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Biophysics Reports 2021年第3期7卷 207-226页

作者： Guangcan Shao Yong Cao Zhenlin Chen Chao Liu Shangtong Li Hao Chi Meng-Qiu Dong School of Life Sciences Peking University National Institute of Biological Sciences Beijing Tsinghua Institute of Multidisciplinary Biomedical Research Tsinghua University Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS) University of CASInstitute of Computing TechnologyCAS University of Chinese Academy of Sciences Beijing Advanced Innovation Center for Big Data-Based Precision Medicine School of Medicine and EngineeringBeihang University

High-throughput proteomics based on mass spectrometry（MS） analysis has permeated biomedical science and propelled numerous research projects. p Find 3 is a database search engine for high-speed and in-depth proteomics data analysis. p Find 3 features a swift open search workflow that is adept at uncovering less obvious information such as unexpected modifications or mutations that would have gone unnoticed using a conventional data analysis pipeline. In this protocol, we provide step-by-step instructions to help users mastering various types of data analysis using p Find 3 in conjunction with p Parse for data pre-processing and if needed, p Quant for quantitation. This streamlined p Parse-p Findp Quant workflow offers exceptional sensitivity, precision, and speed. It can be easily implemented in any laboratory in need of identifying peptides, proteins, or post-translational modifications, or of quantitation based on15N-labeling, SILAC-labeling, or TMT/i TRAQ labeling.

关键词： Mass spectrometry Protein identification Search engine Open-pFind Quantitation

Neuromodulated Meta-Learning

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arXiv 2024年

作者： Wang, Jingyao Guo, Huijie Qiang, Wenwen Li, Jiangmeng Zheng, Changwen Xiong, Hui Hua, Gang University of Chinese Academy of Sciences Beijing China National Key Laboratory of Space Integrated Information System Institute of Software Chinese Academy of Sciences Beijing China Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Beijing China Thrust of Artificial Intelligence Hong Kong University of Science and Technology Guangzhou China Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong Wormpex AI Research LLC BellevueWA98004 United States

Humans excel at adapting perceptions and actions to diverse environments, enabling efficient interaction with the external world. This adaptive capability relies on the biological nervous system (BNS), which activates different brain regions for distinct tasks. Meta-learning similarly trains machines to handle multiple tasks but relies on a fixed network structure, not as flexible as BNS. To investigate the role of flexible network structure (FNS) in meta-learning, we conduct extensive empirical and theoretical analyses, finding that model performance is tied to structure, with no universally optimal pattern across tasks. This reveals the crucial role of FNS in meta-learning, ensuring meta-learning to generate the optimal structure for each task, thereby maximizing the performance and learning efficiency of meta-learning. Motivated by this insight, we propose to define, measure, and model FNS in meta-learning. First, we define that an effective FNS should possess frugality, plasticity, and sensitivity. Then, to quantify FNS in practice, we present three measurements for these properties, collectively forming the structure constraint with theoretical supports. Building on this, we finally propose Neuromodulated Meta-Learning (NeuronML) to model FNS in meta-learning. It utilizes bi-level optimization to update both weights and structure with the structure constraint. Extensive theoretical and empirical evaluations demonstrate the effectiveness of NeuronML on various tasks. Code is publicly available at https://***/WangJingyao07/NeuronML. Copyright © 2024, The Authors. All rights reserved.

关键词： Contrastive Learning

Clairvoyance: Intelligent route planning for electric buses based on urban big data

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arXiv 2021年

作者： Lu, Xiangyong Ota, Kaoru Dong, Mianxiong Yu, Chen Jin, Hai Graduate School of Information Sciences Tohoku University Sendai Japan Serviecs Computing Technology and System Lab Big Data Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan430074 China Department of Information and Electronic Engineering Muroran Institute of Technology Hokkaido Muroran Japan

Nowadays many cities around the world have introduced electric buses to optimize urban traffic and reduce the local carbon emissions. In order to cut the carbon emissions and maximize the utility of electric buses, it is important to choose suitable routes for them. Traditionally, route selection is on the basis of dedicated surveys, which are costly in time and labor. In this paper, we mainly focus attention on planning electric bus routes intelligently, depending on the unique needs of each region throughout the city. We propose Clairvoyance, a route planning system that leverages a deep neural network and a multilayer perceptron to predict the future people’s trips and the future transportation carbon emission in the whole city, respectively. Given the future information of people’s trips and transportation carbon emission, we utilize a greedy mechanism to recommend bus routes for electric buses that will depart in an ideal state. Furthermore, representative features of the two neural networks are extracted from the heterogeneous urban datasets. We evaluate our approach through extensive experiments on the real-world data sources in Zhuhai, China. The results show that our designed neural network-based algorithms are consistently superior to the typical baselines. Additionally, the recommended routes for electric buses are helpful in reducing the peak value of carbon emissions and making full use of electric buses in the city. Copyright © 2021, The Authors. All rights reserved.

关键词： Multilayer neural networks

Robust Self-Expression Learning with Adaptive Noise Perception

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SSRN

SSRN 2023年

作者： Wang, Yangbo Zhou, Jie Lu, Jianglin Wan, Jun Gao, Can Lin, Qingshui College of Computer Science and Software Engineering Shenzhen University Shenzhen518060 China National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Shenzhen518060 China SZU Branch Shenzhen Institute of Artificial Intelligence and Robotics for Society Shenzhen518060 China SMILE Lab Department of ECE College of Engineering Northeastern University Boston02115 United States School of Information and Safety Engineering Zhongnan University of Economics and Law Wuhan430073 China Basic Teaching Department Liaoning Technical University Huludao125105 China

Self-expression learning methods often obtain a coefficient matrix to measure the similarity between pairs of samples. However, directly using the raw data to represent each sample under the self-expression framework may not be ideal, as noise points are inevitably involved in the process of representing clean samples. To address this issue, this work proposes a novel self-expression model called robust Self-Expression learning with adaptive Noise Perception (SENP). SENP decomposes each sample into a clean part and a noisy part, and samples with large self-expression losses can be recognized as the noise points. A reliable coefficient matrix can then be learned by using only the clean points to reconstruct the clean part of each sample. By simultaneously detecting the noisy part of each sample and noise points, and adaptively mitigating their negative impacts, the representative ability of the generated coefficient matrix is improved. Moreover, inspired by the solution of non-negative matrix factorization (NMF), an effective algorithm is formed to optimize SENP. Extensive experiments on well-known benchmark datasets demonstrate the superiority of SENP compared to several state-of-the-art methods. © 2023, The Authors. All rights reserved.

关键词： Non-negative matrix factorization

Fuzzy Granule Density-Based Outlier Detection with Multi-Scale Granular Balls

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arXiv 2025年

作者： Gao, Can Tan, Xiaofeng Zhou, Jie Ding, Weiping Pedrycz, Witold The College of Computer Science and Software Engineering Shenzhen University Shenzhen518060 China Guangdong Key Laboratory of Intelligent Information Processing Shenzhen518060 China The National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Shenzhen518060 China The School of Artificial Intelligence and Computer Science Nantong University Nantong226019 China The Faculty of Data Science City University of Macau Macau999078 China The Department of Electrical and Computer Engineering University of Alberta Edmonton Canada Systems Research Institute Polish Academy of Sciences Warsaw Poland The Department of Electrical and Computer Engineering King Abdulaziz University Jeddah Saudi Arabia The Department of Computer Engineering Istinye University Istanbul Turkey

Outlier detection refers to the identification of anomalous samples that deviate significantly from the distribution of normal data and has been extensively studied and used in a variety of practical tasks. However, most unsupervised outlier detection methods are carefully designed to detect specified outliers, while real-world data may be entangled with different types of outliers. In this study, we propose a fuzzy rough sets-based multi-scale outlier detection method to identify various types of outliers. Specifically, a novel fuzzy rough sets-based method that integrates relative fuzzy granule density is first introduced to improve the capability of detecting local outliers. Then, a multi-scale view generation method based on granular-ball computing is proposed to collaboratively identify group outliers at different levels of granularity. Moreover, reliable outliers and inliers determined by the three-way decision are used to train a weighted support vector machine to further improve the performance of outlier detection. The proposed method innovatively transforms unsupervised outlier detection into a semi-supervised classification problem and for the first time explores the fuzzy rough sets-based outlier detection from the perspective of multi-scale granular balls, allowing for high adaptability to different types of outliers. Extensive experiments carried out on both artificial and UCI datasets demonstrate that the proposed outlier detection method significantly outperforms the state-of-the-art methods, improving the results by at least 8.48% in terms of the Area Under the ROC Curve (AUROC) index. The source codes are released at https://***/Xiaofeng-Tan/MGBOD. © 2025, CC BY.

关键词： Granulation

Why Do Developers Remove Lambda Expressions in Java? 21

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Why Do Developers Remove Lambda Expressions in Java?

IEEE International Conference on Automated Software engineering (ASE)

作者： Mingwei Zheng Jun Yang Ming Wen Hengcheng Zhu Yepang Liu Hai Jin Hubei Engineering Research Center on Big Data Security School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan China National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Huazhong University of Science and Technology Wuhan China School of Electronic Information and Communications Huazhong University of Science and Technology Wuhan China The Hong Kong University of Science and Technology Hong Kong China Southern University of Science and Technology Shenzhen China Cluster and Grid Computing Lab School of Computer Science and Technology HUST Wuhan China

ISBN: (纸本)9781665447843

Java 8 has introduced lambda expressions, a core feature of functional programming. Since its introduction, there is an increasing trend of lambda adoptions in Java projects. Developers often adopt lambda expressions to simplify code, avoid code duplication or simulate other functional features. However, we observe that lambda expressions can also incur different types of side effects (i.e., performance issues and memory leakages) or even severe bugs, and developers also frequently remove lambda expressions in their implementations. Consequently, the advantages of utilizing lambda expressions can be significantly compromised by the collateral side effects. In this study, we present the first large-scale, quantitative and qualitative empirical study to characterize and understand inappropriate usages of lambda expressions. Particularly, we summarized seven main reasons for the removal of lambdas as well as seven common migration patterns. For instance, we observe that lambdas using customized functional interfaces are more likely to be removed by developers. Moreover, from a complementary perspective, we performed a user study over 30 developers to seek the underlying reasons why they remove lambda expressions in practice. Finally, based on our empirical results, we made suggestions on scenarios to avoid lambda usages for Java developers and also pointed out future directions for researchers.

关键词： Java Codes Computer bugs Market research Functional programming Open source software Software engineering

Depth-Aware Multi-Modal Fusion for Generalized Zero-Shot Learning

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Depth-Aware Multi-Modal Fusion for Generalized Zero-Shot Lea...

IEEE International Conference on Industrial Informatics (INDIN)

作者： Weipeng Cao Xuyang Yao Zhiwu Xu Yinghui Pan Yixuan Sun Dachuan Li Bohua Qiu Muheng Wei Guangdong Laboratory of Artificial Intelligence and Digital Economy (Shenzhen) Shenzhen China National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Shenzhen China College of Computer Science and Software Engineering Shenzhen University Shenzhen China Stony Brook University New York United States Research Institute of Trustworthy Autonomous Systems Southern University of Science and Technology Shenzhen China Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen China ZhenDui Industry Artificial Intelligence Co. Ltd Shenzhen China Department of Automation Shanghai Jiao Tong University Shanghai China Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China

ISBN: (数字)9798331527471

ISBN: (纸本)9798331527488

Realizing Generalized Zero-Shot Learning (GZSL) based on large models is emerging as a prevailing trend. However, most existing methods merely regard large models as black boxes, solely leveraging the features output by the final layer while disregarding potential performance enhancements from other layers. Indeed, numerous researchers have visually depicted variations in the features learned across different layers of neural networks. Motivated by this observation, we propose a Vision Transformer (ViT)-based GZSL method named Depth-Aware Multi-Modal ViT (DAM2ViT), which exploits multi-level features of ViT. DAM2ViT incorporates a multi-modal interaction block to align semantic information of categories across multiple layers, thereby augmenting the model's capacity to learn associations between visual and semantic spaces. Extensive experiments conducted on three benchmark datasets (i.e., CUB, SUN, AWA2) have showcased that DAM2ViT achieves competitive results compared to state-of-the-art methods.

关键词： Visualization Adaptation models Semantics Zero shot learning Neural networks Termination of employment Transformers Market research Sun Optimization

Decentralized Task Offloading in Edge computing: A Multi-User Multi-Armed Bandit Approach

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arXiv 2021年

作者： Wang, Xiong Ye, Jiancheng Lui, John C.S. National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China Network Technology Lab Hong Kong Research Center Huawei Technologies Co. Ltd. Hong Kong Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong

Mobile edge computing facilitates users to offload computation tasks to edge servers for meeting their stringent delay requirements. Previous works mainly explore task offloading when system-side information is given (e.g., server processing speed, cellular data rate), or centralized offloading under system uncertainty. But both generally fall short to handle task placement involving many coexisting users in a dynamic and uncertain environment. In this paper, we develop a multi-user offloading framework considering unknown yet stochastic system-side information to enable a decentralized user-initiated service placement. Specifically, we formulate the dynamic task placement as an online multi-user multi-armed bandit process, and propose a decentralized epoch based offloading (DEBO) to optimize user rewards which are subjected under network delay. We show that DEBO can deduce the optimal user-server assignment, thereby achieving a close-to-optimal service performance and tight O(log T) offloading regret. Moreover, we generalize DEBO to various common scenarios such as unknown reward gap, dynamic entering or leaving of clients, and fair reward distribution, while further exploring when users' offloaded tasks require heterogeneous computing resources. Particularly, we accomplish a sub-linear regret for each of these instances. Real measurements based evaluations corroborate the superiority of our offloading schemes over state-of-the-art approaches in optimizing delay-sensitive rewards. Copyright © 2021, The Authors. All rights reserved.

关键词： Stochastic systems

Mandari: Multi-Modal Temporal Knowledge Graph-aware Sub-graph Embedding for Next-POI Recommendation

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Mandari: Multi-Modal Temporal Knowledge Graph-aware Sub-grap...

IEEE International Conference on Multimedia and Expo (ICME)

作者： Xiaoqian Liu Xiuyun Li Yuan Cao Fan Zhang Xiongnan Jin Jinpeng Chen School of Computer Science (National Pilot Software Engineering School) Beijing University of Posts and Telecommunications Beijing China Key Laboratory of Trustworthy Distributed Computing and Service (BUPT) Ministry of Education Beijing China The Technology Innovation Center of Cultural Tourism Big Data of Hebei Province Chengde China Hebei Normal University for Nationalities Chengde China Knowledge Discovery and Data Mining Research Center Zhejiang Lab Hangzhou China

Next-POI recommendation aims to explore from user check-in sequence to predict the next possible location to be visited. Existing methods are often difficult to model the implicit association of multi-modal data with user choices. Moreover, traditional methods struggle to fully explore the variation of user preferences at variable time intervals. To tackle these limitations, we propose a Multi-Modal Temporal Knowledge Graph-aware Sub-graph Embedding approach (Mandari). We first construct a novel Multi-Modal Temporal Knowledge Graph. Based on the proposed knowledge graph, we integrate multi-modal information and leverage the graph attention network to calculate sub-graph prediction probability. Next, we implement a temporal knowledge mining method to model the segmentation and periodicity of user check-in and obtain temporal prediction probability. Finally, we fuse temporal prediction probability with the previous sub-graph prediction probability to obtain the final result. Extensive experiments demonstrate that our approach outperforms existing state-of-the-art methods.

关键词：

Towards High-resolution 3D Anomaly Detection via Group-Level Feature Contrastive Learning

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arXiv 2024年

作者： Zhu, Hongze Xie, Guoyang Hou, Chengbin Dai, Tao Gao, Can Wang, Jinbao Shen, Linlin National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Shenzhen China Department of Computer Science City University of Hong Kong Hong Kong Department of Intelligent Manufacturing CATL Ningde China Fuzhou Fuyao Institute for Advanced Study Fuyao University of Science and Technology Fuzhou China College of Computer Science and Software Engineering Shenzhen University Shenzhen China Guangdong Provincial Key Laboratory of Intelligent Information Processing Shenzhen China Shenzhen University Shenzhen China Shenzhen Institute of Artificial Intelligence and Robotics for Society Shenzhen China

High-resolution point clouds (HRPCD) anomaly detection (AD) plays a critical role in precision machining and high-end equipment manufacturing. Despite considerable 3D-AD methods that have been proposed recently, they still cannot meet the requirements of the HRPCD-AD task. There are several challenges: i) It is difficult to directly capture HRPCD information due to large amounts of points at the sample level;ii) The advanced transformer-based methods usually obtain anisotropic features, leading to degradation of the representation;iii) The proportion of abnormal areas is very small, which makes it difficult to characterize. To address these challenges, we propose a novel group-level feature-based network, called Group3AD, which has a significantly efficient representation ability. First, we design an Intercluster Uniformity Network (IUN) to present the mapping of different groups in the feature space as several clusters, and obtain a more uniform distribution between clusters representing different parts of the point clouds in the feature space. Then, an Intracluster Alignment Network (IAN) is designed to encourage groups within the cluster to be distributed tightly in the feature space. In addition, we propose an Adaptive Group-Center Selection (AGCS) based on geometric information to improve the pixel density of potential anomalous regions during inference. The experimental results verify the effectiveness of our proposed Group3AD, which surpasses Reg3D-AD by the margin of 5% in terms of object-level AUROC on Real3DAD. We provide the code and supplementary information on our website: https://***/M-3lab/Group3AD. Copyright © 2024, The Authors. All rights reserved.

关键词： Anomaly detection