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GMFLDA: Improved prediction of IncRNA-disease association via graph convolutional network

IEEE Access 2025年 13卷 85330-85341页

作者： Kim, Kwangsu Ha, Jihwan Pukyong National University Department of Scientific Computing Busan48513 Korea Republic of Pukyong National University Major of Big Data Convergence Division of Data Information Science Busan48513 Korea Republic of

The rapid expansion of diverse networks has created a growing need to integrate multiple heterogeneous structures to effectively capture both inter- and intra-entity relationships. This integration helps preserve the intrinsic meaning of complex biological interactions. Network-based approaches have been highly effective in predicting node labels and uncovering hidden associations between entities. These methods have been widely applied in areas such as user-item recommendations, gene-gene interactions, and lncRNA-disease association prediction. In this study, we present GMFLDA, an advanced machine learning framework for inferring lncRNA-disease associations (LDA) by synergizing graph convolutional networks (GCNs) with deep matrix factorization. Specifically, GCNs are leveraged to extract and encode high-fidelity feature representations of lncRNAs and diseases, while deep matrix factorization, implemented via a multi-layer perceptron, facilitates the discovery of potential disease-associated lncRNAs. Our model exhibits outstanding predictive performance, achieving AUCs of 0.9183 and 0.9057 in leave-one-out and five-fold cross-validation experiments, respectively. Extensive comparative evaluations demonstrate that GMFLDA surpasses four state-of-the-art methods, underscoring its superior predictive capability. We anticipate that GMFLDA will serve as a powerful computational tool for biomarker discovery, significantly accelerating the identification of disease-associated lncRNAs while mitigating the time and cost constraints of traditional wet-lab experiments. © 2013 IEEE.

关键词： Matrix factorization

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AI-Powered Earth Disaster Management: A Collaborative Innovation Platform 24

AI-Powered Earth Disaster Management: A Collaborative Innova...

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8th International Conference on Innovation in Artificial Intelligence, ICIAI 2024

作者： Huang, Chung-I Sun, Chen-Kai Chang, Jih-Sheng Chang, Wen-Yi Lin, Fang-Pang Wu, Jyh-Horng Chen, Wei-Yu Data Science and Technology Division National Center for High Performance Computing Taiwan High Performance Computing Division National Center for High-performance Computing Taiwan

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Feasibility Study on Restoring Chinese Documents by Convolutional Autoencoder

Feasibility Study on Restoring Chinese Documents by Convolut...

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2023 International Conference on Consumer Electronics - Taiwan, ICCE-Taiwan 2023

作者： Lo, Shi Wei Chou, Hsiu-Mei National Center for High-Performance Computing Data Science and Technology Division Hsinchu Taiwan

ISBN: (纸本)9798350324174

Digitalizing documents has become a crucial aspect of modern information management. However, various factors, such as manual handwriting, stains, and degradation, can significantly impact the quality of digitalized documents. This paper proposes a autoencoder-based network cleaning technology to completely erase manual writing, stains, colors, and background noise from paper documents to enhance their digitalized quality. Our proposed approach utilizes machine learning algorithms to identify and isolate unwanted elements from the document and then replace them with clean and transparent backgrounds. The experimental results demonstrate that our proposed approach significantly improves the digitalized quality of paper documents, making them more suitable for long-term storage and retrieval. Our proposed technology has the potential to revolutionize the field of paper document digitalization and improve the efficiency of information management. © 2023 IEEE.

关键词： Information management

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Inertial mixing of acoustically levitated droplets for time-lapse protein crystallography

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Droplet 2024年第3期3卷 91-101页

作者： Soichiro Tsujino Yohei Sato Shichao Jia Michal W.Kepa Sofia Trampari Takashi Tomizaki Division of Biology and Chemistry Paul Scherrer InstitutVilligenSwitzerland Swiss Nanoscience Institute University of BaselBaselSwitzerland Division Scientific Computing Theory and DataPaul Scherrer InstitutVilligenSwitzerland Biozentrum University of BaselBaselSwitzerland Photon Science Division Paul Scherrer InstitutVilligenSwitzerland

Varying the chemical consistency of acoustically levitated droplets opens up an in situ study of chemical and biochemical reactions in small ***,the opti-mization of the mixing time and the minimization of the positional instability induced by solution dispensing are necessary for practical applications such as the study of the transient state of macromolecules crystallography during the ligand binding *** this purpose,we study the inertial mixing in a configuration compatible with the room-temperature crystallography using the acoustic levitation diffractometer,therein solution drops ejected at high velocity collide and coalesce with droplets dis-pensed on acoustically levitated and rotating polymer thin-film sample *** the proposed method,we are able to achieve the mixing time of∼0.1 s for sub-micro and a few microliter *** observed short mixing time is ascribed to the rapid penetration of the solution into the droplets and confirmed by a computational fluid dynamic *** demonstrated accelerated solution mixing is tested in a pilot time-lapse protein crystallography experiment using the acoustic levitation *** results indicate the detection of transient ligand binding state within 2 s after the solution dispensing,suggesting the feasibility of the proposed method for studying slow biochemical processes.

关键词： mixing droplets transient

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Secure and privacy-preserving federated learning-based resource allocation for next generation networks

Secure and privacy-preserving federated learning-based resou...

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International Conference on Innovation and Technological Advances for Sustainability, ITAS 2023

作者： Dandoush, Abdulhalim Gouissem, Ala Ciftler, Bekir Sait Division of Information Technology College of Computing and Information Technology University of Doha for Science and Technology Doha Qatar ESME Sduria/L2TI at Sorbonne University Paris Nord France Division of Data Science and Artificial Intelligence College of Computing and Information Technology University of Doha for Science and Technology Doha Qatar

ISBN: (纸本)9781032803722

This paper surveys recent research on federated learning-based resource allocation for next-generation networks in order to identify research gaps and potential future directions. We start by outlining the main challenges and requirements for secure and privacy-preserving resource allocation in these networks. The existing solutions and techniques proposed in the literature are then reviewed. The strengths and limitations of these solutions are analyzed, and trade-offs in terms of security, privacy, efficiency, and scalability are discussed. The research gaps and promising directions for future research are identified, such as integrating multiple solutions (e.g., game theory or optimization techniques with federated learning) and developing new models and algorithms for AI-based resource allocation that address specific challenges and requirements of next-generation networks. The goal is to inspire further research in this critical and rapidly evolving field. © 2025 The Author(s).

关键词： Federated learning

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FedDAD: Federated Domain Adaptation for Object Detection

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IEEE Access 2023年 11卷 51320-51330页

作者： Lu, Peggy Joy Jui, Chia-Yung Chuang, Jen-Hui National Yang Ming Chiao Tung University Department of Computer Science Hsinchu30010 Taiwan National Center for High-Performance Computing Data Science and Technology Division Taichung40763 Taiwan

Training an object detection model often requires numerous annotated images on a centralized host, which may violate user privacy and data confidentiality. Federated learning (FL) resolves this issue by allowing multiple clients, e.g., cameras, to collaboratively train a model while protecting user privacy. However, models trained with FL may fail to be generalized for new target domain due to domain shift when the data between source and target domains are statistically different. In this work, we formulate a real-world object detection problem as a source-free multi-domain adaptation problem in FL architecture. Moreover, we propose an adaptive FL algorithm, called FedDAD (Federated Domain Adaptive Detector), which aggregates models with dynamic attention targeting the unsupervised domain on server, and utilize instance-level alignment to alleviate the effects of scene variation on clients. Experimental results show that FedDAD improves the average precision (AP) by up to 10.05% and 19.15% compared to the popular FedAvg for specific object classes in the KAIST and MI3 datasets, respectively. © 2013 IEEE.

关键词： Image annotation

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Solving key challenges in collider physics with foundation models

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Physical Review D 2025年第5期111卷 L051504-L051504页

作者： Vinicius Mikuni Benjamin Nachman National Energy Research Scientific Computing Center Berkeley Lab Berkeley California 94720 USA Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Berkeley Institute for Data Science University of California Berkeley California 94720 USA

Foundation models are neural networks that are capable of simultaneously solving many problems. Large language foundation models like ChatGPT have revolutionized many aspects of daily life, but their impact for science is not yet clear. In this paper, we use a new foundation model for hadronic jets to solve three key challenges in collider physics. In particular, we show how experiments can (1) save significant computing power when developing reconstruction algorithms, (2) perform a complete uncertainty quantification for high-dimensional measurements, and (3) search for new physics with model agnostic methods using low-level inputs. In each case, there are significant computational or methodological challenges with current methods that limit the science potential of deep learning algorithms. By solving each problem, we take jet foundation models beyond proof-of-principle studies and into the toolkit of practitioners.

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Adversarial Machine Learning for Social Good: Reframing the Adversary as an Ally

IEEE Transactions on Artificial Intelligence

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IEEE Transactions on Artificial Intelligence 2024年第9期5卷 4322-4343页

作者： Al-Maliki, Shawqi Qayyum, Adnan Ali, Hassan Abdallah, Mohamed Qadir, Junaid Hoang, Dinh Thai Niyato, Dusit Al-Fuqaha, Ala Division College of Science and Engineering Doha34110 Qatar Information Technology University Lahore54000 Pakistan University of New South Wales Sydney Sydney2052 Australia Qatar University Department of Computer Science and Engineering College of Engineering Doha34110 Qatar University of Technology Sydney School of Electrical and Data Engineering Sydney2052 Australia Nanyang Technological University College of Computing and Data Science 639798 Singapore

Deep neural networks (DNNs) have been the driving force behind many of the recent advances in machine learning. However, research has shown that DNNs are vulnerable to adversarial examples - input samples that have been perturbed to force DNN-based models to make errors. As a result, adversarial machine learning (AdvML) has gained a lot of attention, and researchers have investigated these vulnerabilities in various settings and modalities. In addition, DNNs have also been found to incorporate embedded bias and often produce unexplainable predictions, which can result in antisocial AI applications. The emergence of new AI technologies that leverage large language models (LLMs), such as ChatGPT and GPT-4, increases the risk of producing antisocial applications at scale. AdvML for social good (AdvML4G) is an emerging field that repurposes the AdvML bug to invent prosocial applications. Regulators, practitioners, and researchers should collaborate to encourage the development of prosocial applications and hinder the development of antisocial ones. In this work, we provide the first comprehensive review of the emerging field of AdvML4G. This paper encompasses a taxonomy that highlights the emergence of AdvML4G, a discussion of the differences and similarities between AdvML4G and AdvML, a taxonomy covering social good-related concepts and aspects, an exploration of the motivations behind the emergence of AdvML4G at the intersection of ML4G and AdvML, and an extensive summary of the works that utilize AdvML4G as an auxiliary tool for innovating prosocial applications. Finally, we elaborate upon various challenges and open research issues that require significant attention from the research community. © 2020 IEEE.

关键词： Taxonomies

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Dynamic Charging and Path Planning for UAV-Powered Rechargeable WSNs Using Multi-Agent Deep Reinforcement Learning

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IEEE Transactions on Automation science and Engineering 2025年 22卷 15610-15626页

作者： Betalo, Mesfin Leranso Leng, Supeng Seid, Abegaz Mohammed Abishu, Hayla Nahom Erbad, Aiman Bai, Xiaoshan Shenzhen University College of Mechatronics and Control Engineering Shenzhen518060 China University of Electronic Science and Technology of China School of Information and Communication Engineering Chengdu611731 China Hamad Bin Khalifa University Division of Information and Computing Technology College of Science and Engineering Doha Qatar Shenzhen University College of Mechatronics and Control Engineering National Engineering Laboratory for Big Data System Computing Technology Shenzhen518060 China

Unmanned Aerial Vehicle (UAV)-powered 5G/6G networks integrated with rechargeable wireless sensor networks (RWSNs) offer promising solutions for extending system lifetime, collecting data, and providing computing services and power to sensor nodes (SNs). UAVs offer significant advantages, including exceptional mobility, cost-effective deployment, and the ability to be easily reprogrammed for a wide range of missions. However, the limited onboard power capacity of UAVs, coupled with the lack of dynamic and intelligent charging station (CS) management and inefficient path planning, can lead to SN failure in dynamic mobile environments. To address these challenges, we propose an energy-efficient laser-charged UAV (LCU)-enabled RWSN environment, wherein UAVs, powered by laser beams from ground-based stations, provide services, collect data, and transfer energy to SNs. We formulate a joint optimization problem involving power allocation, dynamic charging strategy (DCS), and path planning to minimize task completion time and sensor node death time. Given the NP-hard nature of the problem, we employ a stochastic game model based on a Markov decision process (MDP) for its solution. To solve this problem, we propose a deep reinforcement learning (DRL) based algorithm that enables real-time charging scheduling decisions while optimizing network performance. We introduce a multi-agent double deep Q-network (MA-DDQN) model to determine the optimal trajectories for all UAVs in large and complex environments. Simulation results demonstrate that the MA-DDQN approach outperforms state-of-the-art techniques, showing significant improvements in terms of average delay, energy consumption, and task completion time. © 2004-2012 IEEE.

关键词： Stochastic models

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Robust Kernel Sparse Subspace Clustering

Robust Kernel Sparse Subspace Clustering

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International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： Ivica Kopriva Division of Computing and Data Science Rudjer Boskovich Institute Zagreb Croatia

ISBN: (数字)9798350368741

ISBN: (纸本)9798350368758

Kernel methods are widely used in pattern recognition, including subspace clustering (SC). They transform nonlinear problems in the input data space into linear ones in a high-dimensional feature space. This transformation, achieved through the kernel trick, makes computationally tractable nonlinear algorithms possible. However, kernelizing linear algorithms through the kernel trick is infeasible in case of gross sparse corruptions that are modeled by the ℓ 1 -norm of the error term. To address this, we propose, for the first time, a robust kernel sparse SC (RKSSC) algorithm for data with gross sparse corruptions. We validated the proposed approach on two well-known datasets, using the linear robust SSC algorithm and nonlinear (kernel-based) SSC algorithm as baseline models. According to the Wilcoxon test, the RKSSC's algorithm clustering performance is statistically significantly better than baselines.

关键词： Computational modeling Clustering algorithms Signal processing algorithms Transforms Signal processing Pattern recognition Sparse matrices Kernel Speech processing Optimization

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