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Journal ArticleDOI

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

12 Jan 2018-ACS central science (American Chemical Society)-Vol. 4, Iss: 2, pp 268-276

Abstract: We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended spaces of chemical compounds. A deep neural network was trained on hundreds of thousands of existing chemical structures to construct three coupled functions: an encoder, a decoder, and a predictor. The encoder converts the discrete representation of a molecule into a real-valued continuous vector, and the decoder converts these continuous vectors back to discrete molecular representations. The predictor estimates chemical properties from the latent continuous vector representation of the molecule. Continuous representations of molecules allow us to automatically generate novel chemical structures by performing simple operations in the latent space, such as decoding random vectors, perturbing known chemical structures, or interpolating between molecules. Continuous represent...
Topics: Encoder (54%)
Citations
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Journal ArticleDOI
Zonghan Wu1, Shirui Pan2, Fengwen Chen1, Guodong Long1  +2 moreInstitutions (3)
TL;DR: This article provides a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields and proposes a new taxonomy to divide the state-of-the-art GNNs into four categories, namely, recurrent GNNS, convolutional GNN’s, graph autoencoders, and spatial–temporal Gnns.
Abstract: Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications, where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on the existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this article, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art GNNs into four categories, namely, recurrent GNNs, convolutional GNNs, graph autoencoders, and spatial–temporal GNNs. We further discuss the applications of GNNs across various domains and summarize the open-source codes, benchmark data sets, and model evaluation of GNNs. Finally, we propose potential research directions in this rapidly growing field.

2,367 citations


Journal ArticleDOI
27 Jul 2018-Science
TL;DR: Methods for achieving inverse design, which aims to discover tailored materials from the starting point of a particular desired functionality, are reviewed.
Abstract: The discovery of new materials can bring enormous societal and technological progress. In this context, exploring completely the large space of potential materials is computationally intractable. Here, we review methods for achieving inverse design, which aims to discover tailored materials from the starting point of a particular desired functionality. Recent advances from the rapidly growing field of artificial intelligence, mostly from the subfield of machine learning, have resulted in a fertile exchange of ideas, where approaches to inverse molecular design are being proposed and employed at a rapid pace. Among these, deep generative models have been applied to numerous classes of materials: rational design of prospective drugs, synthetic routes to organic compounds, and optimization of photovoltaics and redox flow batteries, as well as a variety of other solid-state materials.

688 citations


Journal ArticleDOI
Mariya Popova1, Mariya Popova2, Mariya Popova3, Olexandr Isayev3  +1 moreInstitutions (3)
01 Jul 2018-Science Advances
TL;DR: The ReLeaSE method is used to design chemical libraries with a bias toward structural complexity or toward compounds with maximal, minimal, or specific range of physical properties, such as melting point or hydrophobicity.
Abstract: We have devised and implemented a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). On the basis of deep and reinforcement learning (RL) approaches, ReLeaSE integrates two deep neural networks—generative and predictive—that are trained separately but are used jointly to generate novel targeted chemical libraries. ReLeaSE uses simple representation of molecules by their simplified molecular-input line-entry system (SMILES) strings only. Generative models are trained with a stack-augmented memory network to produce chemically feasible SMILES strings, and predictive models are derived to forecast the desired properties of the de novo–generated compounds. In the first phase of the method, generative and predictive models are trained separately with a supervised learning algorithm. In the second phase, both models are trained jointly with the RL approach to bias the generation of new chemical structures toward those with the desired physical and/or biological properties. In the proof-of-concept study, we have used the ReLeaSE method to design chemical libraries with a bias toward structural complexity or toward compounds with maximal, minimal, or specific range of physical properties, such as melting point or hydrophobicity, or toward compounds with inhibitory activity against Janus protein kinase 2. The approach proposed herein can find a general use for generating targeted chemical libraries of novel compounds optimized for either a single desired property or multiple properties.

480 citations


Journal ArticleDOI
TL;DR: A machine learning model allows the identification of new small-molecule kinase inhibitors in days and is used to discover potent inhibitors of discoidin domain receptor 1 (DDR1), a kinase target implicated in fibrosis and other diseases, in 21 days.
Abstract: We have developed a deep generative model, generative tensorial reinforcement learning (GENTRL), for de novo small-molecule design. GENTRL optimizes synthetic feasibility, novelty, and biological activity. We used GENTRL to discover potent inhibitors of discoidin domain receptor 1 (DDR1), a kinase target implicated in fibrosis and other diseases, in 21 days. Four compounds were active in biochemical assays, and two were validated in cell-based assays. One lead candidate was tested and demonstrated favorable pharmacokinetics in mice.

353 citations


Book ChapterDOI
Martin Simonovsky1, Nikos Komodakis1Institutions (1)
04 Oct 2018-
Abstract: Deep learning on graphs has become a popular research topic with many applications. However, past work has concentrated on learning graph embedding tasks, which is in contrast with advances in generative models for images and text. Is it possible to transfer this progress to the domain of graphs? We propose to sidestep hurdles associated with linearization of such discrete structures by having a decoder output a probabilistic fully-connected graph of a predefined maximum size directly at once. Our method is formulated as a variational autoencoder. We evaluate on the challenging task of molecule generation.

334 citations


References
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Posted Content
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TL;DR: This work introduces a class of CNNs called deep convolutional generative adversarial networks (DCGANs), that have certain architectural constraints, and demonstrates that they are a strong candidate for unsupervised learning.
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Journal ArticleDOI
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Proceedings ArticleDOI
08 Apr 2014-
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Journal ArticleDOI
David Rogers1, Mathew Hahn1Institutions (1)
TL;DR: A description of their implementation has not previously been presented in the literature, and ECFPs can be very rapidly calculated and can represent an essentially infinite number of different molecular features.
Abstract: Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization. Historically, topological fingerprints were developed for substructure and similarity searching. ECFPs were developed specifically for structure−activity modeling. ECFPs are circular fingerprints with a number of useful qualities: they can be very rapidly calculated; they are not predefined and can represent an essentially infinite number of different molecular features (including stereochemical information); their features represent the presence of particular substructures, allowing easier interpretation of analysis results; and the ECFP algorithm can be tailored to generate different types of circular fingerprints, optimized for different uses. While the use of ECFPs has been widely adopted and validated, a description of their implementation has not previously been presented in the literature.

2,865 citations


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No. of citations received by the Paper in previous years
YearCitations
202218
2021443
2020399
2019263
2018134
201728