iBT-Net: an incremental broad transformer network for cancer drug response prediction

DeepDRA: Drug repurposing using multi-omics data integration with autoencoders

Cancer treatment 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, such as machine learning and deep learning, have been suggested to solve these challenges using drug repurposing. 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. Compared to 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 regarding generalization. Using this model, we could 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.

Artificial intelligence approaches for molecular representation in drug response prediction

Drug response prediction is essential for drug development and disease treatment. One key question in predicting drug response is the representation of molecules, which has been greatly advanced by artificial intelligence (AI) techniques in recent years. In this review, we first describe different types of representation methods, pinpointing their key principles and discussing their limitations. Thereafter we discuss potential ways how these methods could be further developed. We expect that this review will provide useful guidance for researchers in the community.