Convolutional Graph Neural Networks

2020 ◽  
pp. 107-123
Author(s):  
J. Joshua Thomas ◽  
Tran Huu Ngoc Tran ◽  
Gilberto Pérez Lechuga ◽  
Bahari Belaton
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Research Area ◽  
Molecular Fingerprints ◽  
Graph Data ◽  
Target Interaction ◽  
Convolutional Networks ◽  
Variational Autoencoder ◽  
Recent Trends ◽  
Graph Neural Networks

Applying deep learning to the pervasive graph data is significant because of the unique characteristics of graphs. Recently, substantial amounts of research efforts have been keen on this area, greatly advancing graph-analyzing techniques. In this study, the authors comprehensively review different kinds of deep learning methods applied to graphs. They discuss with existing literature into sub-components of two: graph convolutional networks, graph autoencoders, and recent trends including chemoinformatics research area including molecular fingerprints and drug discovery. They further experiment with variational autoencoder (VAE) analyze how these apply in drug target interaction (DTI) and applications with ephemeral outline on how they assist the drug discovery pipeline and discuss potential research directions.

scholarly journals Deep learning in bioinformatics: introduction, application, and perspective in big data era

2019 ◽  
Author(s):  
Yu Li ◽  
Chao Huang ◽  
Lizhong Ding ◽  
Zhongxiao Li ◽  
Yijie Pan ◽  
...  
Keyword(s):  
Neural Networks ◽  
Big Data ◽  
Deep Learning ◽  
Generative Adversarial Networks ◽  
Great Success ◽  
Research Directions ◽  
Adversarial Networks ◽  
Variational Autoencoder ◽  
The Common ◽  
Graph Neural Networks

AbstractDeep learning, which is especially formidable in handling big data, has achieved great success in various fields, including bioinformatics. With the advances of the big data era in biology, it is foreseeable that deep learning will become increasingly important in the field and will be incorporated in vast majorities of analysis pipelines. In this review, we provide both the exoteric introduction of deep learning, and concrete examples and implementations of its representative applications in bioinformatics. We start from the recent achievements of deep learning in the bioinformatics field, pointing out the problems which are suitable to use deep learning. After that, we introduce deep learning in an easy-to-understand fashion, from shallow neural networks to legendary convolutional neural networks, legendary recurrent neural networks, graph neural networks, generative adversarial networks, variational autoencoder, and the most recent state-of-the-art architectures. After that, we provide eight examples, covering five bioinformatics research directions and all the four kinds of data type, with the implementation written in Tensorflow and Keras. Finally, we discuss the common issues, such as overfitting and interpretability, that users will encounter when adopting deep learning methods and provide corresponding suggestions. The implementations are freely available at https://github.com/lykaust15/Deep_learning_examples.

scholarly journals Adversarial Examples for Graph Data: Deep Insights into Attack and Defense

2019 ◽  
Author(s):  
Huijun Wu ◽  
Chen Wang ◽  
Yuriy Tyshetskiy ◽  
Andrew Docherty ◽  
Kai Lu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Learning Models ◽  
Graph Data ◽  
Convolutional Networks ◽  
Challenges And Opportunities ◽  
Gradient Technique ◽  
Adversarial Examples ◽  
Discrete Nature ◽  
Attack And Defense ◽  
Attacks And Defenses

Graph deep learning models, such as graph convolutional networks (GCN) achieve state-of-the-art performance for tasks on graph data. However, similar to other deep learning models, graph deep learning models are susceptible to adversarial attacks. However, compared with non-graph data the discrete nature of the graph connections and features provide unique challenges and opportunities for adversarial attacks and defenses. In this paper, we propose techniques for both an adversarial attack and a defense against adversarial attacks. Firstly, we show that the problem of discrete graph connections and the discrete features of common datasets can be handled by using the integrated gradient technique that accurately determines the effect of changing selected features or edges while still benefiting from parallel computations. In addition, we show that an adversarially manipulated graph using a targeted attack statistically differs from un-manipulated graphs. Based on this observation, we propose a defense approach which can detect and recover a potential adversarial perturbation. Our experiments on a number of datasets show the effectiveness of the proposed techniques.

scholarly journals Imitation Learning with Graph Neural Networks for Improving Swarm Robustness under Restricted Communications

2021 ◽  
Vol 11 (19) ◽  
pp. 9055
Author(s):  
Ce Guo ◽  
Pengming Zhu ◽  
Zhiqian Zhou ◽  
Lin Lang ◽  
Zhiwen Zeng ◽  
...  
Keyword(s):  
Neural Networks ◽  
Imitation Learning ◽  
Communication Constraints ◽  
Training Process ◽  
Simulation Experiments ◽  
Graph Data ◽  
Primary Motivation ◽  
Convolutional Networks ◽  
Speed Up ◽  
Graph Neural Networks

This paper focuses on generating distributed flocking strategies via imitation learning. The primary motivation is to improve the swarm robustness and achieve better consistency while respecting the communication constraints. This paper first proposes a quantitative metric of swarm robustness based on entropy evaluation. Then, the graph importance consistency is also proposed, which is one of the critical goals of the flocking task. Moreover, the importance-correlated directed graph convolutional networks (IDGCNs) are constructed for multidimensional feature extraction and structure-related aggregation of graph data. Next, by employing IDGCNs-based imitation learning, a distributed and scalable flocking strategy is obtained, and its performance is very close to the centralized strategy template while considering communication constraints. To speed up and simplify the training process, we train the flocking strategy with a small number of agents and set restrictions on communication. Finally, various simulation experiments are executed to verify the advantages of the obtained strategy in terms of realizing the swarm consistency and improving the swarm robustness. The results also show that the performance is well maintained while the scale of agents expands (tested with 20, 30, 40 robots).

scholarly journals Graph convolutional networks: a comprehensive review

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Si Zhang ◽  
Hanghang Tong ◽  
Jiejun Xu ◽  
Ross Maciejewski
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Network Models ◽  
Representation Learning ◽  
Superior Performance ◽  
Learning Models ◽  
Convolutional Network ◽  
Comprehensive Review ◽  
Convolutional Networks ◽  
Graph Neural Networks

Abstract Graphs naturally appear in numerous application domains, ranging from social analysis, bioinformatics to computer vision. The unique capability of graphs enables capturing the structural relations among data, and thus allows to harvest more insights compared to analyzing data in isolation. However, it is often very challenging to solve the learning problems on graphs, because (1) many types of data are not originally structured as graphs, such as images and text data, and (2) for graph-structured data, the underlying connectivity patterns are often complex and diverse. On the other hand, the representation learning has achieved great successes in many areas. Thereby, a potential solution is to learn the representation of graphs in a low-dimensional Euclidean space, such that the graph properties can be preserved. Although tremendous efforts have been made to address the graph representation learning problem, many of them still suffer from their shallow learning mechanisms. Deep learning models on graphs (e.g., graph neural networks) have recently emerged in machine learning and other related areas, and demonstrated the superior performance in various problems. In this survey, despite numerous types of graph neural networks, we conduct a comprehensive review specifically on the emerging field of graph convolutional networks, which is one of the most prominent graph deep learning models. First, we group the existing graph convolutional network models into two categories based on the types of convolutions and highlight some graph convolutional network models in details. Then, we categorize different graph convolutional networks according to the areas of their applications. Finally, we present several open challenges in this area and discuss potential directions for future research.

scholarly journals DeepDrug: A general graph-based deep learning framework for drug relation prediction

2020 ◽  
Author(s):  
Xusheng Cao ◽  
Rui Fan ◽  
Wanwen Zeng
Keyword(s):  
Deep Learning ◽  
Chemical Properties ◽  
Underlying Mechanism ◽  
Structural Features ◽  
Training Data ◽  
Systematic Evaluation ◽  
Molecular Fingerprints ◽  
Convolutional Networks ◽  
Learning Framework ◽  
Relation Prediction

AbstractComputational approaches for accurate predictions of drug-related interactions such as drug-drug interactions (DDIs) and drug-target interactions (DTIs) are highly demanding for biochemical researchers due to their efficiency and cost-effectiveness. Despite the fact that many methods have been proposed and developed to predict DDIs and DTIs respectively, their success is still limited due to a lack of systematic evaluation of the intrinsic properties embedded in their structure. In this paper, we develop a deep learning framework, named DeepDrug, to overcome these shortcomings by using graph convolutional networks to learn the graphical representations of drugs and proteins such as molecular fingerprints and residual structures in order to boost the prediction accuracy. We benchmark our methods in binary-class DDIs, multi-class DDIs and binary-class DTIs classification tasks using several datasets. We then demonstrate that DeepDrug outperforms other state-of-the-art published methods both in terms of accuracy and robustness in predicting DDIs and DTIs with varying ratios of positive to negative training data. Ultimately, we visualize the structural features learned by DeepDrug, which display compatible and accordant patterns in chemical properties, providing additional evidence to support the strong predictive power of DeepDrug. We believe that DeepDrug is an efficient tool in accurate prediction of DDIs and DTIs and provides a promising path in understanding the underlying mechanism of these biochemical relations. The source code of the DeepDrug can be downloaded from https://github.com/wanwenzeng/deepdrug.

Deep Learning Based High-Resolution Remote Sensing Image classification

2017 ◽  
Vol 7 (10) ◽  
pp. 22
Author(s):  
Sumit Kaur
Keyword(s):  
Machine Learning ◽  
Remote Sensing ◽  
Deep Learning ◽  
Image Classification ◽  
Language Processing ◽  
Object Perception ◽  
Remote Sensing Image ◽  
Research Area ◽  
Remote Sensing Image Classification ◽  
Unsupervised Algorithms

Abstract- Deep learning is an emerging research area in machine learning and pattern recognition field which has been presented with the goal of drawing Machine Learning nearer to one of its unique objectives, Artificial Intelligence. It tries to mimic the human brain, which is capable of processing and learning from the complex input data and solving different kinds of complicated tasks well. Deep learning (DL) basically based on a set of supervised and unsupervised algorithms that attempt to model higher level abstractions in data and make it self-learning for hierarchical representation for classification. In the recent years, it has attracted much attention due to its state-of-the-art performance in diverse areas like object perception, speech recognition, computer vision, collaborative filtering and natural language processing. This paper will present a survey on different deep learning techniques for remote sensing image classification. 

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

scholarly journals Automatic Deep Learning Semantic Segmentation of Ultrasound Thyroid Cineclips using Recurrent Fully Convolutional Networks

IEEE Access ◽  
2020 ◽  
pp. 1-1
Author(s):  
Jeremy M. Webb ◽  
Duane D. Meixner ◽  
Shaheeda A. Adusei ◽  
Eric C. Polley ◽  
Mostafa Fatemi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Semantic Segmentation ◽  
Convolutional Networks ◽  
Fully Convolutional Networks

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.

scholarly journals Random forest classification for predicting lifespan-extending chemical compounds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sofia Kapsiani ◽  
Brendan J. Howlin
Keyword(s):  
Caenorhabditis Elegans ◽  
Random Forest ◽  
Molecular Descriptors ◽  
Area Under The Curve ◽  
Chemical Compounds ◽  
Research Area ◽  
Importance Measure ◽  
Random Forest Algorithm ◽  
Molecular Fingerprints ◽  
Age Related

AbstractAgeing is a major risk factor for many conditions including cancer, cardiovascular and neurodegenerative diseases. Pharmaceutical interventions that slow down ageing and delay the onset of age-related diseases are a growing research area. The aim of this study was to build a machine learning model based on the data of the DrugAge database to predict whether a chemical compound will extend the lifespan of Caenorhabditis elegans. Five predictive models were built using the random forest algorithm with molecular fingerprints and/or molecular descriptors as features. The best performing classifier, built using molecular descriptors, achieved an area under the curve score (AUC) of 0.815 for classifying the compounds in the test set. The features of the model were ranked using the Gini importance measure of the random forest algorithm. The top 30 features included descriptors related to atom and bond counts, topological and partial charge properties. The model was applied to predict the class of compounds in an external database, consisting of 1738 small-molecules. The chemical compounds of the screening database with a predictive probability of ≥ 0.80 for increasing the lifespan of Caenorhabditis elegans were broadly separated into (1) flavonoids, (2) fatty acids and conjugates, and (3) organooxygen compounds.

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