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A novel model-free approach for reconstruction of time-delayed gene regulatory networks

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中国科学：生命科学英文版 2006年第2期49卷 190-200页

作者： JIANG Wei1,2, LI Xia1,2,3,4, GUO zheng1,2,3, LI Chuanxing1, WANG Lihong1 & RAO Shaoqi1,5 1. department of Bioinformatics, Harbin Medical university, Harbin 150086, china 2. department of computer science, Harbin Institute of technology, Harbin 150080, china 3. School of Life science and technology, Tongji university, Shanghai 200092, china 4. Biomedical Engineering Institute, Capital university of Medical sciences, beijing 100054, china 5. departments of Cardiovascular Medicine and Molecular Cardiology, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA department of Bioinformatics Harbin Medical University Harbin China department of computer science Harbin Institute of Technology Harbin China School of Life science and technology Tongji University Shanghai China departments of Cardiovascular Medicine and Molecular Cardiology Cleveland Clinic Foundation Cleveland USA

Reconstruction of genetic networks is one of the key scientific challenges in functional genomics. This paper describes a novel approach for addressing the regulatory dependencies be-tween genes whose activities can be delayed by multiple units of time. The aim of the proposed ap-proach termed TdGRN (time-delayed gene regulatory networking) is to reversely engineer the dy-namic mechanisms of gene regulations, which is realized by identifying the time-delayed gene regu-lations through supervised decision-tree analysis of the newly designed time-delayed gene expres-sion matrix, derived from the original time-series microarray data. A permutation technique is used to determine the statistical classification threshold of a tree, from which a gene regulatory rule(s) is ex-tracted. The proposed TdGRN is a model-free approach that attempts to learn the underlying regula-tory rules without relying on any model assumptions. Compared with model-based approaches, it has several significant advantages: it requires neither any arbitrary threshold for discretization of gene transcriptional values nor the definition of the number of regulators (k). We have applied this novel method to the publicly available data for budding yeast cell cycling. The numerical results demonstrate that most of the identified time-delayed gene regulations have current biological knowledge supports.

关键词： gene regulatory networks, time delayed, decision tree.

A distributed hydrological model with its application to the Jinghe watershed in the Yellow River Basin

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science china(Technological sciences) 2004年第z1期47卷 60-71页

作者： WANG Zhonggen1, zheng Hongxing1, LIU Changming1, , WU Xianfeng2 2 & ZHAO weimin3 1. Key Laboratory of Water Cycle & Related Land Surface Processes, Institute of Geographic science and Natural Resources Research, Chinese Academy of sciences, beijing 100101, china 2. Institute of Environmental science, beijing Normal university, beijing 100875, china 3. Water Resources Conservation Committee of Yellow River, zhengzhou 450003, china Key Laboratory of Water Cycle & Related Land Surface Processes Institute of Geographic Science and Natural Resources Research Chinese Academy of Sciences Institute of Environmental science Beijing Normal University

For the purpose of water resources management in the Yellow River Basin with highly spatial difference, a daily distributed hydrological model was proposed, of which the determination of spatially-distributed parameters and model inputs processing were performed by means of GIS/RS. In the model, the computation of runoff yield was based on the topography index method and flow routing was modeled by Maskingum method. The operation of the model is followed by means of “command structure” technique based upon the topography of river network. A case study using the model was conducted for the Jinghe watershed, which locates at the middle Yellow River Basin. The simulation of the hydrological processes in 1996 has shown that water quantity balance errors were less than 5% and the Nash-Sutcliffe coefficient arrived at 0.7, indicating that the model structure is justifiable, and the precision of the model can satisfy the purpose of water resources management.

关键词： distributed hydrological model, structure and equation, GIS and RS, Jinghe Basin, Yellow River Basin.

Evolution and stability of Linux kernels based on complex networks

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science china(Information sciences) 2012年第9期55卷 1972-1982页

作者： WANG Lei,WANG zheng,YANG Chen & ZHANG Li School of computer science and Engineering,Beihang university,beijing 100191,china School of computer science and Engineering Beihang University Beijing China

This paper presents a novel method to study Linux kernel evolution using complex *** investigated the node degree distribution and average path length of the call graphs corresponding to the kernel modules of 223 different versions(V1.1.0 to V2.4.35),we found that the call graphs are scale-free and smallworld *** on the relationship between average path length and nodes,we propose a method to find unusual points during Linux kernel evolution using the slope of the average path *** the unusual points we identify major structural changes in kernel modules.A stability coefficient is also proposed to describe quantitatively the stability of kernel modules during ***,we verify our result through Vasa’s metrics method.

关键词： complex networks operating system scale-free networks small-world networks average path length

A New Rule-based Method of Automatic Phonetic Notation on Polyphones

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A New Rule-based Method of Automatic Phonetic Notation on Po...

多Agent并行遗传算法在地震勘探属性优化中的应用

第七届国际信号处理会议

作者： zheng Min CAI Lianhong (department of computer science and technology of tsinghua university beijing 100084)

In this paper, a new rule-based method of automatic phonetic notation on the 220 polyphones whose appearing frequency exceeds 99% is proposed. Firstly, all the polyphones in a sentence are classifi

关键词： grapheme-phoneme conversion polyphone prosodic word prosodic functional part of speech feature extracting

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计算机科学 2010年第4期37卷 234-237页

作者：刘其成郑纬民清华大学计算机科学与技术系北京100084 烟台大学计算机学院烟台264005

研究了基于多Agent的并行遗传算法,并将其应用于石油勘探的属性优化。针对常规遗传算法的不足,采用Agent构建多Agent系统实现了基于粗粒度的并行遗传算法,该算法能从进化环境中获取表征当前进化状态的有用信息,智能地监控调度GA的进化操... 详细信息

研究了基于多Agent的并行遗传算法,并将其应用于石油勘探的属性优化。针对常规遗传算法的不足,采用Agent构建多Agent系统实现了基于粗粒度的并行遗传算法,该算法能从进化环境中获取表征当前进化状态的有用信息,智能地监控调度GA的进化操作,在避免早熟的同时加快全局寻优,提高遗传算法搜索的效率,同时具有通讯开销小的特点。将该方法用于地震勘探属性优化,取得了良好的效果。

关键词： Agent 属性优化遗传算法并行

Rhythm dynamics of complex neuronal networks with mixed bursting neurons

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Chinese Physics B 2013年第4期22卷 167-171页

作者：吕永兵石霞郑艳红 School of science Beijing University of Posts and Telecommunications School of Mathematics and computer science Fujian Normal University

The spatiotemporal order and rhythm dynamics of a complex neuronal network with mixed bursting neurons are studied in this paper. A quantitative characteristic, the width factor, is introduced to describe the rhythm dynamics of an individual neuron, and the average width factor is used to characterize the rhythm dynamics of a neuronal network. An r parameter is introduced to denote the ratio of the short bursting neurons in the network. Then we investigate the effect of the ratio on the rhythm dynamics of the neuronal network. The critical value of r is derived, and the neurons in the network always remain short bursting when the r ratio is larger than the critical value.

关键词： rhythm dynamics complex network neuron

ChangeSpider:一个自适应的网页信息跟踪系统

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计算机工程与应用 2003年第34期39卷 160-164页

作者：刘凡陈康郑纬民清华大学计算机科学与技术系高性能计算研究所北京100084

网页信息的更新是网络一个非常重要的性质。同网络的其他应用类似,随着WWW信息内容更新的不断加快,如何有效地跟踪特定网站和页面的更新情况日渐成为人们关心的课题。论文讨论一个自适应的网页信息跟踪系统ChangeSpider,研究其体系结构... 详细信息

网页信息的更新是网络一个非常重要的性质。同网络的其他应用类似,随着WWW信息内容更新的不断加快,如何有效地跟踪特定网站和页面的更新情况日渐成为人们关心的课题。论文讨论一个自适应的网页信息跟踪系统ChangeSpider,研究其体系结构、关键技术等方面的内容。实验表明ChangeSpider能够有效地跟踪网页的信息变化,及时地将变化的内容提交给用户。

关键词：信息更新更新频率信息采集信息分发

Multimedia Forensic technology for Digital Evidence

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Multimedia Forensic Technology for Digital Evidence

A dynamic fuzzy clustering method based on genetic algorithm

第二届和谐人机环境联合学术会议(HHME2006)——第15届中国多媒体学术会议(NCMT'06)

作者： X.B. zheng, L.F. Sun, S.-Q. Yang department of computer science and technology tsinghua university, beijing, china, 100084

Today, worldwide crime and some accidents are more and more serious. Development of Information technology (IT) has increased the need for forensic digital evidence. The amount and quality of digital

关键词： Crime Multimedia Forensic Digital Evidence Forensic Animation

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Progress in Natural science:Materials International 2003年第12期 52-55页

作者： zheng Yan 1*, ZHOU Chunguang 2, LIANG Yanchun 2 and GUO Dongwei 2(1. College of computer science and technology, beijing university of Posts and Telecommunications, beijing 100876, china 2. College of computer science and technology, Jilin university, Changchun 130012, china) College of computer science and technology Beijing University of Posts and Telecommunications Beijing 100876 China College of computer science and technology Jilin University Changchun 130012 China

A dynamic fuzzy clustering method is presented based on the genetic algorithm. By calculating the fuzzy dissimilarity between samples the essential associations among samples are modeled factually. The fuzzy dissimilarity between two samples is mapped into their Euclidean distance, that is, the high dimensional samples are mapped into the two dimensional plane. The mapping is optimized globally by the genetic algorithm, which adjusts the coordinates of each sample, and thus the Euclidean distance, to approximate to the fuzzy dissimilarity between samples gradually. A key advantage of the proposed method is that the clustering is independent of the space distribution of input samples, which improves the flexibility and visualization. This method possesses characteristics of a faster convergence rate and more exact clustering than some typical clustering algorithms. Simulated experiments show the feasibility and availability of the proposed method.

关键词： dynamic fuzzy clustering fuzzy dissimilarity matrix genetic algorithm fuzzy c means clustering.