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Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency

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BMC Medical Genomics 2009年第1期2卷 1-19页

作者： Yeh, Hsiang-Yuan Cheng, Shih-Wu Lin, Yu-Chun Yeh, Cheng-Yu Lin, Shih-Fang Soo, Von-Wun Department of Computer Science National Tsing Hua University HsinChu 300 Taiwan Institute of Information Systems and Applications National Tsing Hua University HsinChu 300 Taiwan Department of Computer Science and Information Engineering National University of Kaohsiung Kaohsiung 811 Taiwan

Background. Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear. We present a computational method for inferring genetic regulatory networks from micorarray data automatically with transcription factor analysis and conditional independence testing to explore the potential significant gene regulatory networks that are correlated with cancer, tumor grade and stage in the prostate cancer. Results. To deal with missing values in microarray data, we used a K-nearest-neighbors (KNN) algorithm to determine the precise expression values. We applied web services technology to wrap the bioinformatics toolkits and databases to automatically extract the promoter regions of DNA sequences and predicted the transcription factors that regulate the gene expressions. We adopt the microarray datasets consists of 62 primary tumors, 41 normal prostate tissues from Stanford Microarray Database (SMD) as a target dataset to evaluate our method. The predicted results showed that the possible biomarker genes related to cancer and denoted the androgen functions and processes may be in the development of the prostate cancer and promote the cell death in cell cycle. Our predicted results showed that sub-networks of genes SREBF1, STAT6 and PBX1 are strongly related to a high extent while ETS transcription factors ELK1, JUN and EGR2 are related to a low extent. Gene SLC22A3 may explain clinically the differentiation associated with the high grade cancer compared with low grade cancer. Enhancer of Zeste Homolg 2 (EZH2) regulated by RUNX1 and STAT3 is correlated to the pathological stage. Conclusions. We provide a computat

关键词： Microarray Data Cluster Coefficient Microarray Dataset Dependent Gene Network Motif

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Personalized facial expression recognition in color image

Personalized facial expression recognition in color image

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2009 4th International Conference on Innovative Computing, Information and Control, ICICIC 2009

作者： Chang, Chuan-Yu Huang, Yan-Chiang Yang, Chi-Lu Department of Computer Science and Information Engineering National Yunlin University of Science and Technology Taiwan Innovative DigitEch-Enabled Applications and Services Institute Institute for Information Industry Taiwan

ISBN: (纸本)9780769538730

Facial expression recognition is one of the most popular topics in emotion analysis. Most facial expression recognition systems are implemented by general expression models. Since facial expressions may be expressed differently by different people, inaccurate results are unavoidable. The proposed facial expression recognition system recognizes facial expressions using facial features of the individual user. Experimental results show that the proposed system can accurately identify the emotions of facial expressions. © 2009 IEEE.

关键词： Face recognition

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A one-time password scheme with QR-code based on mobile phone

A one-time password scheme with QR-code based on mobile phon...

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NCM 2009 - 5th International Joint Conference on Int. Conf. on Networked Computing, Int. Conf. on Advanced Information Management and Service, and Int. Conf. on Digital Content, Multimedia Technology and its applications

作者： Liao, Kuan-Chieh Lee, Wei-Hsun Sung, Min-Hsuan Lin, Ting-Ching Department of Accounting and Information Systems ASIA University Taichung Taiwan Department of Information Science and Applications ASIA University Taichung Taiwan Department of Computer Science and Information Engineering ASIA University Taichung Taiwan

ISBN: (纸本)9780769537696

User authentication is one of the fundamental procedures to ensure secure communications and share system resources over an insecure public network channel. Especially, the purpose of the one-time password is to make it more difficult to gain unauthorized access to restricted resources. Instead of using the password file as conventional authentication systems, many researchers have devoted to implement various one-time password schemes using smart cards, time-synchronized token or short message service in order to reduce the risk of tampering and maintenance cost. However, these schemes are impractical because of the far from ubiquitous hardware devices or the infrastructure requirements. To remedy these weaknesses, the attraction of the QR code technique can be introduced into our one-time password authentication protocol. Not the same as before, the proposed scheme based on QR code not only eliminates the usage of the password verification table, but also is a cost effective solution since most internet users already have mobile phones. © 2009 IEEE.

关键词： Cellular telephones

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SARIDS: A self-adaptive resource index and discovery system

SARIDS: A self-adaptive resource index and discovery system

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10th International Symposium on Pervasive Systems, Algorithms, and Networks, I-SPAN 2009

作者： Lin, Yi-Hsiang Chung, Wu-Chun Lai, Kuan-Chou Li, Kuan-Ching Chung, Yeh-Ching Institute of Information Systems and Applications National Tsing Hua University Hsinchu Taiwan Department of Computer Science National Tsing Hua University Hsinchu Taiwan Department of Computer and Information Science National Taichung University Taichung Taiwan Department of Computer Science and Information Engineering Providence University Taichung Taiwan

ISBN: (纸本)9780769539089

Recently, the resource sharing systems apply the P2P technique to provide scalable multi-attribute range queries. However, due to the heterogeneity of resources and the variation of sharing policies in different providers, current P2P-based resource discovery systems may suffer the load imbalance problem in a large scale distributed system. In this paper, we propose a self-adaptive resource index and discovery system (SARIDS) to achieve load balancing. SARIDS adopts a two-tier architecture based on the structured P2P overlay. The intra-overlay is constructed by normal peers with the same attribute via the locality preserving hash function;and, the inter-overlay is constructed by super-peers with classified attributes in different intra-overlays. SARIDS supports not only the multi-attribute range queries but also the self-adaptive mechanisms for load balancing in the intra-overlay and among the intra-overlays. The simulation results show that SARIDS is scalable and efficient for load balancing even in the nonuniform peer range environment. © 2009 IEEE.

关键词： Hash functions

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Reversible steganography for VQ indices using the modified state codebook

Reversible steganography for VQ indices using the modified s...

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IIH-MSP 2009 - 2009 5th International Conference on Intelligent Information Hiding and Multimedia Signal Processing

作者： Chang, Chin-Chen Chan, Chi-Shiang Wang, Zhi-Hui Li, Ming-Chu Department of Information Engineering and Computer Science Feng Chia University Taichung Taiwan Department of Information Science and Applications Asia University Wufeng Taiwan School of Software Dalian University of Technology Dalian China

ISBN: (纸本)9780769537627

In this paper, we propose an information hiding scheme to embed secret information into the compression code of an index table. First, the codewords neighboring the current processed index along with their closest codewords form a state codebook. Two indices of the state codebook are reserved as indicators. Once the current processed index satisfies some pre-defined conditions, the current processed index can be encoded using the state codebook, and the secret bit can be embedded in the compression code. On the other hand, the reserved indices are taken as indicators to denote that the current processed index is encoded by the VQ mechanism. On the basis of our experimental results, the bit rates of the proposed method are lower than those of related works. The improvements in bit rates increase when the quantity of the embedded bits increases. © 2009 IEEE.

关键词： Steganography

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Experience in parallel computational mechanics on marenostrum

Experience in parallel computational mechanics on marenostru...

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Parallel Computational Fluid Dynamics, Parallel CFD 2007

作者： Houzeaux, G. Vazquez, M. Grima, R. Calmet, H. Cela, J.M. Department of Computer Applications in Science and Engineering Barcelona Supercomputing Center Campus Nord UPC Edificio C1-E201 08034 Barcelona Spain

ISBN: (纸本)9783540927433

We present in this paper the experience of the authors in solving very large problems of computational mechanics on a supercomputer. The authors are researchers of the Barcelona Supercomputing Center-Centro Nacional de Supercomputación (BSC-CNS), a brand new research center in Spain, which hosts the fastest supercomputer in Europe and the fifth in the world: MareNostrum (TOP500, November 2006). A brief presentation of MareNostrum is given in the first section. In the next section, we describe the physical problems we are faced with, followed by the section on the associated numerical strategies. Next section presents the parallelization strategy employed;emphasis will be put on the important aspects to obtain good speed-up results on thousands of processors. We follow the discussion by describing some applications together with speed-up results. We finalize the paper by describing the performance tool used at BSC-CNS and their application in computational mechanics. © 2009 Springer-Verlag Berlin Heidelberg.

关键词： Supercomputers

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Finding behavior patterns and evaluating orderliness of dynamical systems by spanning tree invariants

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Quality and Quantity 2009年第6期43卷 1011-1023页

作者： Shieh, Jiunn-I Wu, Hsin-Hung Yang, Wei-Zu Department of Information Science and Applications Asia University Wufeng Shiang Taichung 413 No. 500 Lioufeng Road Taiwan Department of Business Administration National Changhua University of Education Changhua Taiwan Department of Computer Science and Information Engineering Asia University Taichung Taiwan

Identifying the behavior patterns is the main goal for a dynamical system. It provides the useful information in behavior prediction of a dynamical system. On the other hand, measuring the orderliness of a dynamical system improves the prediction of behavior patterns. In this study, substitution sequences are used to model the long-term correlation of a dynamical system and evaluate the degree of randomness, where the degree of homogeneity is evaluated by the spanning tree invariant. The results show that the more contiguous patterns the sequence has, the smaller the value of the spanning tree invariant is. In fact, the spanning tree invariant can be an effective tool to measure the orderliness of sequences by comparing the computed value with the value of one. © 2008 Springer science+Business Media B.V.

关键词： Behavior patterns Dynamical systems Orderliness Spanning tree invariants

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A RSSI-based algorithm for indoor localization using ZigBee in wireless sensor network 15

A RSSI-based algorithm for indoor localization using ZigBee ...

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15th International Conference on Distributed Multimedia Systems, DMS 2008

作者： Chen, Yu-Tso Yang, Chi-Lu Chang, Yeim-Kuan Chu, Chih-Ping Department of Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan Innovative DigiTech-Enabled Applications and Service Institute Institute for Information Industry Kaohsiung Taiwan

ISBN: (纸本)189170625X

For the various applications in home automation, the service system requires to precisely estimate user’s locations by certain sensors. It is considered as a challenge to automatically serve a mobile user in the house. However, indoor localization cannot be carried out effectively by the well-know Global Positioning System (GPS). In recent years, Wireless Sensor Networks (WSNs) are thus popularly used to locate a mobile object in an indoor environment. Some physical features are widely discussed to solve indoor localization in WSN. In this paper, we inquired about the RSSI solutions on indoor localization, and proposed a Closer Tracking Algorithm (CTA) to locate a mobile user in the house. The proposed CTA was implemented by using ZigBee CC2431 modules. The experimental results show that the proposed CTA can accurately determine the position with error distance less than 1 meter. At the same time, the proposed CTA has at least 85% precision when the distance is less than one meter. © 2009 by Knowledge Systems Institute Graduate School.

关键词： Wireless sensor networks

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Adaptive smartmote in wireless ad-hoc sensor network 15

Adaptive smartmote in wireless ad-hoc sensor network

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15th International Conference on Distributed Multimedia Systems, DMS 2008

作者： Cheng, Sheng-Tzong Zou, Yao-Dong Chou, Ju-Hsien Shih, Jiashing Wu, Mingzoo Department of Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan Innovative DigiTech-Enabled Applications and Services Institute Institute for Information Industry Kaohsiung Taiwan

ISBN: (纸本)189170625X

This paper describes an update mechanism for large wireless ad-hoc sensor networks (WASNs). In wireless sensor networks, the nodes may have to be reprogrammed, especially for design-implement-test iterations. Manually reprogramming is a very cumbersome work, and may be infeasible if nodes of the network are unreachable. Therefore, a wireless update mechanism is needed. Exchanging the running application on a node by transmitting the complete program image is not efficient for small changes in the code. It consumes a lot of bandwidth and time. The proposed framework, Adaptive SmartMote, defines and supports control JOBs that allow computation, behaviors. The goal of this paper is to use programmable packet to update sensor behaviors. To reduce the code transferred and power consumption, we propose a group management architecture. This architecture helps reduce power consumption and increase node number that control by Leader Node in WASNs. The proposed update protocol has been implemented on the Tmote-based Octopus II sensor node, which is named SmartMote, which runs TinyOS [1], a component-based operating system for highly constraint embedded platform. © 2009 by Knowledge Systems Institute Graduate School.

关键词： Electric power utilization

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A Novel Approach to Filter Non-Modified Pages at Remote Site without Downloading during Crawling

A Novel Approach to Filter Non-Modified Pages at Remote Site...

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International Conference on Advances in Recent Technologies in Communication and Computing, ARTCom

作者： Satinder Bal Rajender Nath Department of Computer Science & Applications Vaish College of Engineering Rohtak Haryana India Department of Computer Science & Applications Kurukshetra University Kurukshetra Haryana India

The users to search the required information on the Web extensively use the search engines. These, search engines maintain the index of billions of pages for efficient searching. The crawlers of these search engines have to retrieve the pages continuously to keep the index up-to-date. It is reported in the literature that the 40% of the current Internet traffic and bandwidth consumption is due to these crawlers. These crawlers also cause load on the remote server by using its CPU cycles and memory. The authors of this paper address this problem by proposing a novel indexing system based on mobile crawlers. The proposed approach employs mobile agents to crawl the pages. These mobile crawlers identify the modified pages at the remote site without downloading them. The proposed mobile crawler downloads those pages only, which have actually been modified since last crawl. The simulated results of the proposed mobile crawler have shown the reduction in the Internet traffic and load on the remote site considerably.

关键词： Filters Crawlers Search engines Internet Bandwidth Web server Indexing Mobile agents Telecommunication traffic Traffic control

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