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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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EDSA-Ensemble: an Event Detection Sentiment Analysis Ensemble Architecture

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IEEE Transactions on Affective Computing 2024年第02期16卷 1-18页

作者： PETRESCU, Alexandru TRUICA, Ciprian-Octavian APOSTOL, Elena-Simona PASCHKE, Adrian Computer Science and Engineering Department Faculty of Automatic Control and Computers National University of Science and Technology Politehnica Bucharest Bucharest Romania Fraunhofer Institute for Open Communication Systems Berlin Germany

As global digitization continues to grow, technology becomes more affordable and easier to use, and social media platforms thrive, becoming the new means of spreading information and news. Communities are built around sharing and discussing current events. Within these communities, users are enabled to share their opinions about each event. Using Sentiment Analysis to understand the polarity of each message belonging to an event, as well as the entire event, can help to better understand the general and individual feelings of significant trends and the dynamics on online social networks. In this context, we propose a new ensemble architecture, EDSAEnsemble (Event Detection Sentiment Analysis Ensemble), that uses Event Detection and Sentiment Analysis to improve the detection of the polarity for current events from Social Media. For Event Detection, we use techniques based on Information Diffusion taking into account both the time span and the topics. To detect the polarity of each event, we preprocess the text and employ several Machine and Deep Learning models to create an ensemble model. The preprocessing step includes several word representation models: raw frequency, TFIDF, Word2Vec, and Transformers. The proposed EDSA-Ensemble architecture improves the event sentiment classification over the individual Machine and Deep Learning models. Authors

关键词： Sentiment analysis

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Pneumonia Detection from X-ray Images Using Convolutional Neural Networks 24

Pneumonia Detection from X-ray Images Using Convolutional Ne...

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24th International Conference on control Systems and computer science, CSCS 2023

作者： Dediu, Viorel Udrea, Andreea Faculty of Automatic Control and Computer Science Univesity Politehnica of Bucharest Department of Automatic Control and Systems Engineering Bucharest Romania

ISBN: (纸本)9798350313390

Pneumonia is one of the top causes of death in Romania and early detection of this disease improves the recovery chances and shortens the length of hospitalization. In this work, we develop a solution for automatic pneumonia detection based on convolutional neural networks. Four network models are investigated. They are trained on 4.163 images from a public dataset and tested on 530 images. The best results are obtained by one of the proposed models conducting to a sensitivity of 98.72%, an accuracy of 89.81%, and ROC 93.46%. Thus, this research proposes a lightweight screening tool that can help triaging the patients with pneumonia. © 2023 IEEE.

关键词： Convolution

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STGNN: a new self-trained generalized neural networks task space control for robot manipulators

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Neural Computing and Applications 2025年 1-26页

作者： Elmogy, Ahmed Elawady, Wael El-Ghaish, Hany Computer Engineering Department Prince Sattam Ibn Abdelaziz University Alkharj16273 Saudi Arabia Computers and Automatic Control Department Faculty of Engineering Tanta University Tanta31527 Egypt

The inherent uncertainties in the dynamic and kinematic parameters of robot manipulators pose significant challenges for their control in task space. This paper introduces an innovative adaptive sliding mode control strategy, leveraging self-trained generalized neural networks to enhance the precision and robustness of robot manipulator control. The proposed framework called STGNN integrates deep neural networks for the real-time estimation and adjustment of dynamics’ and kinematics’ parameters. Key contributions of this work include the development of semi-supervised learning models for adaptive dynamics and kinematics estimation. By training the generalized neural network on different trajectories, the same models can be utilized to operate on a variety of tasks, significantly improving the robustness, scalability, and adaptability of the control system. The STGNN approach allows the models to leverage both labeled and unlabeled data, incorporating a self-training mechanism that enhances their ability to generalize and adapt to diverse operational scenarios. This capability is particularly beneficial for real-time applications, where the ability to learn and adapt on the fly is crucial. Simulation results demonstrate the superior performance of the STGNN framework in controlling robot manipulators in operational space, showcasing its potential for real-world applications. The proposed method significantly advances the adaptability, accuracy, and efficiency of robot control systems, offering notable improvements over conventional approaches. © The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2025.

关键词： Self adjusting control systems

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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 Evaluation of the Dual Vectors Based Solutions for Robot-World/Hand-Eye Calibration 1

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25th International Symposium on Measurement and control in Robotics, ISMCR 2023

作者： Ganciu, Aura Burlacu, Adrian Department of Automatic Control and Applied Informatics Faculty of Automatic Control and Computer Engineering "Gheorghe Asachi" Technical University of Iași Iași Romania

ISBN: (数字)9783031510854

ISBN: (纸本)9783031510847

The hand-eye calibration problem represents a major challenge in robotics, arising from the widespread usage of robotic systems along with robot-mounted sensors. Briefly, consisting of estimating the position and orientation of a visual sensor (usually a camera attached to the robot’s end-effector) with respect to the robot itself, calibration is critical in tracking rigid bodies—a common task within mixed reality applications. Hand-eye calibration implies solving the problem formulated as AX = XB or AX = YB equations. The solution lies in computing the unknown homogeneous transformation matrices X and Y, given the A and B parameterizations of rigid body motions. We present the dual vectors based approaches for AX = XB and AX = YB calibration problems, making use of the isomorphism between the special Euclidean group and the orthogonal dual tensor group. Comparisons with state-of-the-art algorithms are used to assess our obtained results. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.

关键词： Mixed reality

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Real-Time Notifier for Blockchain Events 22

Real-Time Notifier for Blockchain Events

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22nd RoEduNet Conference: Networking in Education and Research, RoEduNet 2023

作者： Tanase-Paris, Cristian Carabas, Costin Tapus, Nicolae University Politehnica of Bucharest Faculty of Automatic Control and Computers Computer Science and Engineering Department Bucharest Romania

ISBN: (纸本)9798350393651

Blockchain technology gained much traction in the last few years. These decentralized databases offer security, immutability, and scalability across various applications. Decentralized applications generate vast amounts of data, known as events, that are recorded on the blockchain and are public to anyone. Some people may see opportunities for financial gains in these events and would like to know when they occur. This paper proposes a solution to process and deliver those events as real-time alerts to the users. It uses existing technologies such as message queues, multithreading, and asynchronous processing and integrates them into a scalable architecture. The results we achieved in this paper show that for an evenly distributed network traffic, which does not entirely consists of transaction bursts, the proposed solution offers reliability, efficiency, and a suitable delivery time to those wishing to integrate it into their projects. With time, this solution, or improved architectures, may form the basis of the following big-data architectures for processing blockchain events. © 2023 IEEE.

关键词： Blockchain

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A Distributed automatic Domain-Specific Multi-Word Term Recognition Architecture using Spark Ecosystem 22

A Distributed Automatic Domain-Specific Multi-Word Term Reco...

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22nd International Symposium on Parallel and Distributed Computing, ISPDC 2023

作者： Truica, Ciprian-Octavian Istrate, Neculai-Ovidiu Apostol, Elena-Simona University Politehnica of Bucharest Faculty of Automatic Control and Computers Computer Science and Engineering Department Bucharest Romania

ISBN: (纸本)9798350341270

automatic Term Recognition is used to extract domain-specific terms that belong to a given domain. In order to be accurate, these corpus and language-dependent methods require large volumes of textual data that need to be processed to extract candidate terms that are afterward scored according to a given metric. To improve text preprocessing and candidate terms extraction and scoring, we propose a distributed Spark-based architecture to automatically extract domain-specific terms. The main contributions are as follows: (1) propose a novel distributed automatic domain-specific multi-word term recognition architecture built on top of the Spark ecosystem;(2) perform an in-depth analysis of our architecture in terms of accuracy and scalability;(3) design an easy-to-integrate Python implementation that enables the use of Big Data processing in fields such as Computational Linguistics and Natural Language Processing. We prove empirically the feasibility of our architecture by performing experiments on two real-world datasets. © 2023 IEEE.

关键词： Ecosystems

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Optimizing Artificial Neural Networks Trough Weight Adjustments 28th

Optimizing Artificial Neural Networks Trough Weight Adjustme...

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28th International Conference on Knowledge Based and Intelligent information and engineering Systems, KES 2024

作者： Akber, Syed Muhammad Abrar Szczesna, Agnieszka Kazmi, Sadia Nishat Department of Computer Graphics Vision and Digital Systems Faculty of Automatic Control Electronics and Computer Science Silesian University of Technology Gliwice44-100 Poland Faculty of Automatic Control Electronics and Computer Science Silesian University of Technology Gliwice44-100 Poland

Longer training times pose a significant challenge in artificial neural networks (ANNs) as it may leads to increasing the computational costs and decreasing the effectiveness of the model. Therefore, it is imperative to reduce training times in ANNs to enhance the computational efficiency. The initialization of the weights between the layers in ANN plays a vital role in reducing training times. Appropriate weight initialization can help the network converge faster during the training by providing an optimum starting point for the network. Therefore, weight initialization techniques are essential for efficient training of ANNs. This paper revisits and implements different popular weight initialization techniques in ANNs and analyzes their impact on training time. Specifically, this paper implements Gaussian-based, Kaming-based, and Xavier-based weight initiation atop a popular DNN-based network. The experiments are conducted by employing a well-known dataset. The results show that the scenario when no weight initiation is applied consumed the highest training time, whereas different weight initiation techniques contribute in reducing the training times for the network. © 2024 The Authors.

关键词： Deep neural networks

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UPB at IberLEF-2023 AuTexTification: Detection of Machine-Generated Text using Transformer Ensembles

UPB at IberLEF-2023 AuTexTification: Detection of Machine-Ge...

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2023 Iberian Languages Evaluation Forum, IberLEF 2023

作者： Preda, Andrei-Alexandru Cercel, Dumitru-Clementin Rebedea, Traian Chiru, Costin-Gabriel Computer Science and Engineering Department Faculty of Automatic Control and Computers University Politehnica of Bucharest Bucharest060042 Romania

This paper describes the solutions submitted by the UPB team to the AuTexTification shared task, featured as part of IberLEF-2023. Our team participated in the first subtask, identifying text documents produced by large language models instead of humans. The organizers provided a bilingual dataset for this subtask, comprising English and Spanish texts covering multiple domains, such as legal texts, social media posts, and how-to articles. We experimented mostly with deep learning models based on Transformers, as well as training techniques such as multi-task learning and virtual adversarial training to obtain better results. We submitted three runs, two of which consisted of ensemble models. Our best-performing model achieved macro F1-scores of 66.63% on the English dataset and 67.10% on the Spanish dataset. © 2023 Copyright for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).

关键词： Deep learning

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