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Yang K.-C.,National Yang Ming University | Lin C.-C.,National Yang Ming University | Lin C.-C.,Graduate Institute of Biomedical Electronics and Bioinformatics | Juan H.-F.,Graduate Institute of Biomedical Electronics and Bioinformatics | And 2 more authors.
Bioinformatics | Year: 2014

Summary: Exploring microRNA (miRNA) regulations and protein- protein interactions could reveal the molecular mechanisms responsible for complex biological processes. Mirin is a web-based application suitable for identifying functional modules from protein- protein interaction networks regulated by aberrant miRNAs under user-defined biological conditions such as cancers. The analysis involves combining miRNA regulations, protein-protein interactions between target genes, as well as mRNA and miRNA expression profiles provided by users. Mirin has successfully uncovered oncomirs and their regulatory networks in various cancers, such as gastric and breast cancer. © The Author 2014. Published by Oxford University Press. All rights reserved.

Chang Y.-H.,National Taiwan Ocean University | Chao K.-M.,Graduate Institute of Biomedical Electronics and Bioinformatics | Chao K.-M.,National Taiwan University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2013

As XML data nowadays are extensively used in the applications of data exchange and other fields, supporting efficient query processing on XML data, particularly in determining the structural relationships between two elements, is in great demand recently. To avoid the time-consuming tree traversal tasks, many labeling schemes have been proposed to assign each node a unique label, so that the structural relationships between nodes, such as the ancestor-descendant relationship, can be efficiently determined by comparing their labels. However, to the best of our knowledge, none of the existing labeling schemes can support all structural relationships in constant time and also require the least amount of space. In this paper, we propose a labeling scheme based on the concept of the complete tree, which is called the CT (complete-tree) labeling scheme. This labeling scheme is simple and the resultant labels are compact. We formally analyze its properties and perform an empirical evaluation between the CT labeling scheme and other state-of-the-art labeling schemes on different data sets. The experimental results show that the space requirement of our CT labeling scheme is superior to others in most cases. It is also demonstrated that this scheme can efficiently support all structural relationships and may perform even better than other labeling schemes. © Springer-Verlag 2013.

Lin X.-Y.,Graduate Institute of Biomedical Electronics and Bioinformatics | Ho T.-W.,Graduate Institute of Biomedical Electronics and Bioinformatics | Fang C.-C.,National Taiwan University Hospital | Yen Z.-S.,National Taiwan University Hospital | And 3 more authors.
Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS | Year: 2015

To increase the efficiency in the emergency room, the goal of this research is to implement a mobile-based indoor positioning system using mobile applications (APP) with the iBeacon solution based on the Bluetooth Low Energy (BLE) technology. We use the Received Signal Strength (RSS) based localization method to estimate the patients' locations. Our positioning algorithm achieves 97.22% (95% Confidence Interval = 95.90% - 98.55%) accuracy of classification. As the result, our mechanism is reliable enough to satisfy the need for medical staff to track the locations of their patients. © 2015 IEEE.

Wu Z.-Y.,National Taiwan University | Chung Y.,Tunghai University | Lai F.,National Taiwan University | Lai F.,Graduate Institute of Biomedical Electronics and Bioinformatics | And 2 more authors.
International Journal of Innovative Computing, Information and Control | Year: 2011

Based upon Elliptic Curve Cryptosystem, a simple password user authentication scheme was proposed by Lu et al. for grid computing. In their scheme, Lu et al. not only kept the advantages of Yoon et al.'s scheme, but enhanced the efficiency of mutual authentication and at the same time avoided the stolen-verifier attacks as well. However, their scheme is proven to be unable to resist the off-line password guessing attacks. Apart from that, the problem of people masquerading as a server to communicate with the other users in their scheme is also inevitable. Therefore, an ameliorative password-based authentication scheme is proposed subsequently in this paper to achieve perfect forward secrecy and to resist replay attacks, server spoofing attacks, on-line and off-line password guessing attacks and impersonation attacks. The proposed scheme is shown to be more secure and practical than those previously proposed schemes. © 2011.

Chang Y.-C.,Institute of Information Science | Chang Y.-C.,National Taiwan University | Su Y.-C.,National Taiwan University | Chang N.-W.,Institute of Information Science | And 2 more authors.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2014

Discovering the interactions between proteins mentioned in biomedical literature is one of the core topics of text mining in the life sciences. In this paper, we propose an interaction pattern generation approach to capture frequent PPI patterns in text. We also present an interaction pattern tree kernel method that integrates the PPI pattern with convolution tree kernel to extract protein-protein interactions. Empirical evaluations on LLL, IEPA, and HPRD50 corpora demonstrate that our method is effective and outperforms several wellknown PPI extraction methods. © Springer International Publishing Switzerland 2014.

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