检索结果-内蒙古大学图书馆

PubLabeler: Enhancing Automatic Classification of Publications in UniProtKB Using Protein Textual Description and PubMedBERT

引用

IEEE Journal of Biomedical and Health Informatics 2024年第5期29卷 3782-3791页

作者： Shaojun Wang Junyi Bian Xiaodi Huang Hong Zhou Shanfeng Zhu Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai China School of Computer Science Fudan University Shanghai China School of Computing Mathematics and Engineering Charles Sturt University Albury NSW Australia Atypon Systems LLC Oxford U.K. Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science Fudan University Shanghai China Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Ministry of Education Shanghai China Shanghai Key Laboratory of Intelligent Information Processing Shanghai Institute of Artificial Intelligence Algorithm Fudan University Shanghai China Zhangjiang Fudan International Innovation Center Fudan University Shanghai China

In UniProtKB, each protein is linked to numerous publications covering topics such as sequence, function, and structure, which are annotated manually or through automated methods. Given the vast number of proteins and literature, manual annotation is time-consuming and labour-intensive. Although UniProtKB offers automated annotations, their quality often falls short. Therefore, developing an accurate automated classifier to identify the topics of publications associated with each protein is imperative for advancing biomedical knowledge discovery. Classifying publications in UniProtKB involves protein-publication pairs characterized by multi-label, label co-occurrence, and class imbalance, which increases complexity. This paper proposes a novel method called PubLabeler, which simultaneously considers protein description and scientific literature texts as input. PubLabeler employs the PubMedBERT model to encode input texts and integrates label co-occurrence information into the model parameters. Additionally, it uses focal loss to update parameters, allowing the model to focus more on classes with a few instances. Using newly annotated literature from Swiss-Prot in 2023 as a test set, PubLabeler achieved superior results in both micro and macro metrics, showing a 28.5% improvement in macro-F1 compared to UniProtKB's automated annotation method, UPCLASS. Furthermore, we validated PubLabeler's effectiveness in TrEMBL annotation, showcasing its comprehensive prediction results compared to TrEMBL's automated annotations. These findings highlight PubLabeler's reliability and potential to advance protein-related information extraction and knowledge discovery.

关键词： Proteins Protein engineering Annotations Bioinformatics Training Manuals Biological system modeling Text categorization Predictive models Pipelines

来源：评论

学校读者我要写书评

暂无评论

Timing-Driven High-Level Synthesis for Continuous-Flow Microfluidic Biochips

Timing-Driven High-Level Synthesis for Continuous-Flow Micro...

引用

IEEE International Symposium on Quality Electronic Design

作者： Zhengyang Ye Zhisheng Chen Youlin Pan Genggeng Liu Wenzhong Guo Tsung-Yi Ho Xing Huang College of Computer and Data Science Fuzhou University Fuzhou China Engineering Research Center of Big Data Intelligence Ministry of Education Fuzhou China Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou China School of Informatics Xiamen University Xiamen China Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong China School of Computer Science Northwestern Polytechnical University Xi’an China

ISBN: (数字)9798350309270

ISBN: (纸本)9798350309287

As continuous-flow microfluidic biochips technology rapidly advances, its automated synthesis methods require adapting to increasingly complex and stringent biochemical applications. In particular, with the introduction of time-sensitive bioassays, in this work, we present a timing-driven high-level synthesis method to optimize the resource efficiency of bioassays considering the time constraints. Specifically, we investigate the existing forms of time constraints and propose a corresponding flexible modeling approach based on reaction-control which can achieve downward compatibility for physical design. Additionally, we also analyze the impact of storage and wash on time constraints. The experimental results show that our method achieves efficient execution and low devices cost while satisfying time constraints.

关键词： Costs Biochips Time factors Microfluidics Physical design

来源：评论

学校读者我要写书评

暂无评论

Contrastive Learning for Robust Android Malware Familial Classification

arXiv

引用

arXiv 2021年

作者： Wu, Yueming Dou, Shihan Zou, Deqing Yang, Wei Qiang, Weizhong Jin, Hai National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Hubei Engineering Research Center on Big Data Security School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan430074 China Shanghai Key Laboratory of Intelligent Information Processing School of Computer Science Fudan University Shanghai200433 China University of Texas at Dallas Dallas United States 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 Wuhan430074 China

Due to its open-source nature, Android operating system has been the main target of attackers to exploit. Malware creators always perform different code obfuscations on their apps to hide malicious activities. Features extracted from these obfuscated samples through program analysis contain many useless and disguised features, which leads to many false negatives. To address the issue, in this paper, we demonstrate that obfuscation-resilient malware family analysis can be achieved through contrastive learning. The key insight behind our analysis is that contrastive learning can be used to reduce the difference introduced by obfuscation while amplifying the difference between malware and other types of malware. Based on the proposed analysis, we design a system that can achieve robust and interpretable classification of Android malware. To achieve robust classification, we perform contrastive learning on malware samples to learn an encoder that can automatically extract robust features from malware samples. To achieve interpretable classification, we transform the function call graph of a sample into an image by centrality analysis. Then the corresponding heatmaps can be obtained by visualization techniques. These heatmaps can help users understand why the malware is classified as this family. We implement IFDroid and perform extensive evaluations on two datasets. Experimental results show that IFDroid is superior to state-of-the-art Android malware familial classification systems. Moreover, IFDroid is capable of maintaining a 98.4% F1 on classifying 69,421 obfuscated malware samples. © 2021, CC0.

关键词： Android (operating system)

来源：评论

学校读者我要写书评

暂无评论

A review of big data technology and its application in cancer care

引用

Computers in Biology and Medicine 2024年 176卷 108577-108577页

作者： Xiao, Tianyun Kong, Shanshan Zhang, Zichen Hua, Dianbo Liu, Fengchun Hebei Key Laboratory of Data Science and Application North China University of Science and Technology Hebei Tangshan063210 China The Key Laboratory of Engineering Computing in Tangshan City North China University of Science and Technology Hebei Tangshan063210 China College of Science North China University of Science and Technology Hebei Tangshan063210 China Hebei Engineering Research Center for the Intelligentization of Iron Ore Optimization and Ironmaking Raw Materials Preparation Processes North China University of Science and Technology Hebei Tangshan China Tangshan Intelligent Industry and Image Processing Technology Innovation Center North China University of Science and Technology Hebei Tangshan China Beijing Sitairui Cancer Data Analysis Joint Laboratory Beijing101149 China

The development of modern medical devices and information technology has led to a rapid growth in the amount of data available for health protection information, with the concept of medical big data emerging globally, along with significant advances in cancer care relying on data-driven approaches. However, outstanding issues such as fragmented data governance, low-quality data specification, and data lock-in still make sharing challenging. Big data technology provides solutions for managing massive heterogeneous data while combining artificial intelligence (AI) techniques such as machine learning (ML) and deep learning (DL) to better mine the intrinsic connections between data. This paper surveys and organizes recent articles on big data technology and its applications in cancer, dividing them into three different types to outline their primary content and summarize their critical role in assisting cancer care. It then examines the latest research directions in big data technology in cancer and evaluates the current state of development of each type of application. Finally, current challenges and opportunities are discussed, and recommendations are made for the further integration of big data technology into the medical industry in the future. © 2024 Elsevier Ltd

关键词： Big data

来源：评论

学校读者我要写书评

暂无评论

Inverse system internal model control of DIFG wind power generator system based on matrix converter

引用

Taiyangneng Xuebao/Acta Energiae Solaris Sinica 2012年第11期33卷 1983-1991页

作者： Chen, Caixue Xie, Yunxiang Ma, Xueliang Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan 411105 China School of Electric Power South China University of Technology Guangzhou 510641 China Guangdong MingYang Wind Power Industry Group Co. Ltd Zhongshan 528437 China

Aim to solve the poor dynamic performance and the low disturbance resistance of PI power decoupling controller for DFIG power generator system based on matrix converter, this paper propose a nonlinear control algorithm for the AC-excitation DFIG system. First, we establish the mathematical model of the DFIG, based on the model, use the inverse system theory and deduce the inverse model, add the inverse model in series to the front of the original system model, develop the whole system to a pseudo linear system. Consider the system performance influenced by the parameters of the linearized model, we use the predictive control to improve the robustness. The simulation results show that the control strategy has fast response and good dynamic performance. The off-grid and cut-grid experimental data validate that under sub-synchronous or super-synchronous state, the stator voltage and frequency can maintain stability and achieve variable speed constant frequency operation.

关键词： Model predictive control

来源：评论

学校读者我要写书评

暂无评论

Inferring microRNA-disease association by hybrid recommendation algorithm and unbalanced bi-random walk on heterogeneous network

引用

Scientific reports 2019年第1期9卷 2474页

作者： Dong-Ling Yu Yuan-Lin Ma Zu-Guo Yu Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 P.R. China. yuzuguo@***. School of Electrical Engineering and Computer Science Queensland University of Technology Brisbane Q4001 Australia. yuzuguo@***.

More and more research works have indicated that microRNAs (miRNAs) play indispensable roles in exploring the pathogenesis of diseases. Detecting miRNA-disease associations by experimental techniques in biology is expensive and time-consuming. Hence, it is important to propose reliable and accurate computational methods to exploring potential miRNAs related diseases. In our work, we develop a novel method (BRWHNHA) to uncover potential miRNAs associated with diseases based on hybrid recommendation algorithm and unbalanced bi-random walk. We first integrate the Gaussian interaction profile kernel similarity into the miRNA functional similarity network and the disease semantic similarity network. Then we calculate the transition probability matrix of bipartite network by using hybrid recommendation algorithm. Finally, we adopt unbalanced bi-random walk on the heterogeneous network to infer undiscovered miRNA-disease relationships. We tested BRWHNHA on 22 diseases based on five-fold cross-validation and achieves reliable performance with average AUC of 0.857, which an area under the ROC curve ranging from 0.807 to 0.924. As a result, BRWHNHA significantly improves the performance of inferring potential miRNA-disease association compared with previous methods. Moreover, the case studies on lung neoplasms and prostate neoplasms also illustrate that BRWHNHA is superior to previous prediction methods and is more advantageous in exploring potential miRNAs related diseases. All source codes can be downloaded from https://***/myl446/BRWHNHA .

关键词：

来源：评论

学校读者我要写书评

暂无评论

From social to individuals: A parsimonious path of multi-level models for crowdsourced preference aggregation

arXiv

引用

arXiv 2018年

作者： Xu, Qianqian Xiong, Jiechao Cao, Xiaochun Huang, Qingming Yao, Yuan Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing1000190 China Institute of Information Engineering Chinese Academy of Sciences Beijing100093 China Tencent AI Lab Shenzhen518057 BICMR-LMAM-LMEQF-LMP School of Mathematical Sciences Peking University Beijing100871 China University of Chinese Academy of Sciences Institute of Computing Technology of Chinese Academy of Sciences Beijing100190 China Department of Mathematics and by courtesy Computer Science and Engineering Hong Kong University of Science and Technology Hong Kong Hong Kong

In crowdsourced preference aggregation, it is often assumed that all the annotators are subject to a common preference or social utility function which generates their comparison behaviors in experiments. However, in reality annotators are subject to variations due to multi-criteria, abnormal, or a mixture of such behaviors. In this paper, we propose a parsimonious mixed-effects model, which takes into account both the fixed effect that the majority of annotators follows a common linear utility model, and the random effect that some annotators might deviate from the common significantly and exhibit strongly personalized preferences. The key algorithm in this paper establishes a dynamic path from the social utility to individual variations, with different levels of sparsity on personalization. The algorithm is based on the Linearized Bregman Iterations, which leads to easy parallel implementations to meet the need of large-scale data analysis. In this unified framework, three kinds of random utility models are presented, including the basic linear model with L2 loss, Bradley-Terry model, and Thurstone-Mosteller model. The validity of these multi-level models are supported by experiments with both simulated and real-world datasets, which shows that the parsimonious multi-level models exhibit improvements in both interpretability and predictive precision compared with traditional HodgeRank. Copyright © 2018, The Authors. All rights reserved.

关键词： Crowdsourcing

来源：评论

学校读者我要写书评

暂无评论

Direct clustering algorithm based on generalized information distance

引用

Jisuanji Yanjiu yu Fazhan/Computer Research and Development 2007年第4期44卷 674-679页

作者： Ding, Shifei Shi, Zhongzhi Jin, Fengxiang Xia, Shixiong College of Computer Science and Technology China University of Mining and Technology Xuzhou 221008 China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100080 China College of Geoinformation Science and Engineering Shandong University of Science and Technology Qingdao 266510 China

In this paper a novel direct clustering algorithm based on generalized information distance (GID) is put forward. Firstly, based on information theory, a basic concept of measure of diversity is given and an inequality about measure of diversity is proved. Based on this inequality, a concept of increment of diversity is discussed and a defined. Secondly, by analyzing distance measure, two new concepts of generalized information distance (GID) and improved generalized information distance (IGID) are proposed, and a new direct clustering algorithm based on GID and IGID is designed. Finally this algorithm is applied to soil fertility data processing, and compared with hierarchical clustering algorithm (HCA). The results of simulation application show that the algorithm presented here is feasible and effective. Because of simplicity of algorithm and robustness. It provides a new research approach for studies of pattern recognition theory.

关键词： Clustering algorithms

来源：评论

学校读者我要写书评

暂无评论

Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction

arXiv

引用

arXiv 2023年

作者： Lin, Xuan Dai, Lichang Zhou, Yafang Yu, Zu-Guo Zhang, Wen Shi, Jian-Yu Cao, Dong-Sheng Zeng, Li Chen, Haowen Song, Bosheng Yu, Philip S. Zeng, Xiangxiang Xiangtan China Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University China College of Informatics Huazhong Agricultural University China The Northwestern Polytechnical University Xi’an China The Xiangya School of Pharmaceutical Sciences Central South University China AIDD Department of Yuyao Biotech Shanghai China Hunan University China The College of Information Science and Engineering Hunan University Changsha China Computer Science The University of Illinois Chicago United States

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, NLP based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely-used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction. Copyright © 2023, The Authors. All rights reserved.

关键词： Forecasting

来源：评论

学校读者我要写书评

暂无评论

Real-time Multi-person Eyeblink Detection in the Wild for Untrimmed Video

Real-time Multi-person Eyeblink Detection in the Wild for Un...

引用

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： Wenzheng Zeng Yang Xiao Sicheng Wei Jinfang Gan Xintao Zhang Zhiguo Cao Zhiwen Fang Joey Tianyi Zhou Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China School of Biomedical Engineering Southern Medical University Guangzhou China Department of Rehabilitation Medicine Zhujiang Hospital Southern Medical University Guangzhou China Centre for Frontier AI Research Agency for Science Technology and Research (A*STAR) Singapore Institute of High Performance Computing Agency for Science Technology and Research (A*STAR) Singapore

Real-time eyeblink detection in the wild can widely serve for fatigue detection, face anti-spoofing, emotion analysis, etc. The existing research efforts generally focus on single-person cases towards trimmed video. However, multi-person scenario within untrimmed videos is also important for practical applications, which has not been well concerned yet. To address this, we shed light on this research field for the first time with essential contributions on dataset, theory, and practices. In particular, a large-scale dataset termed MPEblink that involves 686 untrimmed videos with 8748 eyeblink events is proposed under multi-person conditions. The samples are captured from uncon-strainedfilms to reveal “in the wild“ characteristics. Meanwhile, a real-time multi-person eyeblink detection method is also proposed. Being different from the existing counter-parts, our proposition runs in a one-stage spatio-temporal way with end-to-end learning capacity. Specifically, it simultaneously addresses the sub-tasks of face detection, face tracking, and human instance-level eyeblink detection. This paradigm holds 2 main advantages: (1) eyeblink features can be facilitated via the face's global context (e.g., head pose and illumination condition) with joint optimization and interaction, and (2) addressing these sub-tasks in parallel instead of sequential manner can save time remarkably to meet the real-time running requirement. Experiments on MPEblink verify the essential challenges of real-time multi-person eyeblink detection in the wild for untrimmed video. Our method also outperforms existing approaches by large margins and with a high inference speed.

关键词：

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：