scholarly journals DRACON: Disconnected Graph Neural Network for Atom Mapping in Chemical Reactions

2020 ◽  
Author(s):  
Filipp Nikitin ◽  
Olexandr Isayev ◽  
Vadim Strijov
Keyword(s):  
Neural Network ◽  
Chemical Reactions ◽  
Computer Assisted ◽  
Reaction Prediction ◽  
Latent Vector ◽  
Atom Mapping ◽  
Proposed Model ◽  
Unsupervised Approach ◽  
Disconnected Graphs ◽  
Disconnected Graph

Machine learning solved many challenging problems in computer-assisted synthesis prediction (CASP). We formulate a reaction prediction problem in terms of node-classification in a disconnected graph of source molecules and generalize a graph convolution neural network for disconnected graphs. Here we demonstrate that our approach can successfully predict reaction outcome and atom-mapping during a chemical transformation. A set of experiments using the USPTO dataset demonstrates excellent performance and interpretability of the proposed model. Our model uses an unsupervised approach to atom-mapping and bridges the gap between data-driven and traditional rule-based methods. Implicitly learned latent vector representation of chemical reactions strongly correlates with the class of the chemical reaction. Reactions with similar templates group together in the latent vector space.

scholarly journals DRACON: Disconnected Graph Neural Network for Atom Mapping in Chemical Reactions

2020 ◽  
Author(s):  
Filipp Nikitin ◽  
Olexandr Isayev ◽  
Vadim Strijov
Keyword(s):  
Neural Network ◽  
Chemical Reactions ◽  
Computer Assisted ◽  
Excellent Performance ◽  
Reaction Prediction ◽  
Latent Vector ◽  
Atom Mapping ◽  
Proposed Model ◽  
Disconnected Graphs ◽  
Disconnected Graph

<p>Machine learning solved many challenging problems in computer-assisted synthesis prediction (CASP). We formulate a reaction prediction problem in terms of node-classification in a disconnected graph of source molecules and generalize a graph convolution neural network for disconnected graphs. Here we demonstrate that our approach can successfully predict reaction outcome and atom-mapping during a chemical transformation. A set of experiments using the USPTO dataset demonstrates excellent performance and interpretability of the proposed model. Implicitly learned latent vector representation of chemical reactions strongly correlates with the class of the chemical reaction. Reactions with similar templates group together in the latent vector space.</p>

scholarly journals DRACON: Disconnected Graph Neural Network for Atom Mapping in Chemical Reactions

2020 ◽  
Author(s):  
Filipp Nikitin ◽  
Olexandr Isayev ◽  
Vadim Strijov
Keyword(s):  
Neural Network ◽  
Chemical Reactions ◽  
Computer Assisted ◽  
Excellent Performance ◽  
Reaction Prediction ◽  
Latent Vector ◽  
Atom Mapping ◽  
Proposed Model ◽  
Disconnected Graphs ◽  
Disconnected Graph

<p>Machine learning solved many challenging problems in computer-assisted synthesis prediction (CASP). We formulate a reaction prediction problem in terms of node-classification in a disconnected graph of source molecules and generalize a graph convolution neural network for disconnected graphs. Here we demonstrate that our approach can successfully predict reaction outcome and atom-mapping during a chemical transformation. A set of experiments using the USPTO dataset demonstrates excellent performance and interpretability of the proposed model. Implicitly learned latent vector representation of chemical reactions strongly correlates with the class of the chemical reaction. Reactions with similar templates group together in the latent vector space.</p>

scholarly journals DRACON: disconnected graph neural network for atom mapping in chemical reactions

2020 ◽  
Vol 22 (45) ◽  
pp. 26478-26486
Author(s):  
Filipp Nikitin ◽  
Olexandr Isayev ◽  
Vadim Strijov
Keyword(s):  
Neural Network ◽  
Chemical Reactions ◽  
Convolution Neural Network ◽  
Prediction Problem ◽  
Reaction Prediction ◽  
Atom Mapping ◽  
Node Classification ◽  
Disconnected Graphs ◽  
Disconnected Graph

We formulate a reaction prediction problem in terms of node-classification in a disconnected graph of source molecules and generalize a graph convolution neural network for disconnected graphs.

Valence states of atoms and their conversions

1984 ◽  
Vol 49 (5) ◽  
pp. 1247-1261 ◽  
Author(s):  
Jaroslav Koča ◽  
Milan Kratochvíl ◽  
Milan Kunz ◽  
Vladimír Kvasnička
Keyword(s):  
Chemical Reactions ◽  
Computer Assisted ◽  
Efficient Tool ◽  
Common Features ◽  
Systematic Application ◽  
Organic Syntheses ◽  
Valence States ◽  
Algebraic Formalism

The algebraic formalism for the description of valence states of atoms and their interconversions is elaborated. It offers a possibility to construct and trace mechanistic paths of chemical reactions, the problem of which is of great importance in computer-assisted organic syntheses. Its systematic application gives exhaustive lists of possible mechanistic paths, and furthermore, very efficient tool to classify chemical reactions and look for their common features.

scholarly journals Nodule Detection with Convolutional Neural Network Using Apache Spark and GPU Frameworks

2021 ◽  
Vol 11 (6) ◽  
pp. 2838
Author(s):  
Nikitha Johnsirani Venkatesan ◽  
Dong Ryeol Shin ◽  
Choon Sung Nam
Keyword(s):  
Neural Network ◽  
Radiation Dose ◽  
Convolutional Neural Network ◽  
Model Performance ◽  
Performance Comparison ◽  
Apache Spark ◽  
Training Time ◽  
Learning Framework ◽  
Proposed Model

In the pharmaceutical field, early detection of lung nodules is indispensable for increasing patient survival. We can enhance the quality of the medical images by intensifying the radiation dose. High radiation dose provokes cancer, which forces experts to use limited radiation. Using abrupt radiation generates noise in CT scans. We propose an optimal Convolutional Neural Network model in which Gaussian noise is removed for better classification and increased training accuracy. Experimental demonstration on the LUNA16 dataset of size 160 GB shows that our proposed method exhibit superior results. Classification accuracy, specificity, sensitivity, Precision, Recall, F1 measurement, and area under the ROC curve (AUC) of the model performance are taken as evaluation metrics. We conducted a performance comparison of our proposed model on numerous platforms, like Apache Spark, GPU, and CPU, to depreciate the training time without compromising the accuracy percentage. Our results show that Apache Spark, integrated with a deep learning framework, is suitable for parallel training computation with high accuracy.

scholarly journals Natural Disasters Intensity Analysis and Classification Based on Multispectral Images Using Multi-Layered Deep Convolutional Neural Network

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2648
Author(s):  
Muhammad Aamir ◽  
Tariq Ali ◽  
Muhammad Irfan ◽  
Ahmad Shaf ◽  
Muhammad Zeeshan Azam ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Natural Disasters ◽  
Deep Convolutional Neural Network ◽  
Multispectral Images ◽  
Learning Techniques ◽  
Proposed Model ◽  
Disaster Intensity ◽  
And Performance

Natural disasters not only disturb the human ecological system but also destroy the properties and critical infrastructures of human societies and even lead to permanent change in the ecosystem. Disaster can be caused by naturally occurring events such as earthquakes, cyclones, floods, and wildfires. Many deep learning techniques have been applied by various researchers to detect and classify natural disasters to overcome losses in ecosystems, but detection of natural disasters still faces issues due to the complex and imbalanced structures of images. To tackle this problem, we propose a multilayered deep convolutional neural network. The proposed model works in two blocks: Block-I convolutional neural network (B-I CNN), for detection and occurrence of disasters, and Block-II convolutional neural network (B-II CNN), for classification of natural disaster intensity types with different filters and parameters. The model is tested on 4428 natural images and performance is calculated and expressed as different statistical values: sensitivity (SE), 97.54%; specificity (SP), 98.22%; accuracy rate (AR), 99.92%; precision (PRE), 97.79%; and F1-score (F1), 97.97%. The overall accuracy for the whole model is 99.92%, which is competitive and comparable with state-of-the-art algorithms.

scholarly journals Extraction of organic chemistry grammar from unsupervised learning of chemical reactions

2021 ◽  
Vol 7 (15) ◽  
pp. eabe4166
Author(s):  
Philippe Schwaller ◽  
Benjamin Hoover ◽  
Jean-Louis Reymond ◽  
Hendrik Strobelt ◽  
Teodoro Laino
Keyword(s):  
Organic Chemistry ◽  
Neural Networks ◽  
Chemical Synthesis ◽  
Unsupervised Learning ◽  
Chemical Reactions ◽  
Data Driven ◽  
Experimental Task ◽  
Rule Based ◽  
Atom Mapping ◽  
Mapping Information

Humans use different domain languages to represent, explore, and communicate scientific concepts. During the last few hundred years, chemists compiled the language of chemical synthesis inferring a series of “reaction rules” from knowing how atoms rearrange during a chemical transformation, a process called atom-mapping. Atom-mapping is a laborious experimental task and, when tackled with computational methods, requires continuous annotation of chemical reactions and the extension of logically consistent directives. Here, we demonstrate that Transformer Neural Networks learn atom-mapping information between products and reactants without supervision or human labeling. Using the Transformer attention weights, we build a chemically agnostic, attention-guided reaction mapper and extract coherent chemical grammar from unannotated sets of reactions. Our method shows remarkable performance in terms of accuracy and speed, even for strongly imbalanced and chemically complex reactions with nontrivial atom-mapping. It provides the missing link between data-driven and rule-based approaches for numerous chemical reaction tasks.

scholarly journals Predicting the Energy Consumption of a Robot in an Exploration Task Using Optimized Neural Networks

Electronics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 920
Author(s):  
Liesle Caballero ◽  
Álvaro Perafan ◽  
Martha Rinaldy ◽  
Winston Percybrooks
Keyword(s):  
Neural Network ◽  
Energy Consumption ◽  
Mobile Robot ◽  
Energy Budget ◽  
Dynamic Models ◽  
Pearson Correlation ◽  
Experimental Conditions ◽  
Grid Map ◽  
Proposed Model ◽  
Exploration Task

This paper deals with the problem of determining a useful energy budget for a mobile robot in a given environment without having to carry out experimental measures for every possible exploration task. The proposed solution uses machine learning models trained on a subset of possible exploration tasks but able to make predictions on untested scenarios. Additionally, the proposed model does not use any kinematic or dynamic models of the robot, which are not always available. The method is based on a neural network with hyperparameter optimization to improve performance. Tabu List optimization strategy is used to determine the hyperparameter values (number of layers and number of neurons per layer) that minimize the percentage relative absolute error (%RAE) while maximize the Pearson correlation coefficient (R) between predicted data and actual data measured under a number of experimental conditions. Once the optimized artificial neural network is trained, it can be used to predict the performance of an exploration algorithm on arbitrary variations of a grid map scenario. Based on such prediction, it is possible to know the energy needed for the robot to complete the exploration task. A total of 128 tests were carried out using a robot executing two exploration algorithms in a grid map with the objective of locating a target whose location is not known a priori by the robot. The experimental energy consumption was measured and compared with the prediction of our model. A success rate of 96.093% was obtained, measured as the percentage of tests where the energy budget suggested by the model was enough to actually carry out the task when compared to the actual energy consumed in the test, suggesting that the proposed model could be useful for energy budgeting in actual mobile robot applications.

scholarly journals Tomato Leaf Disease Diagnosis Based on Improved Convolution Neural Network by Attention Module

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 651
Author(s):  
Shengyi Zhao ◽  
Yun Peng ◽  
Jizhan Liu ◽  
Shuo Wu
Keyword(s):  
Neural Network ◽  
High Performance ◽  
Model Comparison ◽  
Research Direction ◽  
Disease Diagnosis ◽  
Tomato Leaf ◽  
Identification Accuracy ◽  
Main Research ◽  
Proposed Model ◽  
Complex Features

Crop disease diagnosis is of great significance to crop yield and agricultural production. Deep learning methods have become the main research direction to solve the diagnosis of crop diseases. This paper proposed a deep convolutional neural network that integrates an attention mechanism, which can better adapt to the diagnosis of a variety of tomato leaf diseases. The network structure mainly includes residual blocks and attention extraction modules. The model can accurately extract complex features of various diseases. Extensive comparative experiment results show that the proposed model achieves the average identification accuracy of 96.81% on the tomato leaf diseases dataset. It proves that the model has significant advantages in terms of network complexity and real-time performance compared with other models. Moreover, through the model comparison experiment on the grape leaf diseases public dataset, the proposed model also achieves better results, and the average identification accuracy of 99.24%. It is certified that add the attention module can more accurately extract the complex features of a variety of diseases and has fewer parameters. The proposed model provides a high-performance solution for crop diagnosis under the real agricultural environment.

Data augmentation and transfer learning strategies for reaction prediction in low chemical data regimes

2021 ◽  
Author(s):  
Yun Zhang ◽  
Ling Wang ◽  
Xinqiao Wang ◽  
Chengyun Zhang ◽  
Jiamin Ge ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Deep Learning ◽  
Drug Discovery ◽  
Research And Development ◽  
Learning Strategies ◽  
Transfer Learning ◽  
Chemical Reactions ◽  
Data Augmentation ◽  
Learning Method ◽  
Reaction Prediction

An effective and rapid deep learning method to predict chemical reactions contributes to the research and development of organic chemistry and drug discovery.

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