that outperforms the current state-of-the-art in terms of generalization. Using this model, we were able to assess drug responses and explore drug repurposing, leading to the discovery of novel cancer drugs. Our study highlights the potential for advanced deep learning to advance cancer therapeutic precision
  9. Keywords:
  10. Multimodal Learning ; Data Fusion ; Cancer Treatment ; Deep Learning ; Drug Repurposing

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