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Journal of Cloud Computing 2025年第1期14卷 1-1页

作者： Zhou, Jincheng Lilhore, Umesh Kumar M, Poongodi Hai, Tao Simaiya, Sarita Abang Jawawi, Dayang Norhayati Alsekait, Deema Mohammed Ahuja, Sachin Biamba, Cresantus Hamdi, Mounir School of Computer and Information and Key Laboratory of Complex Systems and Intelligent Optimization of Guizhou Qiannan Normal University for Nationalities Duyun China Department of Computer Science and Engineering Chandigarh University Mohali India College of Science and Engineering Hamad Bin Khalifa University Qatar Foundation Doha Qatar School of Computing Faculty of Engineering Universiti Teknologi Malaysia (UTM) Johor Malaysia Department of Computer Science and Information Technology Princess Nourah Bint Abdul Rahman University Applied College Riyadh Saudi Arabia Department of Culture Studies Religious Studies and Educational Sciences University of Gävle Gävle Sweden

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

sbi reloaded: a toolkit for simulation-based inference workflows

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arXiv 2024年

作者： Boelts, Jan Deistler, Michael Gloeckler, Manuel Tejero-Cantero, Álvaro Lueckmann, Jan-Matthis Moss, Guy Steinbach, Peter Moreau, Thomas Muratore, Fabio Linhart, Julia Durkan, Conor Vetter, Julius Miller, Benjamin Kurt Herold, Maternus Ziaeemehr, Abolfazl Pals, Matthijs Gruner, Theo Bischoff, Sebastian Krouglova, Anastasia N. Gao, Richard Lappalainen, Janne K. Mucsányi, Bálint Pei, Felix Schulz, Auguste Stefanidi, Zinovia Rodrigues, Pedro L.C. Schröder, Cornelius Zaid, Faried Abu Beck, Jonas Kapoor, Jaivardhan Greenberg, David S. Gonçalves, Pedro J. Macke, Jakob H. Machine Learning in Science University of Tübingen Germany Tübingen AI Center Germany TransferLab AppliedAI Institute for Europe Germany ML Colab Cluster ML in Science University of Tübingen Germany Google Research United States Helmholtz-Zentrum Dresden-Rossendorf Germany Université Paris-Saclay INRIA CEA Palaiseau France Robert Bosch GmbH Germany School of Informatics University of Edinburgh United Kingdom University of Amsterdam Netherlands Research and Innovation Center BMW Group Germany Institute for Applied Mathematics and Scientific Computing University of the Bundeswehr Munich Germany Aix Marseille INSERM INS France TU Darmstadt Hessian.AI Germany University Hospital Tübingen M3 Research Center Germany Faculty of Science KU Leuven B-3000 Belgium Imec Belgium Methods of Machine Learning University of Tübingen Germany Neuroscience Institute Carnegie Mellon University United States Université Grenoble Alpes INRIA CNRS Grenoble INP LJK France Hertie Institute for AI in Brain Health University of Tübingen Germany Institute of Coastal Systems - Analysis and Modeling Helmholtz AI Germany Departments of Computer Science Electrical Engineering KU Leuven Belgium Department Empirical Inference Max Planck Institute for Intelligent Systems Tübingen Germany

Scientists and engineers use simulators to model empirically observed phenomena. However, tuning the parameters of a simulator to ensure its outputs match observed data presents a significant challenge. Simulation-based inference (SBI) addresses this by enabling Bayesian inference for simulators, identifying parameters that match observed data and align with prior knowledge. Unlike traditional Bayesian inference, SBI only needs access to simulations from the model and does not require evaluations of the likelihood-function. In addition, SBI algorithms do not require gradients through the simulator, allow for massive parallelization of simulations, and can perform inference for different observations without further simulations or training, thereby amortizing inference. Over the past years, we have developed, maintained, and extended sbi, a PyTorch-based package4 that implements Bayesian SBI algorithms based on neural networks. The sbi toolkit implements a wide range of inference methods, neural network architectures, sampling methods, and diagnostic tools. In addition, it provides well-tested default settings but also offers flexibility to fully customize every step of the simulation-based inference workflow. Taken together, the sbi toolkit enables scientists and engineers to apply state-of-the-art SBI methods to black-box simulators, opening up new possibilities for aligning simulations with empirically observed data. © 2024, CC BY-SA.

关键词： Neural networks

AI-based Fog and Edge Computing: A Systematic Review, Taxonomy and Future Directions

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arXiv 2022年

作者： Iftikhar, Sundas Gill, Sukhpal Singh Song, Chenghao Xu, Minxian Aslanpour, Mohammad Sadegh Toosi, Adel N. Du, Junhui Wu, Huaming Ghosh, Shreya Chowdhury, Deepraj Golec, Muhammed Kumar, Mohit Abdelmoniem, Ahmed M. Cuadrado, Felix Varghese, Blesson Rana, Omer Dustdar, Schahram Uhlig, Steve School of Electronic Engineering and Computer Science Queen Mary University of London London United Kingdom University of Kotli Azad Jammu & Kashmir Azad Kashmir Kotli Pakistan Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Department of Software Systems and Cybersecurity Faculty of Information Technology Monash University Australia Csiro DATA61 Australia Center for Applied Mathematics Tianjin University Tianjin China The Pennsylvania State University PA United States Naya Raipur India Abdullah Gül University Kayseri Turkey Department of Information Technology National Institute of Technology Jalandhar India Spain School of Computer Science University of St Andrews United Kingdom School of Computer Science and Informatics Cardiff University Cardiff United Kingdom Distributed Systems Group Vienna University of Technology Vienna Austria

Resource management in computing is a very challenging problem that involves making sequential decisions. Resource limitations, resource heterogeneity, dynamic and diverse nature of workload, and the unpredictability of fog/edge computing environments have made resource management even more challenging to be considered in the fog landscape. Recently Artificial Intelligence (AI) and Machine Learning (ML) based solutions are adopted to solve this problem. AI/ML methods with the capability to make sequential decisions like reinforcement learning seem most promising for these type of problems. But these algorithms come with their own challenges such as high variance, explainability, and online training. The continuously changing fog/edge environment dynamics require solutions that learn online, adopting changing computing environment. In this paper, we used standard review methodology to conduct this Systematic Literature Review (SLR) to analyze the role of AI/ML algorithms and the challenges in the applicability of these algorithms for resource management in fog/edge computing environments. Further, various machine learning, deep learning and reinforcement learning techniques for edge AI management have been discussed. Furthermore, we have presented the background and current status of AI/ML-based Fog/Edge Computing. Moreover, a taxonomy of AI/ML-based resource management techniques for fog/edge computing has been proposed and compared the existing techniques based on the proposed taxonomy. Finally, open challenges and promising future research directions have been identified and discussed in the area of AI/ML-based fog/edge computing. Copyright © 2022, The Authors. All rights reserved.

关键词： Edge computing

Generalized Sparse Matrix-Matrix Multiplication for Vector Engines and Graph Applications

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Generalized Sparse Matrix-Matrix Multiplication for Vector E...

IEEE/ACM Workshop on Memory Centric High Performance Computing (MCHPC)

作者： Jiayu Li Fugang Wang Takuya Araki Judy Qiu Intelligent Systems Engineering Indiana University Bloomington USA Data Science Research Laboratories NEC Kanagawa Japan

ISBN: (纸本)9781728160085

Generalized sparse matrix-matrix multiplication (SpGEMM) is a key primitive kernel for many high-performance graph algorithms as well as for machine learning and data analysis algorithms. Although many SpGEMM algorithms have been proposed, such as ESC and SPA, there is currently no SpGEMM kernel optimized for vector engines (VEs). NEC SX- Aurora is the new vector computing system that can achieve high performance by leveraging high bandwidth memory of 1.2TB/s and long vector of VEs, where the execution of scientific applications is limited by memory bandwidth. In this paper, we demonstrate significant initial work of SpGEMM kernel for a vector engine and implement it to vectorize several essential graph analysis algorithms: Butterfly counting and Triangle count- ing. We propose a SpGEMM algorithm with a novel hybrid method based on sparse vectors and loop raking to maximize the length of vectorizable code for vector machine architectures. The experimental results show that the vector engine has advantages on more massive data sets. This work contributes to the high performance and portability of the SpGEMM kernel to a new family of heterogeneous computing systems, which is Vector Host (VH) equipped with different accelerators or VEs.

关键词： Engines Sparse matrices Registers Kernel Computer architecture Indexes Machine learning algorithms

Open-SBS: Smart Building Simulator

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Open-SBS: Smart Building Simulator

Information Technology (ACIT)

作者： Houssem Eddine Degha Fatima Zohra Laallam Okba Kazar Issam Khelfaoui Belkacem Athamena Zina Houhamdi Faculty of Sciences and Technology University of Ghardaia Ghardaia Algeria Artificial Intelligence and Information Technologies Laboratory Kasdi Merbah Ouargla University City Algeria Intelligent Computer Science Laboratory LINFI Biskra University Biskra Algeria Department of Information Systems and Security College of Information Technology United Arab Emirate University United Arab Emirates School of Insurance and Economics University of International Business and Economics Beijing China College of Business Al Ain University Al Ain UAE College of engineering Al Ain University Al Ain UAE

ISBN: (数字)9798350320244

ISBN: (纸本)9798350320251

With the rise of machine learning and deep learning techniques in recent years, a representative dataset has become an inspiring source of prediction and knowledge extraction. Furthermore, ambient intelligence environments have emerged as one of the most important research areas. Many complex tasks and challenges face this area to validate and evaluate field research. One of the major challenges in the smart building domain is the lack of a simulation tool capable of simulating complex contexts, executing semantic rules, and collecting representative datasets for experiments. To address these issues, we present in this paper a cross-platform, open-source Smart Building Simulator (Open-SBS). Open-SBS offer an opportunity for researchers in the field of Ambient Intelligence environments to simulate complex contexts and collect representative datasets, save and share their models of experiments. We propose a new simulation process that is divided into four distinct phases: designing, scenario creation, semantic rule addition, and data-set generation. On the System Usability Scale, we conducted a study to assess the ease of use of Open-SBS (SUS).

关键词： Smart buildings Three-dimensional displays Semantics Ontologies data models Ambient intelligence Usability

OLSR+: A new routing method based on fuzzy logic in flying ad-hoc networks (FANETs)

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Vehicular Communications 2022年 36卷

作者： Rahmani, Amir Masoud Ali, Saqib Yousefpoor, Efat Yousefpoor, Mohammad Sadegh Javaheri, Danial Lalbakhsh, Pooia Hassan Ahmed, Omed Hosseinzadeh, Mehdi Lee, Sang-Woong Future Technology Research Center National Yunlin University of Science and Technology Yunlin Taiwan Department of Information Systems College of Economics and Political Science Sultan Qaboos University Al Khoudh Muscat Oman Department of Computer Engineering Dezful Branch Islamic Azad University Dezful Iran Department of Computer Engineering Chosun University Gwangju 61452 South Korea Department of Data Science and Artificial Intelligence Faculty of Information Technology Monash University Clayton 3800 VIC Australia Department of Information Technology University of Human Development Sulaymaniyah Iraq Pattern Recognition and Machine Learning Lab Gachon University 1342 Seongnamdaero Sujeonggu Seongnam 13120 South Korea

Flying ad-hoc networks (FANETs) have many applications in military, industrial and agricultural areas. Due to specific features of FANETs, such as high-speed nodes, low density of nodes in the network, and rapid changes in the topology, most routing protocols designed for mobile ad hoc networks (MANETs) or vehicular ad hoc networks (VANETs) are not compatible with FANETs. In this paper, we propose a fuzzy logic-based routing approach called OLSR+ for FANETs. In this scheme, we seek to improve the optimized link state routing protocol (OLSR) so that it can efficiently be used in FANETs. OLSR+ includes four main phases: 1) Discovering neighboring nodes. In this phase, we propose a new and efficient technique for estimating the lifetime of the link between two unmanned ariel vehicles (UAVs) based on the link quality, distance, relative velocity, and movement direction. 2) Selecting multipoint relays (MPRs). In this phase, we present a fuzzy mechanism for selecting a set of MPR nodes. According to this mechanism, when a node has higher residual energy, higher link lifetime, and more neighborhood degree compared to others, it achieves more fitness to be selected as MPR. 3) Discovering the network topology. In this phase, we modify the format of the topology control (TC) message and add two fields, including route energy and route lifetime to this message. 4) Calculating the routing table. In OLSR+, we consider two parameters, including route energy and route lifetime, for establishing stable paths. Finally, we simulate OLSR+ using NS3 and compare its performance with two methods, namely greedy optimized link state routing (G-OLSR) and optimized link state routing (OLSR). The simulation results show that OLSR+ successfully reduces delay compared to G-OLSR and OLSR. In addition, it has higher packet delivery rate and throughput than others. Also, it improves energy consumption in the network. However, OLSR+ has more routing overhead than G-OLSR. © 2022 Elsevier Inc.

关键词： Artificial intelligence (AI) Flying ad hoc networks (FANETs) Fuzzy logic Routing Unmanned ariel vehicles (UAVs)

Learn to predict sets using feed-forward neural networks

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arXiv 2020年

作者： Rezatofighi, Seyed Hamid Zhu, Alan Tianyu Kaskman, Roman Motlagh, Farbod T. Shi, Javen Qinfeng Milan, Anton Cremers, Daniel Leal-Taixé, Laura Reid, Ian The Department of Data Science and AI Faculty of Information Technology Monash University Melbourne Australia Department of Electrical and Computer Systems Engineering Monash University Melbourne Australia The School of Computer Science The university of Adelaide Australia Amazon Technical University of Munich Germany

This paper addresses the task of set prediction using deep feed-forward neural networks. A set is a collection of elements which is invariant under permutation and the size of a set is not fixed in advance. Many real-world problems, such as image tagging and object detection, have outputs that are naturally expressed as sets of entities. This creates a challenge for traditional deep neural networks which naturally deal with structured outputs such as vectors, matrices or tensors. We present a novel approach for learning to predict sets with unknown permutation and cardinality using deep neural networks. In our formulation we define a likelihood for a set distribution represented by a) two discrete distributions defining the set cardinally and permutation variables, and b) a joint distribution over set elements with a fixed cardinality. Depending on the problem under consideration, we define different training models for set prediction using deep neural networks. We demonstrate the validity of our set formulations on relevant vision problems such as: 1) multi-label image classification where we outperform the other competing methods on the PASCAL VOC and MS COCO datasets, 2) object detection, for which our formulation outperforms popular state-of-the-art detectors, and 3) a complex CAPTCHA test, where we observe that, surprisingly, our set-based network acquired the ability of mimicking arithmetics without any rules being coded. Copyright © 2020, The Authors. All rights reserved.

关键词： Object detection

Correction: PixCUE: Joint Uncertainty Estimation and Image Reconstruction in MRI using Deep Pixel Classification

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Journal of imaging informatics in medicine 2025年 2025 Feb 4页

作者： Mevan Ekanayake Kamlesh Pawar Zhifeng Chen Gary Egan Zhaolin Chen Monash Biomedical Imaging Monash University Clayton VIC 3800 Australia. Department of Electrical and Computer Systems Engineering Monash University Clayton VIC 3800 Australia. Department of Data Science and AI Faculty of IT Monash University Clayton VIC 3800 Australia. School of Psychological Sciences Monash University Clayton VIC 3800 Australia. Monash Biomedical Imaging Monash University Clayton VIC 3800 Australia. zhaolin.chen@monash.edu. Department of Data Science and AI Faculty of IT Monash University Clayton VIC 3800 Australia. zhaolin.chen@monash.edu.

Efficient Recursive Implementation of Spatial-Temporal Gaussian Process Regression

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Efficient Recursive Implementation of Spatial-Temporal Gauss...

Chinese Control Conference (CCC)

作者： Junpeng Zhang Ye Kuang Tianshi Chen Xiaochen Lu Feng Yin Renxin Zhong School of Science and Engineering and Shenzhen Research Institute of Big Data The Chinese University of Hong Kong Shenzhen Shenzhen P. R. China Guangzhou Yunchuang Data Science and Technology Co. Ltd. Guangzhou P. R. China School of Intelligent Systems Engineering Sun Yat-sen University Guangzhou P. R. China

ISBN: (数字)9789881563903

ISBN: (纸本)9781728165233

The current implementation of the spatial-temporal Gaussian process regression has computational complexity O(NM 3 ), where N and M are the number of temporal and spatial data, respectively, and thus can only be applied to data with large N but relatively small M. In this work, we show that by exploring the Kronecker structure in the state-space model realization of the spatial-temporal Gaussian process, we can extend the current implementation with a coordinate transformation and an output transformation (corresponding to data preprocessing), such that the computational complexity is reduced to O(M 3 +NM 2 +NM) and therefore the proposed implementation can be applied to data with large N and moderately large M. Moreover, the proposed implementation can be parallelized and the computational complexity can be further lowered if parallel computing is adopted.

关键词： Gaussian processes Kernel Estimation Computational complexity State-space methods Kalman filters Contracts