We demonstrate a deep learning framework which is inherently based in the highly expressive language of relational logic, enabling to, among other things, capture arbitrarily complex graph structures. We show how Graph Neural Networks and similar models can be easily covered in the framework by specifying the underlying propagation rules in the relational logic. The declarative nature of the used language then allows to easily modify and extend the propagation schemes into complex structures, such as the molecular rings which we choose for a short demonstration in this paper.
Computer Science & Engineering University of Minnesota（明尼苏达大学计算机科学与工程学院）
As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular graphs in which atoms are modeled as nodes. They characterize each atom's chemical environment by modeling its pairwise interactions with other atoms in the molecule. Although these methods achieve a great success, limited amount of works explicitly take many-body interactions, i.e., interactions between three and more atoms, into consideration. In this pap…
Mila（米拉研究所）；Université de Montréal（蒙特利尔大学）；Westfälische Wilhelms-Universität Münster（明斯特大学）；McGill University（麦吉尔大学）；Jagiellonian University（雅盖隆大学）
De novo molecule generation often results in chemically unfeasible molecules. A natural idea to mitigate this problem is to bias the search process towards more easily synthesizable molecules using a proxy for synthetic accessibility. However, using currently available proxies still results in highly unrealistic compounds. We investigate the feasibility of training deep graph neural networks to approximate the outputs of a retrosynthesis planning software, and their use to bias the search process. We evaluate our method on a benchmark involving searching for drug-like molecules with antibiotic…
The dipole moment is a physical quantity indicating the polarity of a molecule and is determined by reflecting the electrical properties of constituent atoms and the geometric properties of the molecule. Most embeddings used to represent graph representations in traditional graph neural network methodologies treat molecules as topological graphs, creating a significant barrier to the goal of recognizing geometric information. Unlike existing embeddings dealing with equivariance, which have been proposed to handle the 3D structure of molecules properly, our proposed embeddings directly express …
An accurate force field is the key to the success of all molecular mechanics simulations on organic polymers and biomolecules. Accuracy beyond density functional theory is often needed to describe the intermolecular interactions, while most correlated wavefunction (CW) methods are prohibitively expensive for large molecules. Therefore, it posts a great challenge to develop an extendible ab initio force field for large flexible organic molecules at CW level of accuracy. In this work, we face this challenge by combining the physics-driven nonbonding potential with a data-driven subgraph neural n…
Multi-Level Fusion Graph Neural Network for Molecule Property Prediction
School of Mathematical Sciences, University of Electronic Science and Technology of China（电子科技大学数学科学学院）；College of Management Science, Chengdu University of Technology（成都理工大学管理科学学院）
Argonne Leadership Computing Facility（阿贡领导力计算设施）；Argonne National Laboratory（阿贡国家实验室）
Bio-oil molecule assessment is essential for the sustainable development of chemicals and transportation fuels. These oxygenated molecules have adequate carbon, hydrogen, and oxygen atoms that can be used for developing new value-added molecules (chemicals or transportation fuels). One motivation for our study stems from the fact that a liquid phase upgrading using mineral acid is a cost-effective chemical transformation. In this chemical upgrading process, adding a proton (positively charged atomic hydrogen) to an oxygen atom is a central step. The protonation energies of oxygen atoms in a mo…
We apply a temporal edge prediction model for weighted dynamic graphs to predict time-dependent changes in molecular structure. Each molecule is represented as a complete graph in which each atom is a vertex and all vertex pairs are connected by an edge weighted by the Euclidean distance between atom pairs. We ingest a sequence of complete molecular graphs into a dynamic graph neural network (GNN) to predict the graph at the next time step. Our dynamic GNN predicts atom-to-atom distances with a mean absolute error of 0.017 Å, which is considered ``chemically accurate'' for molecular simulation…
With the goal of designing novel inhibitors for SARS-CoV-1 and SARS-CoV-2, we propose the general molecule optimization framework, Molecular Neural Assay Search (MONAS), consisting of three components: a property predictor which identifies molecules with specific desirable properties, an energy model which approximates the statistical similarity of a given molecule to known training molecules, and a molecule search method. In this work, these components are instantiated with graph neural networks (GNNs), Deep Energy Estimator Networks (DEEN) and Monte Carlo tree search (MCTS), respectively. Th…
University of Michigan（密歇根大学）；Stanford University（斯坦福大学）
Deep learning based methods have been widely applied to predict various kinds of molecular properties in the pharmaceutical industry with increasingly more success. Solvation free energy is an important index in the field of organic synthesis, medicinal chemistry, drug delivery, and biological processes. However, accurate solvation free energy determination is a time-consuming experimental process. Furthermore, it could be useful to assess solvation free energy in the absence of a physical sample. In this study, we propose two novel models for the problem of free solvation energy predictions, …
University of Wisconsin — Madison（威斯康星大学麦迪逊分校）；Argonne National Laboratory（阿贡国家实验室）
Predicting the properties of a molecule from its structure is a challenging task. Recently, deep learning methods have improved the state of the art for this task because of their ability to learn useful features from the given data. By treating molecule structure as graphs, where atoms and bonds are modeled as nodes and edges, graph neural networks (GNNs) have been widely used to predict molecular properties. However, the design and development of GNNs for a given data set rely on labor-intensive design and tuning of the network architectures. Neural architecture search (NAS) is a promising a…
South China University of Technology（华南理工大学）；Shanghai Jiao Tong University School of Medicine（上海交通大学医学院）
Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements in graph-based molecular property prediction. However, current graph-based deep learning methods neglect the hierarchical information of molecules and the relationships between feature channels. In this study, we propose a well-designed hierarchical informative graph neural networks framework (termed HiGNN) for predicting molecular property by utilizing a co-…
Determining the aqueous solubility of molecules is a vital step in many pharmaceutical, environmental, and energy storage applications. Despite efforts made over decades, there are still challenges associated with developing a solubility prediction model with satisfactory accuracy for many of these applications. The goal of this study is to develop a general model capable of predicting the solubility of a broad range of organic molecules. Using the largest currently available solubility dataset, we implement deep learning-based models to predict solubility from molecular structure and explore …
Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes
The Graduate Center, The City University of New York（纽约市立大学研究生中心）；Hunter College, The City University of New York（纽约市立大学亨特学院）；Weill Cornell Medicine, Cornell University（康奈尔大学威尔医学院）
University of Pittsburgh（匹兹堡大学）；Carnegie Mellon University（卡内基梅隆大学）
To design a drug given a biological molecule by using deep learning methods, there are many successful models published recently. People commonly used generative models to design new molecules given certain protein. LiGAN was regarded as the baseline of deep learning model which was developed on convolutional neural networks. Recently, GraphBP showed its ability to predict innovative "real" chemicals that the binding affinity outperformed with traditional molecular docking methods by using a flow-based generative model with a graph neural network and multilayer perception. However, all those m…
Enhanced Spatial Clustering of Single-Molecule Localizations with Graph Neural Networks
University of Gothenburg（哥德堡大学）；Universitat de Vic – Universitat Central de Catalunya (UVic-UCC)（维克大学–中央加泰罗尼亚大学）；Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC)（加泰罗尼亚中央生命与健康研究所）；Science for Life Laboratory, Department of Physics（生命科学实验室，物理系）
Machine learning techniques have recently been adopted in various applications in medicine, biology, chemistry, and material engineering. An important task is to predict the properties of molecules, which serves as the main subroutine in many downstream applications such as virtual screening and drug design. Despite the increasing interest, the key challenge is to construct proper representations of molecules for learning algorithms. This paper introduces the N-gram graph, a simple unsupervised representation for molecules. The method first embeds the vertices in the molecule graph. It then co…
Wayne State University（韦恩州立大学）；Univ. of Bari Aldo Moro（巴里大学阿尔多·莫罗分校）；National Research Council (CONICET)（国家研究委员会（CONICET））；Daruma Institute for Applied Intelligence（达摩应用智能研究所）
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources, the time and length scales at which these states become detectable are difficult to achieve. One alternative to such methods is based on encoding the atomistic trajectory of molecular dynamics as a shorthand version devoid of physical particles, and then learning to propagate the encoded trajectory through the use of artificial intelligence. Here we show that…
Ionic Liquids (ILs) provide a promising solution for CO$_2$ capture and storage to mitigate global warming. However, identifying and designing the high-capacity IL from the giant chemical space requires expensive, and exhaustive simulations and experiments. Machine learning (ML) can accelerate the process of searching for desirable ionic molecules through accurate and efficient property predictions in a data-driven manner. But existing descriptors and ML models for the ionic molecule suffer from the inefficient adaptation of molecular graph structure. Besides, few works have investigated the e…
Facebook AI Research（Facebook人工智能研究）；Tel Aviv University（特拉维夫大学）
Graph neural networks are currently leading the performance charts in learning-based molecule property prediction and classification. Computational chemistry has, therefore, become the a prominent testbed for generic graph neural networks, as well as for specialized message passing methods. In this work, we demonstrate that the replacement of the underlying networks with hypernetworks leads to a boost in performance, obtaining state of the art results in various benchmarks. A major difficulty in the application of hypernetworks is their lack of stability. We tackle this by combining the curren…
The Graduate Center, The City University of New York（纽约城市大学研究生中心）；Hunter College, The City University of New York（纽约城市大学亨特学院）
The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge. These models improve their expressive power by incorporating auxiliary information in molecules while inevitably increase their computational complexity. In this work, we aim to design a GNN which is both powerful and efficient for molecule structures. To achieve such goal, we propose a molecular mechanics-driven approach by first representing each molecule as a…
Google Research（谷歌研究院）；Arizona State University（亚利桑那州立大学）；University of Toronto（多伦多大学）；Vector Institute for Artificial Intelligence（向量人工智能研究所）；Canadian Institute for Advanced Research（加拿大高等研究院）
Predicting the relationship between a molecule's structure and its odor remains a difficult, decades-old task. This problem, termed quantitative structure-odor relationship (QSOR) modeling, is an important challenge in chemistry, impacting human nutrition, manufacture of synthetic fragrance, the environment, and sensory neuroscience. We propose the use of graph neural networks for QSOR, and show they significantly out-perform prior methods on a novel data set labeled by olfactory experts. Additional analysis shows that the learned embeddings from graph neural networks capture a meaningful odor…
In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. In order to enrich libraries with molecules active towards a given biological target, we propose to fine-tune the model with small …
Beyond Learning on Molecules by Weakly Supervising on Molecules
Helmholtz-Zentrum Berlin für Materialien und Energie GmbH（柏林材料与能源研究中心）；HIPOLE Jena (Helmholtz Institute for Polymers in Energy Applications Jena)（耶拿HIPOLE（聚合物在能源应用中的霍普夫研究所））；Laboratory of Organic and Macromolecular Chemistry (IOMC)（有机与大分子化学实验室）；Center for Energy and Environmental Chemistry Jena (CEEC Jena)（耶拿能源与环境化学中心）；Jena Center for Soft Matter (JCSM)（耶拿软物质中心）
Single molecule localization microscopy is widely used in biological research for measuring the nanostructures of samples smaller than the diffraction limit. This study uses multifocal plane microscopy and addresses the 3D single molecule localization problem, where lateral and axial locations of molecules are estimated. However, when we multifocal plane microscopy is used, the estimation accuracy of 3D localization is easily deteriorated by the small lateral drifts of camera positions. We formulate a 3D molecule localization problem along with the estimation of the lateral drifts as a compres…
Simplified Molecular Input Line Entry System (SMILES) is a single line text representation of a unique molecule. One molecule can however have multiple SMILES strings, which is a reason that canonical SMILES have been defined, which ensures a one to one correspondence between SMILES string and molecule. Here the fact that multiple SMILES represent the same molecule is explored as a technique for data augmentation of a molecular QSAR dataset modeled by a long short term memory (LSTM) cell based neural network. The augmented dataset was 130 times bigger than the original. The network trained wit…
Discovery of atomistic systems with desirable properties is a major challenge in chemistry and material science. Here we introduce a novel, autoregressive, convolutional deep neural network architecture that generates molecular equilibrium structures by sequentially placing atoms in three-dimensional space. The model estimates the joint probability over molecular configurations with tractable conditional probabilities which only depend on distances between atoms and their nuclear charges. It combines concepts from state-of-the-art atomistic neural networks with auto-regressive generative model…
Technische Universität Berlin（柏林工业大学）；University of Luxembourg（卢森堡大学）；Max-Planck-Institut für Informatik（马克斯·普朗克信息学研究所）；Korea University（高丽大学）
Deep Learning has been shown to learn efficient representations for structured data such as image, text or audio. In this chapter, we present neural network architectures that are able to learn efficient representations of molecules and materials. In particular, the continuous-filter convolutional network SchNet accurately predicts chemical properties across compositional and configurational space on a variety of datasets. Beyond that, we analyze the obtained representations to find evidence that their spatial and chemical properties agree with chemical intuition.
With the rapid increase of compound databases available in medicinal and material science, there is a growing need for learning representations of molecules in a semi-supervised manner. In this paper, we propose an unsupervised hierarchical feature extraction algorithm for molecules (or more generally, graph-structured objects with fixed number of types of nodes and edges), which is applicable to both unsupervised and semi-supervised tasks. Our method extends recently proposed Paragraph Vector algorithm and incorporates neural message passing to obtain hierarchical representations of subgraphs…
Neural message passing on molecular graphs is one of the most promising methods for predicting formation energy and other properties of molecules and materials. In this work we extend the neural message passing model with an edge update network which allows the information exchanged between atoms to depend on the hidden state of the receiving atom. We benchmark the proposed model on three publicly available datasets (QM9, The Materials Project and OQMD) and show that the proposed model yields superior prediction of formation energies and other properties on all three datasets in comparison wit…
Novartis Institutes for BioMedical Research（诺华生物医学研究所）
The exploration of novel chemical spaces is one of the most important tasks of cheminformatics when supporting the drug discovery process. Properly designed and trained deep neural networks can provide a viable alternative to brute-force de novo approaches or various other machine-learning techniques for generating novel drug-like molecules. In this article we present a method to generate molecules using a long short-term memory (LSTM) neural network and provide an analysis of the results, including a virtual screening test. Using the network one million drug-like molecules were generated in 2…
Molecular Machine Learning (ML) bears promise for efficient molecule property prediction and drug discovery. However, labeled molecule data can be expensive and time-consuming to acquire. Due to the limited labeled data, it is a great challenge for supervised-learning ML models to generalize to the giant chemical space. In this work, we present MolCLR: Molecular Contrastive Learning of Representations via Graph Neural Networks (GNNs), a self-supervised learning framework that leverages large unlabeled data (~10M unique molecules). In MolCLR pre-training, we build molecule graphs and develop GN…
Technische Universität Berlin（柏林工业大学）；Berlin Institute for the Foundations of Learning and Data（柏林学习与数据基础研究所）；Korea University（高丽大学）；Max-Planck-Institut für Informatik（马克斯·普朗克信息学研究所）
The rational design of molecules with desired properties is a long-standing challenge in chemistry. Generative neural networks have emerged as a powerful approach to sample novel molecules from a learned distribution. Here, we propose a conditional generative neural network for 3d molecular structures with specified chemical and structural properties. This approach is agnostic to chemical bonding and enables targeted sampling of novel molecules from conditional distributions, even in domains where reference calculations are sparse. We demonstrate the utility of our method for inverse design by…
The potential number of drug like small molecules is estimated to be between 10^23 and 10^60 while current databases of known compounds are orders of magnitude smaller with approximately 10^8 compounds. This discrepancy has led to an interest in generating virtual libraries using hand crafted chemical rules and fragment based methods to cover a larger area of chemical space and generate chemical libraries for use in in silico drug discovery endeavors. Here it is explored to what extent a recurrent neural network with long short term memory cells can figure out sensible chemical rules and gener…
Well-designed molecular representations (fingerprints) are vital to combine medical chemistry and deep learning. Whereas incorporating 3D geometry of molecules (i.e. conformations) in their representations seems beneficial, current 3D algorithms are still in infancy. In this paper, we propose a novel molecular representation algorithm which preserves 3D conformations of molecules with a Molecular Hamiltonian Network (HamNet). In HamNet, implicit positions and momentums of atoms in a molecule interact in the Hamiltonian Engine following the discretized Hamiltonian equations. These implicit coor…
Massachusetts Institute of Technology（麻省理工学院）；Rutgers University（罗格斯大学）
Molecules with identical graph connectivity can exhibit different physical and biological properties if they exhibit stereochemistry-a spatial structural characteristic. However, modern neural architectures designed for learning structure-property relationships from molecular structures treat molecules as graph-structured data and therefore are invariant to stereochemistry. Here, we develop two custom aggregation functions for message passing neural networks to learn properties of molecules with tetrahedral chirality, one common form of stereochemistry. We evaluate performance on synthetic dat…
Neural processes (NPs) are models for transfer learning with properties reminiscent of Gaussian Processes (GPs). They are adept at modelling data consisting of few observations of many related functions on the same input space and are trained by minimizing a variational objective, which is computationally much less expensive than the Bayesian updating required by GPs. So far, most studies of NPs have focused on low-dimensional datasets which are not representative of realistic transfer learning tasks. Drug discovery is one application area that is characterized by datasets consisting of many c…
Self-supervised neural language models have recently found wide applications in generative design of organic molecules and protein sequences as well as representation learning for downstream structure classification and functional prediction. However, most of the existing deep learning models for molecule design usually require a big dataset and have a black-box architecture, which makes it difficult to interpret their design logic. Here we propose Generative Molecular Transformer (GMTransformer), a probabilistic neural network model for generative design of molecules. Our model is built on th…
