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Drug–target interactions prediction based on similarity graph features extraction and deep learning

Neural Computing and Applications 2025年第6期37卷 4303-4322页

作者： Torkey, Hanaa El-Behery, Heba Attia, Abdel-Fattah El-Fishawy, Nawal Computer Science and Engineering Department Faculty of Electronic Engineering Menoufia University Menouf Egypt Department of Computer Science and Engineering Faculty of Engineering Kafrelsheikh University Kafrelsheikh Egypt Department of Computer Science College of Computer Engineering and Sciences Prince Sattam Bin Abdulaziz University Al-Kharj Saudi Arabia

Identifying drug–target interactions (DTIs) is a critical step in both drug repositioning. The labor-intensive, time-consuming, and costly nature of classic DTI laboratory studies makes it imperative to create efficient computer algorithms to forecast possible DTIs. However, current computational approaches that predict potential drug–target interactions (DTIs) suffer from some limitations, like finding the best similarity measures or negative samples, and thus require substantial performance improvement. This study proposes an integrated approach based on feature representation and deep learning to predict DTIs. We extract the relevant features of drugs and proteins from heterogeneous networks using graph mining techniques. The proposed approach constructs a heterogeneous graph from the known drug–protein interactions, protein–protein, and drug–drug similarities. Then applying two feature extraction techniques to extract the features, then utilizing these features in training a deep learning model to predict the potential DTIs. Also, a novel algorithm is proposed to find the negative samples based on the drug and protein similarity matrices. Four Benchmark datasets are used to evaluate the proposed approach. Our approach achieves the highest AUC (area under the ROC curve) across all datasets (0.98) with around 2% increases over the existing methods. Experimental results demonstrate that our proposed approach outperforms the baseline methods in predicting DTI, and our negative sample-identifying algorithm could be established as a competitive solution. © The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2024.

关键词： Contrastive Learning

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Image classification of lotus in Nong Han Chaloem Phrakiat Lotus Park using convolutional neural networks

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Artificial Intelligence in Agriculture 2024年第1期11卷 23-33页

作者： Thanawat Phattaraworamet Sawinee Sangsuriyun Phoempol Kutchomsri Susama Chokphoemphun Department of Electrical and Computer Engineering Faculty of Science and EngineeringKasetsart University Chalermphrakiat Sakonnakhon Province Campus SakonnakhonThailand Department of Computer and Information Science Faculty of Science and EngineeringKasetsart University Chalermphrakiat Sakonnakhon Province Campus SakonnakhonThailand

The Nong Han Chaloem Phrakiat Lotus Park is a tourist attraction and a source of learning regarding lotus ***,as a training area,it lacks appeal and learning motivation due to its conventional presentation of information regarding lotus *** current study introduced the concept of smart learning in this setting to increase interest and motivation for *** neural networks(CNNs)were used for the classification of lotus plant species,for use in the development of a mobile application to display details about each *** scope of the study was to classify 11 species of lotus plants using the proposed CNN model based on different techniques(augmentation,dropout,and L2)and hyper parameters(dropout and epoch number).The expected outcome was to obtain a high-performance CNN model with reduced total parameters compared to using three different pre-trained CNN models(Inception V3,VGG16,and VGG19)as *** performance of the model was presented in terms of accuracy,F1-score,precision,and recall *** results showed that the CNN model with the augmentation,dropout,and L2 techniques at a dropout value of 0.4 and an epoch number of 30 provided the highest testing accuracy of *** best proposed model was more accurate than the pre-trained CNN models,especially compared to Inception *** addition,the number of total parameters was reduced by approximately 1.80–2.19 *** findings demonstrated that the proposed model with a small number of total parameters had a satisfactory degree of classification accuracy.

关键词： Lotus Park Classification Smart learning park Convolutional neural network

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Arrhythmia Detection by Using Chaos Theory with Machine Learning Algorithms

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computers, Materials & Continua 2024年第6期79卷 3855-3875页

作者： Maie Aboghazalah Passent El-kafrawy Abdelmoty M.Ahmed Rasha Elnemr Belgacem Bouallegue Ayman El-sayed Math and Computer Science Department Faculty of ScienceMenoufia UniversityShebin El-komEgypt College of Engineering Computer Science DepartmentEffat UniversityJeddahKingdom of Saudi Arabia Department of Computer Engineering College of Computer ScienceKing Khalid UniversityAbha61421Saudi Arabia Computer Science and Engineering Department Faculty of Electronic EngineeringMenoufia UniversityShebin El-komEgypt Climate Change Information Center and Expert Systems Agriculture Research CenterGizaEgypt

Heart monitoring improves life ***(ECGs or EKGs)detect heart *** learning algorithms can create a few ECG diagnosis processing *** first method uses raw ECG and time-series *** second method classifies the ECG by patient *** third technique translates ECG impulses into Q waves,R waves and S waves(QRS)features using richer *** ECG signals vary naturally between humans and activities,we will combine the three feature selection methods to improve classification accuracy and *** using all three approaches have not been examined till *** researchers found that Machine Learning(ML)techniques can improve ECG *** study will compare popular machine learning techniques to evaluate ECG *** algorithms—Support Vector Machine(SVM),Decision Tree,Naive Bayes,and Neural Network—compare categorization *** plus prior knowledge has the highest accuracy(99%)of the four ML *** characteristics failed to identify signals without chaos *** 99.8%classification accuracy,the Decision Tree technique outperformed all previous experiments.

关键词： ECG extraction ECG leads time series prior knowledge and arrhythmia chaos theory QRS complex analysis machine learning ECG classification

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Weighted rank aggregation based on ranker accuracies for feature selection

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Soft Computing 2025年第4期29卷 1981-2001页

作者： Abdolrazzagh-Nezhad, Majid Kherad, Mahdi Faculty of Engineering Department of Computer Engineering Bozorgmehr University of Qaenat Qaen Iran Department of Computer Science Faculty of Computer and Industrial Engineering Birjand University of Technology Birjand Iran Faculty of Engineering Department of Computer Engineering University of Qom Qom Iran

Rank aggregation is the combination of several ranked lists from a set of candidates to achieve a better ranking by combining information from different sources. In feature selection problem, due to the heterogeneity of methods, there are some base rankers (Filter-based methods) that are of diverse quality and usually the ground truth of ratings is not available. Existing rank aggregation methods that take the diverse quality of base rankers into account do not have any explicit approach for appropriate weighting, require prior assumptions, and suffers from high computational complexity. In this paper, to overcome these challenges, an efficient unsupervised method is introduced for estimating the base rankers’ qualities and aggregating the rankers based on the estimated weights. We first compute the ratio of disagreement between base rankers in ordering different element pairs and then estimate the accuracies in a way that to minimize the discrepancy between these computed ratios and their analytical counterparts. We use the weighted majority voting method for obtaining the aggregated results. To resolve the probable inconsistencies in the final aggregation, the result is formed as a graph, and a greedy algorithm is used to find an acyclic subgraph with the highest weigh. To demonstrate the performance of the proposed method, nine standard UCI datasets are used. The obtained results by the proposed method have higher values of classifier measures than the existing baseline Feature Selection methods and rank aggregation-based multi-filter methods in the most datasets. The experiments show that rank aggregation-based Feature Selection methods outperform individual methods. The proposed method also shows the weight of each Filter-based Feature Selection method, in which the MRMR method has a higher weight than other methods. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.

关键词： Wiener filtering

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Rice spikelet’s disease detection using hybrid optimization model and optimized CNN

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Soft Computing 2024年第21期28卷 12787-12806页

作者： Patel, Bharati Department of Computer Science and Engineering Faculty of Science and Technology ICFAI University Raipur India

Rice fields all across the world are affected by spikelet sterility, often known as rice spikelet's disease. It is characterized by the improper development of spikelet’s, which lowers grain output and quality. For optimal management and the avoidance of yield losses, this disease must be discovered early. In this study, a deep learning-based approach utilizing optimization techniques was proposed for accurate segmentation and disease detection in rice crops. The research aimed to address the vulnerability of rice crops to disease attacks from seed germination to mature spikelets. The proposed model consisted of three major phases: pre-processing, segmentation, feature extraction and disease detection. Gaussian filtering was employed to preprocess the raw rice crop images, while a new hybrid Whale Customized Gravitational Optimization Algorithm was utilized for segmentation. Disease detection was performed using a hybrid deep learning model called HybridNet, which combines convolutional neural networks (CNN) with an optimized recurrent neural network (RNN) model. The dataset intended for this proposed project is sourced from the CABI PlantwisePlus Knowledge Bank. The proposed model for rice spikelet disease detection achieved high accuracy with Sensitivity (0.9269), Specificity (0.9756), and Accuracy (0.9634). This indicates that the model effectively identifies and detects diseases in rice spikelets, demonstrating its reliable performance in disease management and crop protection. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.

关键词： Convolutional neural networks

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A State-Migration Particle Swarm Optimizer for Adaptive Latent Factor Analysis of High-Dimensional and Incomplete Data

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IEEE/CAA Journal of Automatica Sinica 2024年第11期11卷 2220-2235页

作者： Jiufang Chen Kechen Liu Xin Luo Ye Yuan Khaled Sedraoui Yusuf Al-Turki MengChu Zhou IEEE the College of Computer Science and Technology Chongqing University of Posts and Telecommunications the Department of Computer Science Columbia University the College of Computer and Information Science Southwest University the Department of Electrical and Computer Engineering Faculty of Engineeringand also with K.A.CARE Energy Research and Innovation CenterKing Abdulaziz University the Center of Research Excellence in Renewable Energy and Power Systems the Department of Electrical and Computer EngineeringFaculty of Engineeringand also with K.A.CARE Energy Research and Innovation CenterKing Abdulaziz University the Department of Electrical and Computer Engineering New Jersey Institute of Technology

High-dimensional and incomplete(HDI) matrices are primarily generated in all kinds of big-data-related practical applications. A latent factor analysis(LFA) model is capable of conducting efficient representation learning to an HDI matrix,whose hyper-parameter adaptation can be implemented through a particle swarm optimizer(PSO) to meet scalable ***, conventional PSO is limited by its premature issues,which leads to the accuracy loss of a resultant LFA model. To address this thorny issue, this study merges the information of each particle's state migration into its evolution process following the principle of a generalized momentum method for improving its search ability, thereby building a state-migration particle swarm optimizer(SPSO), whose theoretical convergence is rigorously proved in this study. It is then incorporated into an LFA model for implementing efficient hyper-parameter adaptation without accuracy loss. Experiments on six HDI matrices indicate that an SPSO-incorporated LFA model outperforms state-of-the-art LFA models in terms of prediction accuracy for missing data of an HDI matrix with competitive computational ***, SPSO's use ensures efficient and reliable hyper-parameter adaptation in an LFA model, thus ensuring practicality and accurate representation learning for HDI matrices.

关键词： Data science generalized momentum high-dimensional and incomplete(HDI)data hyper-parameter adaptation latent factor analysis(LFA) particle swarm optimization(PSO)

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Neutrosophic Fuzzy Power Management (NFPM): Tackling Uncertainty in Energy Harvesting for Sensor Networks

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Neutrosophic Sets and systems 2025年 76卷 99-114页

作者： Alzubi, Musallam M. Mohamed, Mohamed A. Amer, Hanan M. Salama, A.A. Electronics and Communications Engineering Department Faculty of Engineering Mansoura University Mansoura Egypt Department of Mathematics and Computer Science Faculty of Science Port Said University Egypt

This paper presents a novel approach known as Neutrosophic Fuzzy Power Management (NFPM) aimed at addressing the critical challenge of uncertain energy availability in Energy Harvesting Sensor Networks (EHWSNs). The main objective of this research is to enhance the management of energy resources within these networks, which traditional fuzzy logic methods often fail to do, leading to power failures and reduced reliability. NFPM utilizes neutrosophic logic to effectively model uncertainty by representing the degrees of truth, indeterminacy, and falsity of both harvested and residual energy levels. Through a fuzzy inference system, NFPM dynamically allocates energy budgets for each time slot based on these neutrosophic sets, resulting in more adaptive and conservative energy distribution. The results are validated through numerical examples and extensive simulations, demonstrating NFPM's superiority over traditional fuzzy logic, with significant improvements such as a 25% reduction in power failures, 95% enhanced network connectivity, a 15% increase in data transmission success rates, and overall improvements in energy efficiency and robustness to fluctuations and noise. This research establishes NFPM as a promising solution to the uncertainties inherent in EHWSNs. Future research directions include exploring the integration of NFPM with machine learning algorithms for predictive energy management, assessing its scalability in larger networks, and examining its applicability in other domains requiring energy management under uncertainty. © 2025, University of New Mexico. All rights reserved.

关键词： Budget control

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Drug-Target Interactions Prediction Based on Signed Heterogeneous Graph Neural Networks

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Chinese Journal of Electronics 2024年第1期33卷 231-244页

作者： Ming CHEN Yajian JIANG Xiujuan LEI Yi PAN Chunyan JI Wei JIANG College of Information Science and Engineering Hunan Normal University School of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Computer Science Department BNU-HKBU United International College

Drug-target interactions(DTIs) prediction plays an important role in the process of drug *** computational methods treat it as a binary prediction problem, determining whether there are connections between drugs and targets while ignoring relational types information. Considering the positive or negative effects of DTIs will facilitate the study on comprehensive mechanisms of multiple drugs on a common target, in this work, we model DTIs on signed heterogeneous networks, through categorizing interaction patterns of DTIs and additionally extracting interactions within drug pairs and target protein pairs. We propose signed heterogeneous graph neural networks(SHGNNs), further put forward an end-to-end framework for signed DTIs prediction, called SHGNN-DTI,which not only adapts to signed bipartite networks, but also could naturally incorporate auxiliary information from drug-drug interactions(DDIs) and protein-protein interactions(PPIs). For the framework, we solve the message passing and aggregation problem on signed DTI networks, and consider different training modes on the whole networks consisting of DTIs, DDIs and PPIs. Experiments are conducted on two datasets extracted from Drug Bank and related databases, under different settings of initial inputs, embedding dimensions and training modes. The prediction results show excellent performance in terms of metric indicators, and the feasibility is further verified by the case study with two drugs on breast cancer.

关键词： Drug-target interactions Signed heterogeneous network Link sign prediction Graph neural networks

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An Encoding-Decoding Framework Based on CNN for circ RNA-RBP Binding Sites Prediction

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Chinese Journal of Electronics 2024年第1期33卷 256-263页

作者： Yajing GUO Xiujuan LEI Yi PAN School of Computer Science Shaanxi Normal University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Department of Computer Science Georgia State University

Predicting RNA binding protein(RBP) binding sites on circular RNAs(circ RNAs) is a fundamental step to understand their interaction mechanism. Numerous computational methods are developed to solve this problem, but they cannot fully learn the features. Therefore, we propose circ-CNNED, a convolutional neural network(CNN)-based encoding and decoding framework. We first adopt two encoding methods to obtain two original matrices. We preprocess them using CNN before fusion. To capture the feature dependencies, we utilize temporal convolutional network(TCN) and CNN to construct encoding and decoding blocks, respectively. Then we introduce global expectation pooling to learn latent information and enhance the robustness of circ-CNNED. We perform circ-CNNED across 37 datasets to evaluate its effect. The comparison and ablation experiments demonstrate that our method is superior. In addition, motif enrichment analysis on four datasets helps us to explore the reason for performance improvement of circ-CNNED.

关键词： Circular RNAs (circRNAs) RNA binding proteins Convolutional neural network Temporal convolutional network Encoder-decoder network

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A new bi-level deep human action representation structure based on the sequence of sub-actions

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Neural Computing and Applications 2025年第2期37卷 985-1008页

作者： Akhlaghian Tab, Fardin Ramezani, Mohsen Afshoon, Hadi Seyedi, Seyed Amjad Moradyani, Atefeh Department of Computer Engineering Faculty of Engineering University of Kurdistan Sanandaj Iran Department of Computer Science University of Kurdistan Sanandaj Iran

Human action recognition is applicable in different domains. Previously proposed methods cannot appropriately consider the sequence of sub-actions. Herein, we propose a semantical action model based on the sequence of sub-actions. A technique is used to segment actions on the time axis based on body movements via an energy diagram. After dividing actions into sub-actions, a novel bi-level deep structure is used to extract their features. Then, the sequence of sub-action features is modeled by a deep network to create the action model. As extracted sub-actions have fewer variations in execution manner, their representation is more stable, and modeling their sequence would be an efficient model. Experimental results on UCF-YouTube, UCF-Sport, and Human Motion DataBase (HMDB) datasets indicate the sustainable performance of this method. Overall, the accuracy of the proposed method is 0.972 on average, while the value for the second-best method is 0.925. © The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2024.

关键词： Human form models

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