Autonomous deep learning for continual learning in complex data stream environment

2021 ◽  
Author(s):  
◽  
Andri Ashfahani
Keyword(s):  
Deep Learning ◽  
Data Stream ◽  
Complex Data ◽  
Continual Learning

Deep Learning in the Study of Protein-Related Interactions

2020 ◽  
Vol 27 (5) ◽  
pp. 359-369 ◽  
Author(s):  
Cheng Shi ◽  
Jiaxing Chen ◽  
Xinyue Kang ◽  
Guiling Zhao ◽  
Xingzhen Lao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Physiological Data ◽  
Great Promise ◽  
Complex Data ◽  
Protein Protein Interactions ◽  
Learning Patterns ◽  
Introductory Overview ◽  
Protein Research ◽  
Neural Network Theory

: Protein-related interaction prediction is critical to understanding life processes, biological functions, and mechanisms of drug action. Experimental methods used to determine proteinrelated interactions have always been costly and inefficient. In recent years, advances in biological and medical technology have provided us with explosive biological and physiological data, and deep learning-based algorithms have shown great promise in extracting features and learning patterns from complex data. At present, deep learning in protein research has emerged. In this review, we provide an introductory overview of the deep neural network theory and its unique properties. Mainly focused on the application of this technology in protein-related interactions prediction over the past five years, including protein-protein interactions prediction, protein-RNA\DNA, Protein– drug interactions prediction, and others. Finally, we discuss some of the challenges that deep learning currently faces.

scholarly journals Deep Transfer Learning Based Intrusion Detection System for Electric Vehicular Networks

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4736
Author(s):  
Sk. Tanzir Mehedi ◽  
Adnan Anwar ◽  
Ziaur Rahman ◽  
Kawsar Ahmed
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Intrusion Detection ◽  
Real Time ◽  
Transfer Learning ◽  
Security Requirements ◽  
Detection Accuracy ◽  
Area Network ◽  
Complex Data ◽  
Network Intrusion

The Controller Area Network (CAN) bus works as an important protocol in the real-time In-Vehicle Network (IVN) systems for its simple, suitable, and robust architecture. The risk of IVN devices has still been insecure and vulnerable due to the complex data-intensive architectures which greatly increase the accessibility to unauthorized networks and the possibility of various types of cyberattacks. Therefore, the detection of cyberattacks in IVN devices has become a growing interest. With the rapid development of IVNs and evolving threat types, the traditional machine learning-based IDS has to update to cope with the security requirements of the current environment. Nowadays, the progression of deep learning, deep transfer learning, and its impactful outcome in several areas has guided as an effective solution for network intrusion detection. This manuscript proposes a deep transfer learning-based IDS model for IVN along with improved performance in comparison to several other existing models. The unique contributions include effective attribute selection which is best suited to identify malicious CAN messages and accurately detect the normal and abnormal activities, designing a deep transfer learning-based LeNet model, and evaluating considering real-world data. To this end, an extensive experimental performance evaluation has been conducted. The architecture along with empirical analyses shows that the proposed IDS greatly improves the detection accuracy over the mainstream machine learning, deep learning, and benchmark deep transfer learning models and has demonstrated better performance for real-time IVN security.

scholarly journals DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity

2021 ◽  
Vol 15 ◽  
pp. 117793222110303
Author(s):  
Asad Ahmed ◽  
Bhavika Mam ◽  
Ramanathan Sowdhamini
Keyword(s):  
Deep Learning ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Chemical Space ◽  
Biological Significance ◽  
Protein Crystal ◽  
Ligand Docking ◽  
Complex Data ◽  
Binding Prediction ◽  
Data Set

Protein-ligand binding prediction has extensive biological significance. Binding affinity helps in understanding the degree of protein-ligand interactions and is a useful measure in drug design. Protein-ligand docking using virtual screening and molecular dynamic simulations are required to predict the binding affinity of a ligand to its cognate receptor. Performing such analyses to cover the entire chemical space of small molecules requires intense computational power. Recent developments using deep learning have enabled us to make sense of massive amounts of complex data sets where the ability of the model to “learn” intrinsic patterns in a complex plane of data is the strength of the approach. Here, we have incorporated convolutional neural networks to find spatial relationships among data to help us predict affinity of binding of proteins in whole superfamilies toward a diverse set of ligands without the need of a docked pose or complex as user input. The models were trained and validated using a stringent methodology for feature extraction. Our model performs better in comparison to some existing methods used widely and is suitable for predictions on high-resolution protein crystal (⩽2.5 Å) and nonpeptide ligand as individual inputs. Our approach to network construction and training on protein-ligand data set prepared in-house has yielded significant insights. We have also tested DEELIG on few COVID-19 main protease-inhibitor complexes relevant to the current public health scenario. DEELIG-based predictions can be incorporated in existing databases including RSCB PDB, PDBMoad, and PDBbind in filling missing binding affinity data for protein-ligand complexes.

scholarly journals Synthesis of Prostate MR Images for Classification Using Capsule Network-Based GAN Model

Sensors ◽  
2020 ◽  
Vol 20 (20) ◽  
pp. 5736
Author(s):  
Houqiang Yu ◽  
Xuming Zhang
Keyword(s):  
Prostate Cancer ◽  
Deep Learning ◽  
Data Augmentation ◽  
Spatial Relationship ◽  
Health Concern ◽  
Complex Data ◽  
Mr Images ◽  
Generative Adversarial Network ◽  
Generation Task ◽  
Leibler Divergence

Prostate cancer remains a major health concern among elderly men. Deep learning is a state-of-the-art technique for MR image-based prostate cancer diagnosis, but one of major bottlenecks is the severe lack of annotated MR images. The traditional and Generative Adversarial Network (GAN)-based data augmentation methods cannot ensure the quality and the diversity of generated training samples. In this paper, we have proposed a novel GAN model for synthesis of MR images by utilizing its powerful ability in modeling the complex data distributions. The proposed model is designed based on the architecture of deep convolutional GAN. To learn the more equivariant representation of images that is robust to the changes in the pose and spatial relationship of objects in the images, the capsule network is applied to replace CNN used in the discriminator of regular GAN. Meanwhile, the least squares loss has been adopted for both the generator and discriminator in the proposed GAN to address the vanishing gradient problem of sigmoid cross entropy loss function in regular GAN. Extensive experiments are conducted on the simulated and real MR images. The results demonstrate that the proposed capsule network-based GAN model can generate more realistic and higher quality MR images than the compared GANs. The quantitative comparisons show that among all evaluated models, the proposed GAN generally achieves the smallest Kullback–Leibler divergence values for image generation task and provides the best classification performance when it is introduced into the deep learning method for image classification task.

scholarly journals Complex Data Imputation by Auto-Encoders and Convolutional Neural Networks—A Case Study on Genome Gap-Filling

Computers ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 37 ◽  
Author(s):  
Luca Cappelletti ◽  
Tommaso Fontana ◽  
Guido Walter Di Donato ◽  
Lorenzo Di Tucci ◽  
Elena Casiraghi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Missing Data ◽  
State Of The Art ◽  
The State ◽  
Complex Data ◽  
Data Imputation ◽  
Genome Sequences ◽  
Missing Data Imputation ◽  
The Past ◽  
Learning Techniques

Missing data imputation has been a hot topic in the past decade, and many state-of-the-art works have been presented to propose novel, interesting solutions that have been applied in a variety of fields. In the past decade, the successful results achieved by deep learning techniques have opened the way to their application for solving difficult problems where human skill is not able to provide a reliable solution. Not surprisingly, some deep learners, mainly exploiting encoder-decoder architectures, have also been designed and applied to the task of missing data imputation. However, most of the proposed imputation techniques have not been designed to tackle “complex data”, that is high dimensional data belonging to datasets with huge cardinality and describing complex problems. Precisely, they often need critical parameters to be manually set or exploit complex architecture and/or training phases that make their computational load impracticable. In this paper, after clustering the state-of-the-art imputation techniques into three broad categories, we briefly review the most representative methods and then describe our data imputation proposals, which exploit deep learning techniques specifically designed to handle complex data. Comparative tests on genome sequences show that our deep learning imputers outperform the state-of-the-art KNN-imputation method when filling gaps in human genome sequences.

Application of deep learning methods in biological networks

2020 ◽  
Author(s):  
Shuting Jin ◽  
Xiangxiang Zeng ◽  
Feng Xia ◽  
Wei Huang ◽  
Xiangrong Liu
Keyword(s):  
Deep Learning ◽  
Biological Networks ◽  
Learning Algorithm ◽  
Biological Data ◽  
Training Data ◽  
Learning Ability ◽  
Network Data ◽  
Complex Data ◽  
Layer By Layer ◽  
Information Layer

Abstract The increase in biological data and the formation of various biomolecule interaction databases enable us to obtain diverse biological networks. These biological networks provide a wealth of raw materials for further understanding of biological systems, the discovery of complex diseases and the search for therapeutic drugs. However, the increase in data also increases the difficulty of biological networks analysis. Therefore, algorithms that can handle large, heterogeneous and complex data are needed to better analyze the data of these network structures and mine their useful information. Deep learning is a branch of machine learning that extracts more abstract features from a larger set of training data. Through the establishment of an artificial neural network with a network hierarchy structure, deep learning can extract and screen the input information layer by layer and has representation learning ability. The improved deep learning algorithm can be used to process complex and heterogeneous graph data structures and is increasingly being applied to the mining of network data information. In this paper, we first introduce the used network data deep learning models. After words, we summarize the application of deep learning on biological networks. Finally, we discuss the future development prospects of this field.

scholarly journals A Guide for Using Deep Learning for Complex Trait Genomic Prediction

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 553 ◽  
Author(s):  
Pérez-Enciso ◽  
Zingaretti
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Genomic Prediction ◽  
Genetic Risk ◽  
Complex Trait ◽  
Molecular Data ◽  
Multilayer Perceptrons ◽  
Complex Data ◽  
Theoretical Foundations

Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability to predict phenotypic values from molecular data is less well studied. Here, we describe the theoretical foundations of DL and provide a generic code that can be easily modified to suit specific needs. DL comprises a wide variety of algorithms which depend on numerous hyperparameters. Careful optimization of hyperparameter values is critical to avoid overfitting. Among the DL architectures currently tested in genomic prediction, convolutional neural networks (CNNs) seem more promising than multilayer perceptrons (MLPs). A limitation of DL is in interpreting the results. This may not be relevant for genomic prediction in plant or animal breeding but can be critical when deciding the genetic risk to a disease. Although DL technologies are not ”plug-and-play”, they are easily implemented using Keras and TensorFlow public software. To illustrate the principles described here, we implemented a Keras-based code in GitHub.

scholarly journals Towards Repayment Prediction in Peer-to-Peer Social Lending Using Deep Learning

Mathematics ◽  
2019 ◽  
Vol 7 (11) ◽  
pp. 1041 ◽  
Author(s):  
Kim ◽  
Cho
Keyword(s):  
Deep Learning ◽  
Design Feature ◽  
Feature Space ◽  
Peer To Peer ◽  
Complex Data ◽  
Complex Information ◽  
Social Lending ◽  
P2p Lending ◽  
Complex Features ◽  
Deep Learning Model

Peer-to-Peer (P2P) lending transactions take place by the lenders choosing a borrower and lending money. It is important to predict whether a borrower can repay because the lenders must bear the credit risk when the borrower defaults, but it is difficult to design feature extractors with very complex information about borrowers and loan products. In this paper, we present an architecture of deep convolutional neural network (CNN) for predicting the repayment in P2P social lending to extract features automatically and improve the performance. CNN is a deep learning model for classifying complex data, which extracts discriminative features automatically by convolution operation on lending data. We classify the borrower’s loan status by capturing the robust features and learning the patterns. Experimental results with 5-fold cross-validation show that our method automatically extracts complex features and is effective in repayment prediction on Lending Club data. In comparison with other machine learning methods, the standard CNN has achieved the highest performance with 75.86%. Exploiting various CNN models such as Inception, ResNet, and Inception-ResNet results in the state-of-the-art performance of 77.78%. We also demonstrate that the features extracted by our model are better performed by projecting the samples into the feature space.

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