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Register a new userLearning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning
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Added by
Vijaya Sai Krishna Gottipati
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Over the last decade, there has been significant progress in the field of machine learning for de novo drug design, particularly in deep generative models. However, current generative approaches exhibit a significant challenge as they do not ensure that the proposed molecular structures can be feasibly synthesized nor do they provide the synthesis routes of the proposed small molecules, thereby seriously limiting their practical applicability. In this work, we propose a novel forward synthesis framework powered by reinforcement learning (RL) for de novo drug design, Policy Gradient for Forward Synthesis (PGFS), that addresses this challenge by embedding the concept of synthetic accessibility directly into the de novo drug design system. In this setup, the agent learns to navigate through the immense synthetically accessible chemical space by subjecting commercially available small molecule building blocks to valid chemical reactions at every time step of the iterative virtual multi-step synthesis process. The proposed environment for drug discovery provides a highly challenging test-bed for RL algorithms owing to the large state space and high-dimensional continuous action space with hierarchical actions. PGFS achieves state-of-the-art performance in generating structures with high QED and penalized clogP. Moreover, we validate PGFS in an in-silico proof-of-concept associated with three HIV targets. Finally, we describe how the end-to-end training conceptualized in this study represents an important paradigm in radically expanding the synthesizable chemical space and automating the drug discovery process.
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Learning in environments with large state and action spaces, and sparse rewards, can hinder a Reinforcement Learning (RL) agents learning through trial-and-error. For instance, following natural language instructions on the Web (such as booking a flight ticket) leads to RL settings where input vocabulary and number of actionable elements on a page can grow very large. Even though recent approaches improve the success rate on relatively simple environments with the help of human demonstrations to guide the exploration, they still fail in environments where the set of possible instructions can reach millions. We approach the aforementioned problems from a different perspective and propose guided RL approaches that can generate unbounded amount of experience for an agent to learn from. Instead of learning from a complicated instruction with a large vocabulary, we decompose it into multiple sub-instructions and schedule a curriculum in which an agent is tasked with a gradually increasing subset of these relatively easier sub-instructions. In addition, when the expert demonstrations are not available, we propose a novel meta-learning framework that generates new instruction following tasks and trains the agent more effectively. We train DQN, deep reinforcement learning agent, with Q-value function approximated with a novel QWeb neural network architecture on these smaller, synthetic instructions. We evaluate the ability of our agent to generalize to new instructions on World of Bits benchmark, on forms with up to 100 elements, supporting 14 million possible instructions. The QWeb agent outperforms the baseline without using any human demonstration achieving 100% success rate on several difficult environments.
Learning to autonomously navigate the web is a difficult sequential decision making task. The state and action spaces are large and combinatorial in nature, and websites are dynamic environments consisting of several pages. One of the bottlenecks of training web navigation agents is providing a learnable curriculum of training environments that can cover the large variety of real-world websites. Therefore, we propose using Adversarial Environment Generation (AEG) to generate challenging web environments in which to train reinforcement learning (RL) agents. We provide a new benchmarking environment, gMiniWoB, which enables an RL adversary to use compositional primitives to learn to generate arbitrarily complex websites. To train the adversary, we propose a new technique for maximizing regret using the difference in the scores obtained by a pair of navigator agents. Our results show that our approach significantly outperforms prior methods for minimax regret AEG. The regret objective trains the adversary to design a curriculum of environments that are just-the-right-challenge for the navigator agents; our results show that over time, the adversary learns to generate increasingly complex web navigation tasks. The navigator agents trained with our technique learn to complete challenging, high-dimensional web navigation tasks, such as form filling, booking a flight etc. We show that the navigator agent trained with our proposed Flexible b-PAIRED technique significantly outperforms competitive automatic curriculum generation baselines -- including a state-of-the-art RL web navigation approach -- on a set of challenging unseen test environments, and achieves more than 80% success rate on some tasks.
Computer-aided design of molecules has the potential to disrupt the field of drug and material discovery. Machine learning, and deep learning, in particular, have been topics where the field has been developing at a rapid pace. Reinforcement learning is a particularly promising approach since it allows for molecular design without prior knowledge. However, the search space is vast and efficient exploration is desirable when using reinforcement learning agents. In this study, we propose an algorithm to aid efficient exploration. The algorithm is inspired by a concept known in the literature as curiosity. We show on three benchmarks that a curious agent finds better performing molecules. This indicates an exciting new research direction for reinforcement learning agents that can explore the chemical space out of their own motivation. This has the potential to eventually lead to unexpected new molecules that no human has thought about so far.
Quantum computers can offer dramatic improvements over classical devices for data analysis tasks such as prediction and classification. However, less is known about the advantages that quantum computers may bring in the setting of reinforcement learning, where learning is achieved via interaction with a task environment. Here, we consider a special case of reinforcement learning, where the task environment allows quantum access. In addition, we impose certain naturalness conditions on the task environment, which rule out the kinds of oracle problems that are studied in quantum query complexity (and for which quantum speedups are well-known). Within this framework of quantum-accessible reinforcement learning environments, we demonstrate that quantum agents can achieve exponential improvements in learning efficiency, surpassing previous results that showed only quadratic improvements. A key step in the proof is to construct task environments that encode well-known oracle problems, such as Simons problem and Recursive Fourier Sampling, while satisfying the above naturalness conditions for reinforcement learning. Our results suggest that quantum agents may perform well in certain game-playing scenarios, where the game has recursive structure, and the agent can learn by playing against itself.
In recent years deep reinforcement learning (RL) systems have attained superhuman performance in a number of challenging task domains. However, a major limitation of such applications is their demand for massive amounts of training data. A critical present objective is thus to develop deep RL methods that can adapt rapidly to new tasks. In the present work we introduce a novel approach to this challenge, which we refer to as deep meta-reinforcement learning. Previous work has shown that recurrent networks can support meta-learning in a fully supervised context. We extend this approach to the RL setting. What emerges is a system that is trained using one RL algorithm, but whose recurrent dynamics implement a second, quite separate RL procedure. This second, learned RL algorithm can differ from the original one in arbitrary ways. Importantly, because it is learned, it is configured to exploit structure in the training domain. We unpack these points in a series of seven proof-of-concept experiments, each of which examines a key aspect of deep meta-RL. We consider prospects for extending and scaling up the approach, and also point out some potentially important implications for neuroscience.
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