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

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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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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Predicting circRNA-Disease Associations by Using Multi-Biomolecular Networks Based on Variational Graph Auto-Encoder with Attention Mechanism

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Chinese Journal of Electronics 2024年第6期33卷 1526-1537页

作者： Jing YANG 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 Shenzhen Key Laboratory of Intelligent Bioinformatics Shenzhen Institute of Advanced Technology

CircRNA-disease association(CDA) can provide a new direction for the treatment of diseases. However,traditional biological experiment is time-consuming and expensive, this urges us to propose the reliable computational model to predict the associations between circRNAs and diseases. And there is existing more and more evidence indicates that the combination of multi-biomolecular information can improve the prediction accuracy. We propose a novel computational model for CDA prediction named MBCDA, we collect the multi-biomolecular information including circRNA, disease, miRNA and lncRNA based on 6 databases, and construct three heterogeneous network among them, then the multi-heads graph attention networks are applied to these three networks to extract the features of circRNAs and diseases from different views, the obtained features are put into variational graph auto-encoder(VGAE) network to learn the latent distributions of the nodes, a fully connected neural network is adopted to further process the output of VGAE and uses sigmoid function to obtain the predicted probabilities of circRNA-disease *** a result, MBCDA achieved the values of AUC and AUPR under 5-fold cross-validation of 0.893 and 0.887. MBCDA was applied to the analysis of the top-25 predicted associations between circRNAs and diseases, these experimental results show that our proposed MBCDA is a powerful computational model for CDA prediction.

关键词： Knowledge engineering Attention mechanisms Computational modeling Biological system modeling Predictive models Feature extraction Heterogeneous networks Topology Data mining Diseases

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Improving agility in projects using machine learning algorithm

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Multimedia Tools and Applications 2024年第38期83卷 85987-86005页

作者： Varun, Janani Karthika, R.A. Department of Computer Science and Engineering Vels Institute of Science Technology and Advanced Studies Chennai India Department of Computer Science and Engineering Saveetha School of Engineering SIMATS Chennai India

All the software products developed will need testing to ensure the quality and accuracy of the product. It makes the life of testers much easier when they can optimize on the effort spent and predict defects for the upcoming modules in the Agile era. The functionality being discussed in this paper is to predict the defects using Random Forest Algorithm. Predictive analytics draws on information from the past to create forecasts about the outcomes of future events. Product team always have the difficulty in delivering the product as per schedule. As we are in the agile era, the requirement keeps changing and team is unsure on upcoming releases. Prediction helps the team to focus on the complex and error prone modules in upcoming releases. The Predictive analytics model designed, can predict defects with an accuracy rate of 88% with the help of historical data. By predicting, testers can focus on the module where there are a greater number of defects predicted by the model and left shift the delivery. © The Author(s), under exclusive licence to Springer science+Business Media, LLC, part of Springer Nature 2024.

关键词： Predictive analytics

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Highly Efficient Back‑End‑of‑Line Compatible Flexible Si‑Based Optical Memristive Crossbar Array for Edge Neuromorphic Physiological Signal Processing and Bionic Machine Vision

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Nano-Micro Letters 2024年第11期16卷 323-339页

作者： Dayanand Kumar Hanrui Li Dhananjay D.Kumbhar Manoj Kumar Rajbhar Uttam Kumar Das Abdul Momin Syed Georgian Melinte Nazek El‑Atab Smart Advanced Memory Devices and Applications(SAMA)LaboratoryElectrical and Computer EngineeringComputer Electrical Mathematical Science and EngineeringKing Abdullah University of Science and Technology(KAUST)23955‑6900 ThuwalSaudi Arabia

The emergence of the Internet-of-Things is anticipated to create a vast market for what are known as smart edge devices,opening numerous opportunities across countless domains,including personalized healthcare and advanced *** 3D integration,edge devices can achieve unprecedented miniaturization while simultaneously boosting processing power and minimizing energy ***,we demonstrate a back-end-of-line compatible optoelectronic synapse with a transfer learning method on health care applications,including electroencephalogram(EEG)-based seizure prediction,electromyography(EMG)-based gesture recognition,and electrocardiogram(ECG)-based arrhythmia *** experiments on three biomedical datasets,we observe the classification accuracy improvement for the pretrained model with 2.93%on EEG,4.90%on ECG,and 7.92%on EMG,*** optical programming property of the device enables an ultralow power(2.8×10^(-13) J)fine-tuning process and offers solutions for patient-specific issues in edge computing ***,the device exhibits impressive light-sensitive characteristics that enable a range of light-triggered synaptic functions,making it promising for neuromorphic vision *** display the benefits of these intricate synaptic properties,a 5×5 optoelectronic synapse array is developed,effectively simulating human visual perception and memory *** proposed flexible optoelectronic synapse holds immense potential for advancing the fields of neuromorphic physiological signal processing and artificial visual systems in wearable applications.

关键词： Neuromorphic computing Electrophysiological signal Artificial vision system Image recognition Memristor

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Multi-Scale Time Series Segmentation Network Based on Eddy Current Testing for Detecting Surface Metal Defects

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IEEE/CAA Journal of Automatica Sinica 2025年第3期12卷 528-538页

作者： Xiaorui Li Xiaojuan Ban Haoran Qiao Zhaolin Yuan Hong-Ning Dai Chao Yao Yu Guo Mohammad S.Obaidat George Q.Huang the School of Intelligence Science and Technology University of Science and Technology Beijing the Beijing Advanced Innovation Center for Materials Genome Engineering the Key Laboratory of Intelligent Bionic Unmanned Systems and the Institute of Materials Intelligent Technology Liaoning Academy of Materials IEEE the Department of Computer Science Hong Kong Baptist University the School of Computer and Communication Engineering Key Laboratory of Advanced Materials and Devices for Post-Moore Chips Ministry of Education University of Science and Technology Beijing the Beijing Advanced Innovation Center for Materials Genome Engineering University of Science and Technology Beijing the School of Computer and Communication Engineering University of Science and Technology Beijing the King Abdullah Ⅱ School of Information Technology The University of Jordan the Department of Computational Intelligence the School of Computing SRM University the School of Engineering The Amity University The Hong Kong Polytechnic University

In high-risk industrial environments like nuclear power plants, precise defect identification and localization are essential for maintaining production stability and safety. However, the complexity of such a harsh environment leads to significant variations in the shape and size of the defects. To address this challenge, we propose the multivariate time series segmentation network(MSSN), which adopts a multiscale convolutional network with multi-stage and depth-separable convolutions for efficient feature extraction through variable-length templates. To tackle the classification difficulty caused by structural signal variance, MSSN employs logarithmic normalization to adjust instance distributions. Furthermore, it integrates classification with smoothing loss functions to accurately identify defect segments amid similar structural and defect signal subsequences. Our algorithm evaluated on both the Mackey-Glass dataset and industrial dataset achieves over 95% localization and demonstrates the capture capability on the synthetic dataset. In a nuclear plant's heat transfer tube dataset, it captures 90% of defect instances with75% middle localization F1 score.

关键词： Eddy current testing nondestructive testing semantic segmentation time series analysis

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Molecular Generation and Optimization of Molecular Properties Using a Transformer Model

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Big Data Mining and Analytics 2024年第1期7卷 142-155页

作者： Zhongyin Xu Xiujuan Lei Mei Ma Yi Pan School of Computer Science Shaanxi Normal UniversityXi'an 710119China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Generating novel molecules to satisfy specific properties is a challenging task in modern drug discovery,which requires the optimization of a specific objective based on satisfying chemical ***,we aim to optimize the properties of a specific molecule to satisfy the specific properties of the generated *** Matched Molecular Pairs(MMPs),which contain the source and target molecules,are used herein,and logD and solubility are selected as the optimization *** main innovative work lies in the calculation related to a specific transformer from the perspective of a matrix *** intervals and state changes are then used to encode logD and solubility for subsequent *** the experiments,we screen the data based on the proportion of heavy atoms to all atoms in the groups and select 12365,1503,and 1570 MMPs as the training,validation,and test sets,*** models are compared with the baseline models with respect to their abilities to generate molecules with specific *** show that the transformer model can accurately optimize the source molecules to satisfy specific properties.

关键词： molecular optimization transformer Matched Molecular Pairs(MMPs) logD solubility

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Highly-efficient(>70%)and Wide-spectral(400-1700 nm)sub-micron-thick InGaAs photodiodes for future high-resolution image sensors

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Light(science & Applications) 2024年第12期13卷 3224-3235页

作者： Dae-Myeong Geum Jinha Lim Junho Jang Seungyeop Ahn SeongKwang Kim Joonsup Shim Bong Ho Kim Juhyuk Park Woo Jin Baek Jaeyong Jeong SangHyeon Kim School of Electrical Engineering Korea Advanced Institute of Science and Technology(KAIST)Daejeon 34141Republic of Korea Department of Electrical and Computer Engineering Inha UniversityIncheon 22212Republic of Korea

This paper demonstrates the novel approach of sub-micron-thick InGaAs broadband photodetectors(PDs)designed for high-resolution imaging from the visible to short-wavelength infrared(SWIR)*** approaches encounter challenges such as low resolution and crosstalk issues caused by a thick absorption layer(AL).Therefore,we propose a guided-mode resonance(GMR)structure to enhance the quantum efficiency(QE)of the InGaAs PDs in the SWIR region with only sub-micron-thick *** TiOx/Au-based GMR structure compensates for the reduced AL thickness,achieving a remarkably high QE(>70%)from 400 to 1700 nm with only a 0.98μm AL InGaAs PD(defined as 1μm AL PD).This represents a reduction in thickness by at least 2.5 times compared to previous results while maintaining a high ***,the rapid transit time is highly expected to result in decreased electrical *** effectiveness of the GMR structure is evident in its ability to sustain QE even with a reduced AL thickness,simultaneously enhancing the transit *** breakthrough offers a viable solution for high-resolution and low-noise broadband image sensors.

关键词： thick resolution image

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circ2CBA: prediction of circRNA-RBP binding sites combining deep learning and attention mechanism

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Frontiers of computer science 2023年第5期17卷 217-225页

作者： Yajing GUO Xiujuan LEI Lian LIU Yi PAN School of Computer Science Shaanxi Normal UniversityXi’an 710119China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Circular RNAs(circRNAs)are RNAs with closed circular structure involved in many biological processes by key interactions with RNA binding proteins(RBPs).Existing methods for predicting these interactions have limitations in feature *** view of this,we propose a method named circ2CBA,which uses only sequence information of circRNAs to predict circRNA-RBP binding *** have constructed a data set which includes eight ***,circ2CBA encodes circRNA sequences using the one-hot ***,a two-layer convolutional neural network(CNN)is used to initially extract the *** CNN,circ2CBA uses a layer of bidirectional long and short-term memory network(BiLSTM)and the self-attention mechanism to learn the *** AUC value of circ2CBA reaches *** of circ2CBA with other three methods on our data set and an ablation experiment confirm that circ2CBA is an effective method to predict the binding sites between circRNAs and RBPs.

关键词： circRNAs RBPs CNN BiLSTM self-attention mechanism

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Artificial visual perception neural system using a solution-processable MoS_(2)-based in-memory light sensor

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Light(science & Applications) 2023年第8期12卷 1583-1594页

作者： Dayanand Kumar Lana Joharji Hanrui Li Ayman Rezk Ammar Nayfeh Nazek El-Atab Smart Advanced Memory Devices and Applications(SAMA)LaboratoryElectrical and Computer Engineering ProgramComputer Electrical Mathematical Science and Engineering DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955Kingdom of Saudi Arabia Department of Electrical Engineering and Computer Science Khalifa UniversityAbu Dhabi 127788United Arab Emirates

Optoelectronic devices are advantageous in in-memory light sensing for visual information processing,recognition,and storage in an energy-efficient ***,in-memory light sensors have been proposed to improve the energy,area,and time efficiencies of neuromorphic computing *** study is primarily focused on the development of a single sensing-storage-processing node based on a two-terminal solution-processable MoS2 metal-oxide-semiconductor(MOS)charge-trapping memory structure—the basic structure for charge-coupled devices(CCD)—and showing its suitability for in-memory light sensing and artificial visual *** memory window of the device increased from 2.8 V to more than 6V when the device was irradiated with optical lights of different wavelengths during the program ***,the charge retention capability of the device at a high temperature(100 ℃)was enhanced from 36 to 64%when exposed to a light wavelength of 400 *** larger shift in the threshold voltage with an increasing operating voltage confirmed that more charges were trapped at the Al_(2)O_(3)/MoS_(2) interface and in the MoS_(2) layer.A small convolutional neural network was proposed to measure the optical sensing and electrical programming abilities of the *** array simulation received optical images transmitted using a blue light wavelength and performed inference computation to process and recognize the images with 91%*** study is a significant step toward the development of optoelectronic MOS memory devices for neuromorphic visual perception,adaptive parallel processing networks for in-memory light sensing,and smart CCD cameras with artificial visual perception capabilities.

关键词： visual neural process

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