Molecular Graph Generation with Deep Reinforced Multitask Network and Adversarial Imitation Learning

Molecular graph generation aims to design molecules with desired biochemical properties, which is promising in drug discovery. Existing methods typically combine deep reinforcement models with adversarial training. However, the reinforced rewards in molecule generation are delayed and sparse while adversarial training suffers mode collapse issue. Moreover, they optimize multiple properties with a linear combination manner, where the models get distracted by potentially conflicting objectives. To tackle the above challenges, we propose a Deep Reinforced framework with Adversarial Imitation and Multitask learning (DR-AIM). First, the reinforced agent generates discrete molecular graphs via deep Q-learning, where the trajectories of high rewards are cached as experts. Then policies are extracted directly from expert trajectories by adversarial imitation learning, in which the discriminator delivers behavior distribution signals to the agent as dense rewards. Second, we propose to realize multi-goal molecule generation as a multitask learning process, where different property optimizations are treated as different tasks to be trained jointly. Extensive experiments demonstrate the effectiveness of DR-AIM in molecule generation.

[1]  Wojciech Zaremba,et al.  Improved Techniques for Training GANs , 2016, NIPS.

[2]  Tom Schaul,et al.  Dueling Network Architectures for Deep Reinforcement Learning , 2015, ICML.

[3]  David Rogers,et al.  Extended-Connectivity Fingerprints , 2010, J. Chem. Inf. Model..

[4]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[5]  Anind K. Dey,et al.  Modeling Interaction via the Principle of Maximum Causal Entropy , 2010, ICML.

[6]  Andrew W. Moore,et al.  Prioritized Sweeping: Reinforcement Learning with Less Data and Less Time , 1993, Machine Learning.

[7]  Daniel C. Elton,et al.  Deep learning for molecular generation and optimization - a review of the state of the art , 2019, Molecular Systems Design & Engineering.

[8]  Nicola De Cao,et al.  MolGAN: An implicit generative model for small molecular graphs , 2018, ArXiv.

[9]  Pavlo O. Dral,et al.  Quantum chemistry structures and properties of 134 kilo molecules , 2014, Scientific Data.

[10]  Alexandre Varnek,et al.  Estimation of the size of drug-like chemical space based on GDB-17 data , 2013, Journal of Computer-Aided Molecular Design.

[11]  Niloy Ganguly,et al.  Designing Random Graph Models Using Variational Autoencoders With Applications to Chemical Design , 2018, ArXiv.

[12]  Michael H. Bowling,et al.  Apprenticeship learning using linear programming , 2008, ICML '08.

[13]  Bin Li,et al.  Applications of machine learning in drug discovery and development , 2019, Nature Reviews Drug Discovery.

[14]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[15]  G. V. Paolini,et al.  Quantifying the chemical beauty of drugs. , 2012, Nature chemistry.

[16]  Regina Barzilay,et al.  Junction Tree Variational Autoencoder for Molecular Graph Generation , 2018, ICML.

[17]  Zois Boukouvalas,et al.  Deep learning for molecular generation and optimization - a review of the state of the art , 2019, Molecular Systems Design & Engineering.

[18]  Alán Aspuru-Guzik,et al.  Objective-Reinforced Generative Adversarial Networks (ORGAN) for Sequence Generation Models , 2017, ArXiv.

[19]  Satinder Singh,et al.  Generative Adversarial Self-Imitation Learning , 2018, ArXiv.

[20]  Qi Liu,et al.  Advances and challenges in deep generative models for de novo molecule generation , 2018, WIREs Computational Molecular Science.

[21]  Jure Leskovec,et al.  Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation , 2018, NeurIPS.