Optimizing Recurrent Neural Network Architectures for De Novo Drug Design

• Main Authors: Santos, Beatriz P., Abbasi, Maryam, Pereira, Tiago, Ribeiro, Bernardete, Arrais, Joel P.
• Format: Conference Proceeding
• Language: English
• Subjects: Biological system modeling; Computer architecture; Deep Learning; Drug Design; Drug Generation; Drugs; Encoding; GRU; Libraries; LSTM; Recurrent neural networks; RNN; SMILES; Syntactics
• ISSN: 2372-9198
• DOI: 10.1109/CBMS52027.2021.00067

In drug discovery, Deep Learning algorithms are emerging as a potential method to generate novel chemical structures since they can speed up the traditional process and decrease expenditure. Recurrent architectures are amongst the most promising methods for computational de novo drug design. One current challenge consists in finding the optimal architecture and parameters for the recurrent network that assures the generation of valid molecules that span the chemical space. In this work we perform an evaluation on Recurrent Neural Networks which can learn the syntax of molecular representation in terms of SMILES notation. We optimize the computational framework based on the recurrent architecture and its hyper-parameters. Moreover, we evaluate the performance of two types of encoding and spatial arrangement of molecules: Embedding and One-hot Encoding, and datasets with and without stereo-chemical information, respectively. The proposed model showed improved performance when compared to the current literature, both in terms of percentage of valid generated SMILES and diversity with 98.7% and 0.88, for the ChEMBL dataset, respectively. Even when considering the ZINC biogenic library, with stereochemical information, the values were 94.5% and 0.90. The obtained results reveal the potential of the recurrent architectures in learning the SMILES syntax and adding novelty to generate promising compounds.