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Metacognition Inspired Reflective Chain-of-Thought for Knowledge-Based VQA
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作者 Zhongfan Sun Kan Guo +1 位作者 Yongli Hu Yong Zhang 《Computers, Materials & Continua》 2026年第4期1909-1933,共25页
Knowledge-based VisualQuestion Answering(VQA)requires the integration of visual information with external knowledge reasoning.Existing approaches typically retrieve information from external corpora and rely on pretra... Knowledge-based VisualQuestion Answering(VQA)requires the integration of visual information with external knowledge reasoning.Existing approaches typically retrieve information from external corpora and rely on pretrained language models for reasoning.However,their performance is often hindered by the limited capabilities of retrievers and the constrained size of knowledge bases.Moreover,relying on image captions to bridge the modal gap between visual and language modalities can lead to the omission of critical visual details.To address these limitations,we propose the Reflective Chain-of-Thought(ReCoT)method,a simple yet effective framework inspired by metacognition theory.ReCoT effectively activates the reasoning capabilities ofMultimodal Large LanguageModels(MLLMs),providing essential visual and knowledge cues required to solve complex visual questions.It simulates a metacognitive reasoning process that encompasses monitoring,reflection,and correction.Specifically,in the initial generation stage,an MLLM produces a preliminary answer that serves as the model’s initial cognitive output.During the reflective reasoning stage,this answer is critically examined to generate a reflective rationale that integrates key visual evidence and relevant knowledge.In the final refinement stage,a smaller language model leverages this rationale to revise the initial prediction,resulting in amore accurate final answer.By harnessing the strengths ofMLLMs in visual and knowledge grounding,ReCoT enables smaller language models to reason effectively without dependence on image captions or external knowledge bases.Experimental results demonstrate that ReCoT achieves substantial performance improvements,outperforming state-of-the-art methods by 2.26%on OK-VQA and 5.8%on A-OKVQA. 展开更多
关键词 knowledge-based VQA METACOGNITION reflective chain-of-thought answer refinement
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A physics knowledge-based surrogate model framework for timedependent slope deformation:Considering water effect and sliding states
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作者 Wenyu Zhuang Yaoru Liu +3 位作者 Kai Zhang Qingchao Lyu Shaokang Hou Qiang Yang 《Journal of Rock Mechanics and Geotechnical Engineering》 2025年第9期5416-5436,共21页
The surrogate model serves as an efficient simulation tool during the slope parameter inversion process.However,the creep constitutive model integrated with dynamic damage evolution poses challenges in development of ... The surrogate model serves as an efficient simulation tool during the slope parameter inversion process.However,the creep constitutive model integrated with dynamic damage evolution poses challenges in development of the required surrogate model.In this study,a novel physics knowledge-based surrogate model framework is proposed.In this framework,a Transformer module is employed to capture straindriven softening-hardening physical mechanisms.Positional encoding and self-attention are utilized to transform the constitutive parameters associated with shear strain,which are not directly time-related,into intermediate latent features for physical loss calculation.Next,a multi-layer stacked GRU(gated recurrent unit)network is built to provide input interfaces for time-dependent intermediate latent features,hydraulic boundary conditions,and water-rock interaction degradation equations,with static parameters introduced via external fully-connected layers.Finally,a combined loss function is constructed to facilitate the collaborative training of physical and data loss,introducing time-dependent weight adjustments to focus the surrogate model on accurate deformation predictions during critical phases.Based on the deformation of a reservoir bank landslide triggered by impoundment and subsequent restabilization,an elasto-viscoplastic constitutive model that considers water effect and sliding state dependencies is developed to validate the proposed surrogate model framework.The results indicate that the framework exhibits good performance in capturing physical mechanisms and predicting creep behavior,reducing errors by about 30 times compared to baseline models such as GRU and LSTM(long short-term memory),meeting the precision requirements for parameter inversion.Ablation experiments also confirmed the effectiveness of the framework.This framework can also serve as a reference for constructing other creep surrogate models that involve non-time-related across dimensions. 展开更多
关键词 Reservoir bank slope Time-dependent deformation Elasto-viscoplastic constitutive model Physics knowledge-based deep learning Surrogate model
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Triple-helix knowledge-based Sino-Nordic Arctic relationships for trust and sustainable development
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作者 Rasmus Gjedsso Bertelsen 《Advances in Polar Science》 2016年第3期180-184,共5页
This paper goes beyond Sino-Nordic Arctic science diplomacy and looks at Sino-Nordic Arctic triple-helix knowledge- based collaborations among academia, business, civil society (the inclusion of which moves beyond th... This paper goes beyond Sino-Nordic Arctic science diplomacy and looks at Sino-Nordic Arctic triple-helix knowledge- based collaborations among academia, business, civil society (the inclusion of which moves beyond the original triple-helix concept), and government. In light of the potential of science diplomacy for building Sino-Arctic trust under systemic international conditions of power transition and globalization, this is the natural next step toward exploring triple-helix collaborations. Knowledge-based collaborations between academia, business, civil society, and government also open up avenues for innovation and entrepreneurship by both Arctic societies and Chinese society in attempts to address major challenges to sustainable development in these societies. This paper discusses possible triple-helix knowledge-based collaborations with China by each of the five Nordic countries, and highlights the innovation and entrepreneurial talents of summer school students at the University of International Relations in Beijing in developing projects as part of a course entitled "The Global Arctic". 展开更多
关键词 international relations power transition trust science diplomacy TRIPLE-HELIX NORDIC China
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Blockchain-Enabled Trusted Virtual Network Embedding in Intelligent Cyber-Physical Systems
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作者 Zhu Hailong Huang Tao +2 位作者 Zhang Yi Chen Ning Zhang Peiying 《China Communications》 2026年第1期175-188,共14页
With the rapid development of intelligent cyber-physical systems(ICPS),diverse services with varying Quality of Service(QoS)requirements have brought great challenges to traditional network resource allocation.Further... With the rapid development of intelligent cyber-physical systems(ICPS),diverse services with varying Quality of Service(QoS)requirements have brought great challenges to traditional network resource allocation.Furthermore,given the open environment and a multitude of devices,enhancing the security of ICPS is an urgent concern.To address these issues,this paper proposes a novel trusted virtual network embedding(T-VNE)approach for ICPS based combining blockchain and edge computing technologies.Additionally,the proposed algorithm leverages a deep reinforcement learning(DRL)model to optimize decision-making processes.It employs the policygradient-based agent to compute candidate embedding nodes and utilizes a breadth-first search(BFS)algorithm to determine the optimal embedding paths.Finally,through simulation experiments,the efficacy of the proposed method was validated,demonstrating outstanding performance in terms of security,revenue generation,and virtual network request(VNR)acceptance rate. 展开更多
关键词 blockchain cyber-physical system trusted embedding virtual network
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A Year of Deepening China-Africa Bonds--Political trust,economic collaboration and cultural exchanges further solidify China-Africa ties
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作者 HE WENPING 《ChinAfrica》 2026年第1期20-22,共3页
The year 2025 marks both the 25th anniversary of the Forum on China-Africa Cooperation(FOCAC)and the first year of implementation of the outcomes of the 2024 FOCAC Beijing Summit.Throughout the year,China has supporte... The year 2025 marks both the 25th anniversary of the Forum on China-Africa Cooperation(FOCAC)and the first year of implementation of the outcomes of the 2024 FOCAC Beijing Summit.Throughout the year,China has supported Africa in addressing historical injustices at diplomatic and political levels and firmly backed South Africa in hosting the G20 Leaders’Summit,further deepening China-Africa strategic mutual trust. 展开更多
关键词 Political trust Forum China Africa Cooperation addressing historical injustices FOCAC China Africa Cooperation Strategic Mutual trust Economic Collaboration Diplomatic Support
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Anomaly Detection Method of Power Internet of Things Terminals in Zero-Trust Environment
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作者 Sun Pengzhan Ren Yinlin +2 位作者 Shao Sujie Yang Chao Qiu Xuesong 《China Communications》 2026年第1期290-305,共16页
With more and more IoT terminals being deployed in various power grid business scenarios,terminal reliability has become a practical challenge that threatens the current security protection architecture.Most IoT termi... With more and more IoT terminals being deployed in various power grid business scenarios,terminal reliability has become a practical challenge that threatens the current security protection architecture.Most IoT terminals have security risks and vulnerabilities,and limited resources make it impossible to deploy costly security protection methods on the terminal.In order to cope with these problems,this paper proposes a lightweight trust evaluation model TCL,which combines three network models,TCN,CNN,and LSTM,with stronger feature extraction capability and can score the reliability of the device by periodically analyzing the traffic behavior and activity logs generated by the terminal device,and the trust evaluation of the terminal’s continuous behavior can be achieved by combining the scores of different periods.After experiments,it is proved that TCL can effectively use the traffic behaviors and activity logs of terminal devices for trust evaluation and achieves F1-score of 95.763,94.456,99.923,and 99.195 on HDFS,BGL,N-BaIoT,and KDD99 datasets,respectively,and the size of TCL is only 91KB,which can achieve similar or better performance than CNN-LSTM,RobustLog and other methods with less computational resources and storage space. 展开更多
关键词 anomaly detection distributed machine learning power internet of Things zero trust
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Promoting psychological well-being in AI-enhanced english as a foreign language learning:A mixed-methods study of motivation,language learning anxiety and trust in higher education
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作者 Zhiyong Sun 《Journal of Psychology in Africa》 2026年第1期33-43,共11页
This mixed-methods study investigated how AI-enhanced English as a Foreign Language(EFL)learning environments influence students’psychological well-being through the mediating roles of motivation and language learnin... This mixed-methods study investigated how AI-enhanced English as a Foreign Language(EFL)learning environments influence students’psychological well-being through the mediating roles of motivation and language learning anxiety and the moderating role of trust.Participants were Chinese university students(N=310,62%female,mean age=18.9,SD=0.8),of whom 15 completed interviews to both add to and to clarify the evidence from the surveys.Structural equation modeling results revealed that AI use had significant indirect effects on well-being through increased motivation and reduced language learning anxiety.Trust in AI significantly moderated both paths,amplifying the motivational benefits and anxiety reduction associated with AI use.Thematic analysis supported these results,identifying three experiential themes:(1)motivational empowerment through personalization,(2)anxiety regulation through safe practice and feedback,and(3)trust as the emotional bridge between AI and well-being.The study extends AI psychology applications by empirically linking technology engagement with affective outcomes and underscores the need for human-centered and trust-enhancing design in AI-supported education.From these findings,we conclude that adaptive,transparent,and autonomy-supportive AI systems promote self-determined motivation,emotional safety,and overall psychological health among EFL learners. 展开更多
关键词 Artificial intelligence psychology EFL learning MOTIVATION anxiety trust WELL-BEING mixed methods self-determination theory
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国际档案领域人工智能研究进展及启示——基于I Trust AI项目五项课题研究的述评 被引量:1
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作者 潘未梅 曹飞羽 张佳琦 《北京档案》 北大核心 2025年第8期12-18,共7页
伴随着人工智能技术的发展与普及,人工智能技术对档案学学科的影响已成为档案领域深入研究与探讨的热点议题。为推动我国档案学领域人工智能相关研究的创新性发展,本文对国际档案领域规模最大、持续时间最长、影响最为深远的跨国跨学科... 伴随着人工智能技术的发展与普及,人工智能技术对档案学学科的影响已成为档案领域深入研究与探讨的热点议题。为推动我国档案学领域人工智能相关研究的创新性发展,本文对国际档案领域规模最大、持续时间最长、影响最为深远的跨国跨学科项目InterPARES第五期——I(nterPARES)Trust AI项目的部分前沿成果进行介绍,旨在为我国档案学界的理论探索与实践应用提供参考。 展开更多
关键词 InterPARES I trust AI 人工智能 档案
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Knowledge-Based Classification in Automated Soil Mapping 被引量:10
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作者 ZHOU BIN and WANG RENCHAOInstitute of Agricultural Remote Sensing and Information Technology Application, Zhejiang University, Hangzhou 310029 (China) 《Pedosphere》 SCIE CAS CSCD 2003年第3期209-218,共10页
A machine-learning approach was developed for automated building of knowledgebases for soil resources mapping by using a classification tree to generate knowledge from trainingdata. With this method, building a knowle... A machine-learning approach was developed for automated building of knowledgebases for soil resources mapping by using a classification tree to generate knowledge from trainingdata. With this method, building a knowledge base for automated soil mapping was easier than usingthe conventional knowledge acquisition approach. The knowledge base built by classification tree wasused by the knowledge classifier to perform the soil type classification of Longyou County,Zhejiang Province, China using Landsat TM bi-temporal images and CIS data. To evaluate theperformance of the resultant knowledge bases, the classification results were compared to existingsoil map based on a field survey. The accuracy assessment and analysis of the resultant soil mapssuggested that the knowledge bases built by the machine-learning method was of good quality formapping distribution model of soil classes over the study area. 展开更多
关键词 CLASSIFICATION classification tree knowledge-based rule extracting soilmapping
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Knowledge-based bridge detection from SAR images 被引量:5
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作者 Wang Wenguang Sun Jinping +1 位作者 Hu Rui Mao Shiyi 《Journal of Systems Engineering and Electronics》 SCIE EI CSCD 2009年第5期929-936,共8页
Automatic bridge detection is an important application of SAR images.Differed from the classical CFAR method,a new knowledge-based bridge detection approach is proposed.The method not only uses the backscattering inte... Automatic bridge detection is an important application of SAR images.Differed from the classical CFAR method,a new knowledge-based bridge detection approach is proposed.The method not only uses the backscattering intensity difference between targets and background but also applies the contextual information and spatial relationship between objects.According to bridges'special characteristics and scattering properties in SAR images,the new knowledge-based method includes three processes:river segmentation,potential bridge areas detection and bridge discrimination.The application to AIRSAR data shows that the new method is not sensitive to rivers'shape.Moreover,this method can detect bridges successfully when river segmentation is not very exact and is more robust than the radius projection method. 展开更多
关键词 knowledge-based bridge detection SAR contextual information mathematical morphology.
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New Knowledge-based Genetic Algorithm for Excavator Boom Structural Optimization 被引量:6
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作者 HUA Haiyan LIN Shuwen 《Chinese Journal of Mechanical Engineering》 SCIE EI CAS CSCD 2014年第2期392-401,共10页
Due to the insufficiency of utilizing knowledge to guide the complex optimal searching, existing genetic algorithms fail to effectively solve excavator boom structural optimization problem. To improve the optimization... Due to the insufficiency of utilizing knowledge to guide the complex optimal searching, existing genetic algorithms fail to effectively solve excavator boom structural optimization problem. To improve the optimization efficiency and quality, a new knowledge-based real-coded genetic algorithm is proposed. A dual evolution mechanism combining knowledge evolution with genetic algorithm is established to extract, handle and utilize the shallow and deep implicit constraint knowledge to guide the optimal searching of genetic algorithm circularly. Based on this dual evolution mechanism, knowledge evolution and population evolution can be connected by knowledge influence operators to improve the conflgurability of knowledge and genetic operators. Then, the new knowledge-based selection operator, crossover operator and mutation operator are proposed to integrate the optimal process knowledge and domain culture to guide the excavator boom structural optimization. Eight kinds of testing algorithms, which include different genetic operators, arc taken as examples to solve the structural optimization of a medium-sized excavator boom. By comparing the results of optimization, it is shown that the algorithm including all the new knowledge-based genetic operators can more remarkably improve the evolutionary rate and searching ability than other testing algorithms, which demonstrates the effectiveness of knowledge for guiding optimal searching. The proposed knowledge-based genetic algorithm by combining multi-level knowledge evolution with numerical optimization provides a new effective method for solving the complex engineering optimization problem. 展开更多
关键词 boom structural optimization dual evolution mechanism knowledge-based genetic strategies deep implicit knowledge domain culture
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TrustZone半虚拟化与容器化实现机制
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作者 余发江 王朝州 《信息网络安全》 北大核心 2025年第10期1523-1536,共14页
TrustZone广泛应用于移动平台,随着ARM CPU在云服务中大量部署,利用TrustZone增强虚拟机计算环境和数据的安全性需求日益凸显。但基础的TrustZone提供的硬件可信执行环境通常仅支持主机上的应用程序使用。为解决这一问题,文章提出一种Tr... TrustZone广泛应用于移动平台,随着ARM CPU在云服务中大量部署,利用TrustZone增强虚拟机计算环境和数据的安全性需求日益凸显。但基础的TrustZone提供的硬件可信执行环境通常仅支持主机上的应用程序使用。为解决这一问题,文章提出一种TrustZone半虚拟化与容器化实现机制pvTEE,使虚拟机或容器中的客户能够高效、并行利用主机平台的可信执行环境运行可信应用。pvTEE通过前端驱动vTEEdriver、虚拟设备vTEE、主机代理程序vTEEproxy以及后端驱动TEEdriver,将虚拟机或容器内客户的调用请求转发至可信执行环境中的可信应用执行。主机、虚拟机和容器中的客户仅可调用自身场景的可信应用,无法访问其他应用。同时,主机、虚拟机及容器各自有独立的日志获取能力与安全存储服务。pvTEE基于ARMv8.2 CPU服务器、QEMU KVM虚拟机和Docker容器实现,实验结果表明,客户在虚拟机中调用可信应用完成一次RSA加解密操作,相比在主机场景中仅增加约6%的时间开销。 展开更多
关键词 trustZONE 可信执行环境 虚拟化 容器化 云服务
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Structural Topology Design of Container Ship Based on Knowledge-Based Engineering and Level Set Method 被引量:5
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作者 崔进举 王德禹 史琪琪 《China Ocean Engineering》 SCIE EI CSCD 2015年第4期551-564,共14页
Knowledge-Based Engineering (KBE) is introduced into the ship structural design in this paper. From the implementation of KBE, the design solutions for both Rules Design Method (RDM) and Interpolation Design Meth... Knowledge-Based Engineering (KBE) is introduced into the ship structural design in this paper. From the implementation of KBE, the design solutions for both Rules Design Method (RDM) and Interpolation Design Method (IDM) are generated. The corresponding Finite Element (FE) models are generated. Topological design of the longitudinal structures is studied where the Gaussian Process (GP) is employed to build the surrogate model for FE analysis. Multi-objective optimization methods inspired by Pareto Front are used to reduce the design tank weight and outer surface area simultaneously. Additionally, an enhanced Level Set Method (LSM) which employs implicit algorithm is applied to the topological design of typical bracket plate which is used extensively in ship structures. Two different sets of boundary conditions are considered. The proposed methods show satisfactory efficiency and accuracy. 展开更多
关键词 knowledge-based Engineering (KBE) Level Set Method (LSM) Gaussian Process GP)
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FAULT DIAGNOSIS OF ROTATING MACHINERY USING KNOWLEDGE-BASED FUZZY NEURAL NETWORK 被引量:2
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作者 李如强 陈进 伍星 《Applied Mathematics and Mechanics(English Edition)》 SCIE EI 2006年第1期99-108,共10页
A novel knowledge-based fuzzy neural network (KBFNN) for fault diagnosis is presented. Crude rules were extracted and the corresponding dependent factors and antecedent coverage factors were calculated firstly from ... A novel knowledge-based fuzzy neural network (KBFNN) for fault diagnosis is presented. Crude rules were extracted and the corresponding dependent factors and antecedent coverage factors were calculated firstly from the diagnostic sample based on rough sets theory. Then the number of rules was used to construct partially the structure of a fuzzy neural network and those factors were implemented as initial weights, with fuzzy output parameters being optimized by genetic algorithm. Such fuzzy neural network was called KBFNN. This KBFNN was utilized to identify typical faults of rotating machinery. Diagnostic results show that it has those merits of shorter training time and higher right diagnostic level compared to general fuzzy neural networks. 展开更多
关键词 rotating machinery fault diagnosis rough sets theory fuzzy sets theory generic algorithm knowledge-based fuzzy neural network
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Knowledge-based potentials in bioinformatics: From a physicist's viewpoint 被引量:1
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作者 郑伟谋 《Chinese Physics B》 SCIE EI CAS CSCD 2015年第12期22-27,共6页
Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis o... Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint. 展开更多
关键词 knowledge-based potentials for proteins protein native structures sequence signals
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A Knowledge-based System for the Analysis of the Ability of Paying back Loans 被引量:1
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作者 Zhu Ming(朱明) +1 位作者 Yang Baoan(杨保安) 《Journal of Donghua University(English Edition)》 EI CAS 2001年第1期123-126,共4页
This paper describes the development of a knowledgebased system (KBS) for determining whether or not, and under what conditions, a bank Ioan officer should grant a business loan to a company. The prototype system deve... This paper describes the development of a knowledgebased system (KBS) for determining whether or not, and under what conditions, a bank Ioan officer should grant a business loan to a company. The prototype system developed focuses on what is bank loans risks management, how to prevent risk by the analysis of the ability of paying back loans. The paper makes the structural analysis involved in the system's decision situation, the structured situation diagram or model, dependency diagram and the document needed by the KBS prototype system thus are developed. Through testing the samples from loan business, the quality for the analysis of the ability of paying back loans can be effectively evaluated by the KBS prototype system. 展开更多
关键词 knowledge-based SYSTEM (KBS) the KBS prototype system the ABILITY of paying BACK loans bank LOANS risk management.
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Integration of Decision-Support and Knowledge-Based Techniques in a Problem-Solving Strategy for Selection Problems 被引量:1
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作者 David McSherry(School of Information and Software Engineering,Faculty of Informatics, University of Ulster,Coleraine BT52 1SA, Northern Ireland) 《Journal of Systems Engineering and Electronics》 SCIE EI CSCD 1996年第2期35-54,共20页
The limitations of traditional approaches to selection problems are examined. A problemsolving strategy is presented in which decision-support and knowledge-based techniques play complementary roles. An approach to th... The limitations of traditional approaches to selection problems are examined. A problemsolving strategy is presented in which decision-support and knowledge-based techniques play complementary roles. An approach to the representation of knowledge to support the problem-solving strategy is presented which avoids commitment to a specific programming language or implementation environment. The problem of choosing a home is used to illustrate the representation of knowledge in a specific problem domain. Techniques for implementation of the problem-solving strategy are described. Knowledge elicitation techniques and their implementation in a development shell for application of the problem-solving strategy to any selection problem are also described. 展开更多
关键词 knowledge-based systems Decision-support systems Knowledge acquisition Multiple criteria decision making Operational research Analytic hierarchy process
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Yarn Quality Prediction and Diagnosis Based on Rough Set and Knowledge-Based Artificial Neural Network 被引量:1
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作者 杨建国 徐兰 +1 位作者 项前 刘彬 《Journal of Donghua University(English Edition)》 EI CAS 2014年第6期817-823,共7页
In the spinning process, some key process parameters( i. e.,raw material index inputs) have very strong relationship with the quality of finished products. The abnormal changes of these process parameters could result... In the spinning process, some key process parameters( i. e.,raw material index inputs) have very strong relationship with the quality of finished products. The abnormal changes of these process parameters could result in various categories of faulty products. In this paper, a hybrid learning-based model was developed for on-line intelligent monitoring and diagnosis of the spinning process. In the proposed model, a knowledge-based artificial neural network( KBANN) was developed for monitoring the spinning process and recognizing faulty quality categories of yarn. In addition,a rough set( RS)-based rule extraction approach named RSRule was developed to discover the causal relationship between textile parameters and yarn quality. These extracted rules were applied in diagnosis of the spinning process, provided guidelines on improving yarn quality,and were used to construct KBANN. Experiments show that the proposed model significantly improve the learning efficiency, and its prediction precision is improved by about 5. 4% compared with the BP neural network model. 展开更多
关键词 yarn quality prediction rough set(RS) knowledge discovery knowledge-based artificial neural network(KBANN)
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MY PERSONAL STUDY ON KNOWLEDGE-BASED ECONOMY 被引量:2
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作者 Deng Shuhui(Institute of Systems Science, the CAS) 《Bulletin of the Chinese Academy of Sciences》 1999年第2期119-120,共2页
The Financial Crisis in Asia is having a negative impacion the economic development of China, but it also enlightens us. It makes us consider and take measures to avoid such a crisis. I have put forward six measures, ... The Financial Crisis in Asia is having a negative impacion the economic development of China, but it also enlightens us. It makes us consider and take measures to avoid such a crisis. I have put forward six measures, one of which is to promote the transformation of S&T knowledge into productive forces. 展开更多
关键词 MODE MY PERSONAL STUDY ON knowledge-based ECONOMY
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Optimizing the atom types of proteins through iterative knowledge-based potentials
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作者 汪心享 黄胜友 《Chinese Physics B》 SCIE EI CAS CSCD 2018年第2期43-50,共8页
Knowledge-based scoring functions have been widely used for protein structure prediction, protein-small molecule, and protein-nucleic acid interactions, in which one critical step is to find an appropriate representat... Knowledge-based scoring functions have been widely used for protein structure prediction, protein-small molecule, and protein-nucleic acid interactions, in which one critical step is to find an appropriate representation of protein structures. A key issue is to determine the minimal protein representations, which is important not only for developing of scoring func- tions but also for understanding the physics of protein folding. Despite significant progresses in simplifying residues into alphabets, few studies have been done to address the optimal number of atom types for proteins. Here, we have investigated the atom typing issue by classifying the 167 heavy atoms of proteins through 11 schemes with 1 to 20 atom types based on their physicochemical and functional environments. For each atom typing scheme, a statistical mechanics-based iterative method was used to extract atomic distance-dependent potentials from protein structures. The atomic distance-dependent pair potentials for different schemes were illustrated by several typical atom pairs with different physicochemical proper- ties. The derived potentials were also evaluated on a high-resolution test set of 148 diverse proteins for native structure recognition. It was found that there was a crossover around the scheme of four atom types in terms of the success rate as a function of the number of atom types, which means that four atom types may be used when investigating the basic folding mechanism of proteins. However, it was revealed by a close examination of typical potentials that 14 atom types were needed to describe the protein interactions at atomic level. The present study will be beneficial for the development of protein related scoring functions and the understanding of folding mechanisms. 展开更多
关键词 atom types knowledge-based potentials statistical mechanics ITERATION
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