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Predicting Transcription Factor Binding Sites using Transformer based Capsule Network

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arXiv 2023年

作者： Ghosh, Nimisha Santoni, Daniele Saha, Indrajit Felici, Giovanni Odisha Bhubaneswar751030 India Institute for System Analysis and Computer Science "Antonio Ruberti" National Research Council of Italy Via dei Taurini Rome00185 Italy Department of Computer Science and Engineering National Institute of Technical Teachers' Training and Research West Bengal Kolkata700106 India

Motivation: Prediction of binding sites for transcription factors is important to understand how they regulate gene expression and how this regulation can be modulated for therapeutic purposes. Although in the past few years there are significant works addressing this issue, there is still space for improvement. In this regard, a transformer based capsule network viz. DNABERT-Cap is proposed in this work to predict transcription factor binding sites mining ChIPseq datasets. DNABERT-Cap is a bidirectional encoder pre-trained with large number of genomic DNA sequences, empowered with a capsule layer responsible for the final prediction. Results: The proposed model builds a predictor for transcription factor binding sites using the joint optimisation of features encompassing both bidirectional encoder and capsule layer, along with convolutional and bidirectional long-short term memory layers. To evaluate the efficiency of the proposed approach, we use a benchmark ChIP-seq datasets of five cell lines viz. A549, GM12878, Hep-G2, H1-hESC and Hela, available in the ENCODE repository. The results show that the average area under the receiver operating characteristic curve score exceeds 0.91 for all such five cell lines. DNABERT-Cap is also compared with existing state-of-the-art deep learning based predictors viz. DeepARC, DeepTF, CNN-Zeng and DeepBind, and is seen to outperform them. Availability and implementation: The datasets used in this work along with code are available at https://***/NimishaGhosh/DNABERT-Cap/tree/main. © 2023, CC BY.

关键词： DNA sequences

A Comprehensive Study on Drones and Big Data for Supply Chain Optimization Using a Novel Approach

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A Comprehensive Study on Drones and Big Data for Supply Chai...

Advanced Computing and Emerging Technologies (ACET), International Conference on

作者： Dankan Gowda V D Palanikkumar Suganthi. N A.S. Malleswari Sanjog Thapa Rama Chaithanya Tanguturi Department of Electronics and Communication Engineering BMS Institute of Technology and Management Bangalore Karnataka Department of Computer Science and Engineering Dr NGP Institute of Technology Coimbatore Tamilnadu India Department of Electrical and Electronics Engineering Dayananda Sagar College of Engineering Bangalore Karnataka India Department of Computer Science & Engineering Aditya College of Engineering and Technology Surampalem Andhra Pradesh India Department of Information System and Analysis Lamar University Beaumont Texas USA School of Business Woxsen University Hyderabad India

ISBN: (数字)9798350367720

ISBN: (纸本)9798350367737

This research paper aims to provide qualitative and quantitative insights regarding the application of drones and big data techniques in the SCM field through a new scientific method. The proposed method exploits the opportunities of drones for real-time data capturing and big data technologies to enrich decision making in supply chain. The study is pertinent to modern tendencies in supply chain systems and proves the efficiency of the new method through the precise calculations and contrastive analysis. The following are some of the findings that suggest efficiency, cost decrease, and outstanding performance of the supply chain. The studies being offered in this research will prove beneficial for practitioners and researchers who endeavor to advance the concepts and practice of logistics and supply chain management.

关键词： Costs Supply chain management Supply chains Demand forecasting Big Data Real-time systems Security Reliability Drones Resilience

Continual Test-Time Adaptation for Single Image Defocus Deblurring via Causal Siamese Networks

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arXiv 2025年

作者： Cui, Shuang Li, Yi Li, Jiangmeng Tang, Xiongxin Su, Bing Xu, Fanjiang Xiong, Hui National Key Laboratory of Space Integrated Information System Institute of Software Chinese Academy of Sciences University of Chinese Academy of Sciences China Beijing Key Laboratory of Big Data Management and Analysis Methods Gaoling School of Artificial Intelligence Renmin University of China China Department of Computer Science & Engineering the Hong Kong University of Science and Technology Hong Kong

Single image defocus deblurring (SIDD) aims to restore an all-in-focus image from a defocused one. Distribution shifts in defocused images generally lead to performance degradation of existing methods during out-of-distribution inferences. In this work, we gauge the intrinsic reason behind the performance degradation, which is identified as the heterogeneity of lens-specific point spread functions. Empirical evidence supports this finding, motivating us to employ a continual test-time adaptation (CTTA) paradigm for SIDD. However, traditional CTTA methods, which primarily rely on entropy minimization, cannot sufficiently explore task-dependent information for pixel-level regression tasks like SIDD. To address this issue, we propose a novel Siamese networks-based continual test-time adaptation framework, which adapts source models to continuously changing target domains only requiring unlabeled target data in an online manner. To further mitigate semantically erroneous textures introduced by source SIDD models under severe degradation, we revisit the learning paradigm through a structural causal model and propose Causal Siamese networks (CauSiam). Our method leverages large-scale pre-trained vision-language models to derive discriminative universal semantic priors and integrates these priors into Siamese networks, ensuring causal identifiability between blurry inputs and restored images. Extensive experiments demonstrate that CauSiam effectively improves the generalization performance of existing SIDD methods in continuously changing domains. Copyright © 2025, The Authors. All rights reserved.

关键词： Semantics

A Blockchain Approach to IoT Security and Reliability analysis 3

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A Blockchain Approach to IoT Security and Reliability Analys...

3rd International Conference on Intelligent Engineering and Management, ICIEM 2022

作者： Jain, Nilesh Wahid, Nazia Al-Farhani, Liwa H. Manideep, A. Sai Bhardwaj, Vikash Sangeeth Kumar, M. Mandsaur University Department of Computer Applications Madhya Pradesh Mandsaur India Vishwakarma University Faculty of Science & Technology Department of Mathematics & Statistics Maharashtra Pune India RDUN University System Analysis Control and Information Processing Academy of Engineering Moscow Russia Vignan's Foundation for Science Technology and Research Department of Management Studies Andhra Pradesh Guntur India Dewan VS Institute of Engineering & Technology Uttar Pradesh Meerut India Sona College of Technology Mechanical Engineering Department Tamilnadu Salem India

ISBN: (数字)9781665467568

ISBN: (纸本)9781665467568

An investigation area of interest including the use of blockchain technology to address Internet of Things security concerns (IoT). Despite the fact that numerous relevant ideas have been offered, there are few published works that provide hypothetical and information backing. The examination of model building and execution assessment is the focus of this research. First, an IoT security paradigm is outlined, using blockchain and the Inter-Planetary-File-system (IPFS) in a view. Many of the security risks associated with traditional IoT designs can be avoided with this paradigm, and framework execution is entirely focused on distributed large limit stockpiling, simultaneity, and query. In addition, the suggested model's display is evaluated using normal idleness and throughput, which are important for further investigation and enhancement of this course. The blockchain-based security model's feasibility has been demonstrated via analysis and experiments. © 2022 IEEE.

关键词： Blockchain

A Survey of Fault Tolerance in Cloud Computing

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A Survey of Fault Tolerance in Cloud Computing

systems, Advanced Technologies and Knowledge (ISSATK), International Symposium of

作者： Om Kolthoum Elhajjej Nouha Alyaoui Samia Dardouri Karim Chabir Research Laboratory Modeling Aanalysis Control of System (MACS) LR16ES22 National engineering school of Gabes (ENIG) University of Gabes Tunisia Computer Science and Telecommunications Department Laboratory of Modeling Analysis and Control of Systems (MACS) Higher Institute of Applied Sciences and Technology Zarroug Gafsa Gafsa University Tunisia Department of Computer Science College of Computing and Information Technology Shaqra University Saudi Arabia InnoV’COM Laboratory-Sup’Com University of Carthage Tunisia

ISBN: (数字)9798331540173

ISBN: (纸本)9798331540180

This paper is designed to provide a comprehensive overview of the latest developments in fault tolerance methods for cloud computing. Maintaining high availability and reliability of cloud environments requires fault tolerance. This paper explores fault tolerance in the context of cloud computing and discusses recent challenges and innovations in the field. Moreover, it examines the ongoing research efforts to improve fault-tolerance architectures. At the end of the paper, the paper presents system-level metrics that are relevant to fault tolerance.

关键词： Measurement Surveys Cloud computing Fault tolerance Technological innovation Scalability Fault tolerant systems computer architecture Software Software reliability

The geographic proximity effect on domestic cross-sector vis-à-vis intra-sector research collaborations

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arXiv 2022年

作者： Abramo, Giovanni Apponi, Francesca D'Angelo, Ciriaco Andrea Laboratory for Studies in Research Evaluation Institute for System Analysis and Computer Science IASI CNR National Research Council of Italy Italy Department of Engineering and Management University of Rome "Tor Vergata" Italy

Geographic proximity is acknowledged to be a key factor in research collaborations. Specifically, it can work as a possible substitute for institutional proximity. The present study investigates the relevance of the "proximity" effect for different types of national research collaborations. We apply a bibliometric approach based on the Italian 2010-2017 scientific production indexed in the Web of science. On such dataset, we apply statistical tools for analyzing if and to what extent geographical distance between co-authors in the byline of a publication varies across collaboration types, scientific disciplines, and along time. Results can inform policies aimed at effectively stimulating cross-sector collaborations, and also bear direct practical implications for research performance assessments. Copyright © 2022, The Authors. All rights reserved.

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Simplify Implant Depth Prediction as Video Grounding: A Texture Perceive Implant Depth Prediction Network

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arXiv 2024年

作者： Yang, Xinquan Li, Xuguang Luo, Xiaoling Zeng, Leilei Zhang, Yudi Shen, Linlin Deng, Yongqiang College of Computer Science and Software Engineering Shenzhen University Shenzhen China AI Research Center for Medical Image Analysis and Diagnosis Shenzhen University Shenzhen China National Engineering Laboratory for Big Data System Computing Technology Shenzhen University China Department of Stomatology Shenzhen University General Hospital Shenzhen China

Surgical guide plate is an important tool for the dental implant surgery. However, the design process heavily relies on the dentist to manually simulate the implant angle and depth. When deep neural networks have been applied to assist the dentist quickly locates the implant position, most of them are not able to determine the implant depth. Inspired by the video grounding task which localizes the starting and ending time of the target video segment, in this paper, we simplify the implant depth prediction as video grounding and develop a Texture Perceive Implant Depth Prediction Network (TPNet), which enables us to directly output the implant depth without complex measurements of oral bone. TPNet consists of an implant region detector (IRD) and an implant depth prediction network (IDPNet). IRD is an object detector designed to crop the candidate implant volume from the CBCT, which greatly saves the computation resource. IDPNet takes the cropped CBCT data to predict the implant depth. A Texture Perceive Loss (TPL) is devised to enable the encoder of IDPNet to perceive the texture variation among slices. Extensive experiments on a large dental implant dataset demonstrated that the proposed TPNet achieves superior performance than the existing methods. Copyright © 2024, The Authors. All rights reserved.

关键词： Forecasting

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IEEE International Conference on Multimedia and Expo (ICME)

作者： Xiaoke Zhu Danyang Li Xiaopan Chen Fumin Qi Fan Zhang Xiao-Yuan Jing School of Computer and Information Engineering Henan University Kaifeng China Henan Engineering Research Center of Intelligent Technology and Application Henan University Kaifeng China Department of System Operation National Supercomuting Center in Shenzhen Shenzhen China Henan Key Laboratory of Big Data Analysis and Processing Henan University Kaifeng China School of Computer Science Wuhan University Wuhan China

ISBN: (数字)9798350390155

ISBN: (纸本)9798350390162

Facial image based kinship verification aims to decide whether there exists kinship between the given facial images. In practice, the cross-generation differences will cause adverse effects on kinship verification, which limits the performance. Therefore, how to mine the implied similarity from facial images with large cross-generation divergence is an important problem in kinship verification, which has not yet been well studied. In view of this, we propose a Similarity Mining via Implicit matching pattern LEarning (SMILE) approach for kinship verification. Specifically, SMILE mainly consists of two modules, including a Semi-coupled Multi-pattern Similarity Learning (SMSL) module and a Cross-Generation Feature Normalization (CGFN) module. The SMSL module is designed to learn multiple semi-coupled matching patterns for mining the implicit facial similarity information from different perspectives. The CGFN module aims to reduce the divergence between facial images of parent and child. Extensive experiments demonstrate that the proposed approach outperforms the existing state-of-the-art methods.

关键词： Pattern matching Similarity learning

Fog-Cloud-IoT Enabled WSN Architecture 3

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Fog-Cloud-IoT Enabled WSN Architecture

3rd International Conference on Intelligent Engineering and Management, ICIEM 2022

作者： Anitha Christy Angelin, P. Samuel Devakumar, P.V. Al-Farhani, Liwa H. Kumar, Gandam Vijay Deep, Shaurya Mohammad, Shoaib PSNA College of Engineering and Technology Tamilnadu Dindigul India Karunya Institute of Technology and Sciences Tamilnadu Coimbatore India RUDN University System Analysis Control and Information Processing Academy of Engineering Moscow Russia Career Point University Computer Science and Engineering Rajasthan India IIMT College of Management Greater Noida India IMS Unison University Department of Law Uttarakhand Dehradun India

ISBN: (数字)9781665467568

ISBN: (纸本)9781665467568

Remote Because of the exciting innovation it introduces, the WSN likely to be a subject of research in recent time. Because of the impromptu distant connections, adaptability, and simplicity of execution, this has all the makings of becoming the most maintainable innovation for ecological detecting, whether it's about limited or huge scope watching. In any case, the main drawbacks stem from the limited capacity, processing, and accessibility of organization centers for information. Virtual machines resources have been adopted to overcome such constraints, devices to expanded capacity, computation, and easy-to-understand availability. This was a natural progression from traditional WSN designs among pattern in recent theories evolved along advent of Internet-of-Things advancements. Against the growing popularity of WSN associated cloud checking frameworks, still the issues are detected because of the distributed comp ting's disadvantages, like dormancy with the capacity charges. In this paper, the advancements achieved to a fog-cloud-IoT associated with WSN architecture of putting a bit of computing at the network part are elaborated, a process, which follows the smart Fog associated with Cloud-computing concept of dissecting also following up on IoT data. A similar investigation was carried out to illustrate the improvements made possible by processing at the organization's edge. © 2022 IEEE.

关键词： Fog computing