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Deep Inverse Reinforcement Learning for Structural Evolution of Small Molecules
Jul 24, 2020
The size and quality of chemical libraries to the drug discovery pipeline are crucial for developing new drugs or repurposing existing drugs. Existing techniques such as combinatorial organic synthesis and High-Throughput Screening usually make the process extraordinarily tough and complicated since the search space of synthetically feasible drugs is exorbitantly huge. While reinforcement learning has been mostly exploited in the literature for generating novel compounds, the requirement of designing a reward function that succinctly represents the learning objective could prove daunting in certain complex domains. Generative Adversarial Network-based methods also mostly discard the discriminator after training and could be hard to train. In this study, we propose a framework for training a compound generator and learning a transferable reward function based on the entropy maximization inverse reinforcement learning paradigm. We show from our experiments that the inverse reinforcement learning route offers a rational alternative for generating chemical compounds in domains where reward function engineering may be less appealing or impossible while data exhibiting the desired objective is readily available.
Drug-Target Indication Prediction by Integrating End-to-End Learning and Fingerprints
Dec 06, 2019
Computer-Aided Drug Discovery research has proven to be a promising direction in drug discovery. In recent years, Deep Learning approaches have been applied to problems in the domain such as Drug-Target Interaction Prediction and have shown improvements over traditional screening methods. An existing challenge is how to represent compound-target pairs in deep learning models. While several representation methods exist, such descriptor schemes tend to complement one another in many instances, as reported in the literature. In this study, we propose a multi-view architecture trained adversarially to leverage this complementary behavior by integrating both differentiable and predefined molecular descriptors. We conduct experiments on clinically relevant benchmark datasets to demonstrate the potential of our approach.