Memory augmented recurrent neural networks for de-novo drug design

Naveen Suresh, Neelesh Chinnakonda Ashok Kumar, Srikumar Subramanian and Gowri Srinivasa

PLOS ONE, 2022, vol. 17, issue 6, 1-21

Abstract: A recurrent neural network (RNN) is a machine learning model that learns the relationship between elements of an input series, in addition to inferring a relationship between the data input to the model and target output. Memory augmentation allows the RNN to learn the interrelationships between elements of the input over a protracted length of the input series. Inspired by the success of stack augmented RNN (StackRNN) to generate strings for various applications, we present two memory augmented RNN-based architectures: the Neural Turing Machine (NTM) and the Differentiable Neural Computer (DNC) for the de-novo generation of small molecules. We trained a character-level convolutional neural network (CNN) to predict the properties of a generated string and compute a reward or loss in a deep reinforcement learning setup to bias the Generator to produce molecules with the desired property. Further, we compare the performance of these architectures to gain insight to their relative merits in terms of the validity and novelty of the generated molecules and the degree of property bias towards the computational generation of de-novo drugs. We also compare the performance of these architectures with simpler recurrent neural networks (Vanilla RNN, LSTM, and GRU) without an external memory component to explore the impact of augmented memory in the task of de-novo generation of small molecules.

Date: 2022
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0269461

DOI: 10.1371/journal.pone.0269461

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