Predicting drug-target affinity based on recurrent neural networks and graph convolutional neural networks

Background: Drug development requires a lot of money and time, and the outcome of the challenge is unknown. So, there is an urgent need for researchers to find a new approach that can reduce costs. Therefore, the identification of drug-target interactions (DTIs) has been a critical step in the early stages of drug discovery. These computational methods aim to narrow the search space for novel DTIs and to elucidate the functional background of drugs. Most of the methods developed so far use binary classification to predict the presence or absence of interactions between the drug and the target. However, it is more informative, but also more challenging, to predict the strength of the binding between a drug and its target. If the strength is not strong enough, such a DTI may not be useful. Hence, the development of methods to predict drug-target affinity (DTA) is of significant importance. Method: We have improved the Graph DTA model from a dual-channel model to a triple-channel model. We interpreted the target/protein sequences as time series and extracted their features using the LSTM network. For the drug, we considered both the molecular structure and the local chemical background, retaining the four variant networks used in Graph DTA to extract the topological features of the drug and capturing the local chemical background of the atoms in the drug by using BiGRU. Thus, we obtained the latent features of the target and two latent features of the drug. The connection of these three feature vectors is then input into a 2-layer FC network, and a valuable binding affinity is output. Result: We use the Davis and Kiba datasets, using 80% of the data for training and 20% of the data for validation. Our model shows better performance by comparing it with the experimental results of Graph DTA. Conclusion: In this paper, we altered the Graph DTA model to predict drug-target affinity. It represents the drug as a graph, and extracts the two-dimensional drug information using a graph convolutional neural network. Simultaneously, the drug and protein targets are represented as a word vector, and the convolutional neural network is used to extract the time series information of the drug and the target. We demonstrate that our improved method has better performance than the original method. In particular, our model has better performance in the evaluation of benchmark databases.

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Convolutional Neural Network Classification of Telematics Car Driving Data

Risks ◽

10.3390/risks7010006 ◽

2019 ◽

Vol 7 (1) ◽

pp. 6 ◽

Cited By ~ 9

Author(s):

Guangyuan Gao ◽

Mario Wüthrich

Keyword(s):

Neural Network ◽

Neural Networks ◽

Time Series ◽

Convolutional Neural Network ◽

High Frequency ◽

Location Data ◽

Neural Network Classification ◽

Feature Information ◽

Car Driving

The aim of this project is to analyze high-frequency GPS location data (second per second) of individual car drivers (and trips). We extract feature information about speeds, acceleration, deceleration, and changes of direction from this high-frequency GPS location data. Time series of this feature information allow us to appropriately allocate individual car driving trips to selected drivers using convolutional neural networks.

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Economic Structure Analysis Based on Neural Network and Bionic Algorithm

Complexity ◽

10.1155/2021/9925823 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Yanjun Dai ◽

Lin Su

Keyword(s):

Neural Network ◽

Neural Networks ◽

Convolutional Neural Network ◽

Optimization Algorithm ◽

Economic Structure ◽

Search Space ◽

Weight Space ◽

Neural Structure ◽

Migration Strategy ◽

Structure Space

In this article, an in-depth study and analysis of economic structure are carried out using a neural network fusion release algorithm. The method system defines the weight space and structure space of neural networks from the perspective of optimization theory, proposes a bionic optimization algorithm under the weight space and structure space, and establishes a neuroevolutionary method with shallow neural network and deep neural network as the research objects. In the shallow neuroevolutionary, the improved genetic algorithm (IGA) based on elite heuristic operation and migration strategy and the improved coyote optimization algorithm (ICOA) based on adaptive influence weights are proposed, and the shallow neuroevolutionary method based on IGA and the shallow neuroevolutionary method based on ICOA are applied to the weight space of backpropagation (BP) neural networks. In deep neuroevolutionary method, the structure space of convolutional neural network is proposed to solve the search space design of neural structure search (NAS), and the GA-based deep neuroevolutionary method under the structure space of convolutional neural network is proposed to solve the problem that numerous hyperparameters and network structure parameters can produce explosive combinations when designing deep learning models. The neural network fusion bionic algorithm used has the application value of exploring the spatial structure and dynamics of the socioeconomic system, improving the perception of the socioeconomic situation, and understanding the development law of society, etc. The idea is also verifiable through the present computer technology.

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Convolutional Neural Network Coupled with a Transfer-Learning Approach for Time-Series Flood Predictions

Water ◽

10.3390/w12010096 ◽

2019 ◽

Vol 12 (1) ◽

pp. 96 ◽

Cited By ~ 5

Author(s):

Nobuaki Kimura ◽

Ikuo Yoshinaga ◽

Kenji Sekijima ◽

Issaku Azechi ◽

Daichi Baba

Keyword(s):

Neural Network ◽

Neural Networks ◽

Time Series ◽

Convolutional Neural Network ◽

Transfer Learning ◽

Learning Approach ◽

Target Domain ◽

Training Time ◽

Source Domain ◽

Flood Model

East Asian regions in the North Pacific have recently experienced severe riverine flood disasters. State-of-the-art neural networks are currently utilized as a quick-response flood model. Neural networks typically require ample time in the training process because of the use of numerous datasets. To reduce the computational costs, we introduced a transfer-learning approach to a neural-network-based flood model. For a concept of transfer leaning, once the model is pretrained in a source domain with large datasets, it can be reused in other target domains. After retraining parts of the model with the target domain datasets, the training time can be reduced due to reuse. A convolutional neural network (CNN) was employed because the CNN with transfer learning has numerous successful applications in two-dimensional image classification. However, our flood model predicts time-series variables (e.g., water level). The CNN with transfer learning requires a conversion tool from time-series datasets to image datasets in preprocessing. First, the CNN time-series classification was verified in the source domain with less than 10% errors for the variation in water level. Second, the CNN with transfer learning in the target domain efficiently reduced the training time by 1/5 of and a mean error difference by 15% of those obtained by the CNN without transfer learning, respectively. Our method can provide another novel flood model in addition to physical-based models.

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Structural-parametric synthesis of deep learning neural networks

Artificial Intelligence ◽

10.15407/jai2020.04.042 ◽

2020 ◽

Vol 25 (4) ◽

pp. 42-51

Author(s):

Sineglazov V.M. ◽

◽

Chumachenko O.I. ◽

Keyword(s):

Neural Network ◽

Genetic Algorithm ◽

Neural Networks ◽

Deep Learning ◽

Convolutional Neural Network ◽

Convolutional Neural Networks ◽

Search Space ◽

Training Sample ◽

Parametric Synthesis ◽

Encoding Method

The structural-parametric synthesis of neural networks of deep learning, in particular convolutional neural networks used in image processing, is considered. The classification of modern architectures of convolutional neural networks is given. It is shown that almost every convolutional neural network, depending on its topology, has unique blocks that determine its essential features (for example, Squeeze and Excitation Block, Convolutional Block of Attention Module (Channel attention module, Spatial attention module), Residual block, Inception module, ResNeXt block. It is stated the problem of structural-parametric synthesis of convolutional neural networks, for the solution of which it is proposed to use a genetic algorithm. The genetic algorithm is used to effectively overcome a large search space: on the one hand, to generate possible topologies of the convolutional neural network, namely the choice of specific blocks and their locations in the structure of the convolutional neural network, and on the other hand to solve the problem of structural-parametric synthesis of convolutional neural network of selected topology. The most significant parameters of the convolutional neural network are determined. An encoding method is proposed that allows to repre- sent each network structure in the form of a string of fixed length in binary format. After that, several standard genetic operations were identified, i.e. selection, mutation and crossover, which eliminate weak individuals of the previous generation and use them to generate competitive ones. An example of solving this problem is given, a database (ultrasound results) of patients with thyroid disease was used as a training sample.

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Multi-State Household Appliance Identification Based on Convolutional Neural Networks and Clustering

Energies ◽

10.3390/en13040792 ◽

2020 ◽

Vol 13 (4) ◽

pp. 792 ◽

Cited By ~ 2

Author(s):

Ying Zhang ◽

Bo Yin ◽

Yanping Cong ◽

Zehua Du

Keyword(s):

Neural Network ◽

Neural Networks ◽

Time Series ◽

Energy Consumption ◽

Convolutional Neural Network ◽

Neural Network Model ◽

Clustering Algorithm ◽

Identification Accuracy ◽

Household Appliance ◽

Load Monitoring

Non-intrusive load monitoring, a convenient way to discern the energy consumption of a house, has been studied extensively. However, most research works have been carried out based on a hypothetical condition that each electric appliance has only one running state. This leads to low identification accuracy for multi-state electric appliances. To deal with this problem, a method for identifying the type and state of electric appliances based on a power time series is proposed in this paper. First, to identify the type of appliance, a convolutional neural network model was constructed that incorporated residual modules. Then, a k-means clustering algorithm was applied to calculate the number of states of the appliance. Finally, in order to identify the states of the appliances, different k-means clustering models were established for different multi-state electric appliances. Experimental results show effectiveness of the proposed method in identifying both the type and the running state of electric appliances.

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Neural Network Techniques for Time Series Prediction: A Review

JOIV International Journal on Informatics Visualization ◽

10.30630/joiv.3.3.281 ◽

2019 ◽

Vol 3 (3) ◽

Author(s):

Muhammad Faheem Mushtaq ◽

Urooj Akram ◽

Muhammad Aamir ◽

Haseeb Ali ◽

Muhammad Zulqarnain

Keyword(s):

Neural Network ◽

Neural Networks ◽

Time Series ◽

Time Series Data ◽

Weather Prediction ◽

Time Series Prediction ◽

Series Data ◽

Prediction Problem ◽

Neural Network Models ◽

Physical Time

It is important to predict a time series because many problems that are related to prediction such as health prediction problem, climate change prediction problem and weather prediction problem include a time component. To solve the time series prediction problem various techniques have been developed over many years to enhance the accuracy of forecasting. This paper presents a review of the prediction of physical time series applications using the neural network models. Neural Networks (NN) have appeared as an effective tool for forecasting of time series. Moreover, to resolve the problems related to time series data, there is a need of network with single layer trainable weights that is Higher Order Neural Network (HONN) which can perform nonlinearity mapping of input-output. So, the developers are focusing on HONN that has been recently considered to develop the input representation spaces broadly. The HONN model has the ability of functional mapping which determined through some time series problems and it shows the more benefits as compared to conventional Artificial Neural Networks (ANN). The goal of this research is to present the reader awareness about HONN for physical time series prediction, to highlight some benefits and challenges using HONN.

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Using Convolutional Neural Network and Candlestick Representation to Predict Sports Match Outcomes

Applied Sciences ◽

10.3390/app11146594 ◽

2021 ◽

Vol 11 (14) ◽

pp. 6594

Author(s):

Yu-Chia Hsu

Keyword(s):

Neural Network ◽

Time Series ◽

Pattern Recognition ◽

Logistic Regression ◽

Regression Model ◽

Convolutional Neural Network ◽

Logistic Regression Model ◽

National Football League ◽

Performance Metrics ◽

Betting Market

The interdisciplinary nature of sports and the presence of various systemic and non-systemic factors introduce challenges in predicting sports match outcomes using a single disciplinary approach. In contrast to previous studies that use sports performance metrics and statistical models, this study is the first to apply a deep learning approach in financial time series modeling to predict sports match outcomes. The proposed approach has two main components: a convolutional neural network (CNN) classifier for implicit pattern recognition and a logistic regression model for match outcome judgment. First, the raw data used in the prediction are derived from the betting market odds and actual scores of each game, which are transformed into sports candlesticks. Second, CNN is used to classify the candlesticks time series on a graphical basis. To this end, the original 1D time series are encoded into 2D matrix images using Gramian angular field and are then fed into the CNN classifier. In this way, the winning probability of each matchup team can be derived based on historically implied behavioral patterns. Third, to further consider the differences between strong and weak teams, the CNN classifier adjusts the probability of winning the match by using the logistic regression model and then makes a final judgment regarding the match outcome. We empirically test this approach using 18,944 National Football League game data spanning 32 years and find that using the individual historical data of each team in the CNN classifier for pattern recognition is better than using the data of all teams. The CNN in conjunction with the logistic regression judgment model outperforms the CNN in conjunction with SVM, Naïve Bayes, Adaboost, J48, and random forest, and its accuracy surpasses that of betting market prediction.

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System for Forecasting COVID-19 Cases Using Time-Series and Neural Networks Models

Engineering Proceedings ◽

10.3390/engproc2021005046 ◽

2021 ◽

Vol 5 (1) ◽

pp. 46

Author(s):

Mostafa Abotaleb ◽

Tatiana Makarovskikh

Keyword(s):

Neural Network ◽

Neural Networks ◽

Time Series ◽

Time Series Models ◽

Third Wave ◽

The Third ◽

Modeling And Forecasting ◽

Auto Regressive ◽

The Russian Federation ◽

R Programming

COVID-19 is one of the biggest challenges that countries face at the present time, as infections and deaths change daily and because this pandemic has a dynamic spread. Our paper considers two tasks. The first one is to develop a system for modeling COVID-19 based on time-series models due to their accuracy in forecasting COVID-19 cases. We developed an “Epidemic. TA” system using R programming for modeling and forecasting COVID-19 cases. This system contains linear (ARIMA and Holt’s model) and non-linear (BATS, TBATS, and SIR) time-series models and neural network auto-regressive models (NNAR), which allows us to obtain the most accurate forecasts of infections, deaths, and vaccination cases. The second task is the implementation of our system to forecast the risk of the third wave of infections in the Russian Federation.

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Classification of Skin Disease Using Deep Learning Neural Networks with MobileNet V2 and LSTM

Sensors ◽

10.3390/s21082852 ◽

2021 ◽

Vol 21 (8) ◽

pp. 2852

Author(s):

Parvathaneni Naga Srinivasu ◽

Jalluri Gnana SivaSai ◽

Muhammad Fazal Ijaz ◽

Akash Kumar Bhoi ◽

Wonjoon Kim ◽

...

Keyword(s):

Neural Network ◽

Neural Networks ◽

Deep Learning ◽

Convolutional Neural Network ◽

Skin Disease ◽

Network Architecture ◽

Large Scale ◽

Short Term Memory ◽

Convolutional Networks ◽

Occurrence Matrix

Deep learning models are efficient in learning the features that assist in understanding complex patterns precisely. This study proposed a computerized process of classifying skin disease through deep learning based MobileNet V2 and Long Short Term Memory (LSTM). The MobileNet V2 model proved to be efficient with a better accuracy that can work on lightweight computational devices. The proposed model is efficient in maintaining stateful information for precise predictions. A grey-level co-occurrence matrix is used for assessing the progress of diseased growth. The performance has been compared against other state-of-the-art models such as Fine-Tuned Neural Networks (FTNN), Convolutional Neural Network (CNN), Very Deep Convolutional Networks for Large-Scale Image Recognition developed by Visual Geometry Group (VGG), and convolutional neural network architecture that expanded with few changes. The HAM10000 dataset is used and the proposed method has outperformed other methods with more than 85% accuracy. Its robustness in recognizing the affected region much faster with almost 2× lesser computations than the conventional MobileNet model results in minimal computational efforts. Furthermore, a mobile application is designed for instant and proper action. It helps the patient and dermatologists identify the type of disease from the affected region’s image at the initial stage of the skin disease. These findings suggest that the proposed system can help general practitioners efficiently and effectively diagnose skin conditions, thereby reducing further complications and morbidity.

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Nonlinear Time-Series Analysis of Pulsation of Post-AGB Stars by Genetic Algorithm/Neural Network Hybrid Systems

International Astronomical Union Colloquium ◽

10.1017/s0252921100057419 ◽

2000 ◽

Vol 176 ◽

pp. 135-136

Author(s):

Toshiki Aikawa

Keyword(s):

Neural Network ◽

Genetic Algorithm ◽

Neural Networks ◽

Time Series ◽

Artificial Neural Networks ◽

Hybrid System ◽

Nonlinear Time Series ◽

Photometric Data ◽

Nonlinear Time Series Analysis ◽

Agb Stars

AbstractSome pulsating post-AGB stars have been observed with an Automatic Photometry Telescope (APT) and a considerable amount of precise photometric data has been accumulated for these stars. The datasets, however, are still sparse, and this is a problem for applying nonlinear time series: for instance, modeling of attractors by the artificial neural networks (NN) to the datasets. We propose the optimization of data interpolations with the genetic algorithm (GA) and the hybrid system combined with NN. We apply this system to the Mackey–Glass equation, and attempt an analysis of the photometric data of post-AGB variables.

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