|
Comparative study of network-based prioritization
of protein domains associated with human complex diseases
Wangshu ZHANG, Rui JIANG, Yong CHEN,
Front. Electr. Electron. Eng.. 2010, 5 (2): 107-118.
https://doi.org/10.1007/s11460-010-0018-x
Domains are basic structural and functional unit of proteins, and, thus, exploring associations between protein domains and human inherited diseases will greatly improve our understanding of the pathogenesis of human complex diseases and further benefit the medical prevention, diagnosis and treatment of these diseases. Based on the assumption that deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) underlying human complex diseases may actually change structures of protein domains, affect functions of corresponding proteins, and finally result in these diseases, we compile a dataset that contains 1174 associations between 433 protein domains and 848 human disease phenotypes. With this dataset, we compare two approaches (guilt-by-association and correlation coefficient) that use a domain-domain interaction network and a phenotype similarity network to prioritize associations between candidate domains and human disease phenotypes. We implement these methods with three distance measures (direct neighbor, shortest path with Gaussian kernel, and diffusion kernel), demonstrate the effectiveness of these methods using three large-scale leave-one-out cross-validation experiments (random control, simulated linkage interval, and whole-genome scan), and evaluate the performance of these methods in terms of three criteria (mean rank ratio, precision, and AUC score). Results show that both methods can effectively prioritize domains that are associated with human diseases at the top of the candidate list, while the correlation coefficient approach can achieve slightly higher performance in most cases. Finally, taking the advantage that the correlation coefficient method does not require known disease-domain associations, we calculate a genome-wide landscape of associations between 4036 protein domains and 5080 human disease phenotypes using this method and offer a freely accessible web interface for this landscape.
References |
Related Articles |
Metrics
|
|
An adaptive region growing algorithm for breast
masses in mammograms
Ying CAO, Xin HAO, Xiaoen ZHU, Shunren XIA,
Front. Electr. Electron. Eng.. 2010, 5 (2): 128-136.
https://doi.org/10.1007/s11460-010-0017-y
This study attempted to accurately segment the mammographic masses and distinguish malignant from benign tumors. An adaptive region growing algorithm with hybrid assessment function combined with maximum likelihood analysis and maximum gradient analysis was developed in this paper. In order to accommodate different situations of masses, the likelihood and the edge gradients of segmented masses were weighted adaptively by the use of information entropy. 106 benign and 110 malignant tumors were included in this study. We found that the proposed algorithm obtained segmentation contour more accurately and delineated the tumor body as well as tumor peripheral regions covering typical mass boundaries and some spiculation patterns. Then the segmented results were evaluated by the classification accuracy. 42 features including age, intensity, shape and texture were extracted from each segmented mass and support vector machine (SVM) was used as a classifier. The classification accuracy was evaluated using the area (Az) under the receiver operating characteristic (ROC) curve. It was found that the maximum likelihood analysis achieved an Az value of 0.835, the maximum gradient analysis got an Az value of 0.932 and the hybrid assessment function performed the best classification result where the value of Az was 0.948. In addition, compared with traditional region growing algorithm, our proposed algorithm is more adaptive and provides a better performance for future works.
References |
Related Articles |
Metrics
|
|
A framework to express variant and invariant
functional spaces for binary logic
Jeffrey Zhi J. ZHENG, Christian H. ZHENG,
Front. Electr. Electron. Eng.. 2010, 5 (2): 163-172.
https://doi.org/10.1007/s11460-010-0011-4
A new framework has been developed to express variant and invariant properties of functions operating on a binary vector space. This framework allows for manipulation of dynamic logic using basic operations and permutations. Novel representations of binary functional spaces are presented. Current ideas of binary functional spaces are extended and additional conditions are added to describe new function representation schemes: F code and C code. Sizes of the proposed functional space representation schemes were determined. It was found that the complete representation for any set of functions operating on a binary sequence of numbers is larger than previously thought. The complete representation can only be described using a structure having a space of size for any given space of functions acting on a binary sequence of length n. The framework, along with the proposed coding schemes provides a foundational theory of variant and invariant logic in software and electric-electronic technology and engineering, and has uses in the analysis of the stability of rule-based, dynamic binary systems such as cellular automata.
References |
Related Articles |
Metrics
|
|
A feedback control mechanism for adaptive SLO
maintenance in dynamic service level management
Fei GAO, Xuesong QIU,
Front. Electr. Electron. Eng.. 2010, 5 (2): 188-196.
https://doi.org/10.1007/s11460-010-0003-4
With the increasing scale of information technology (IT) service system, traditional threshold-based static service level management (SLM) solution appears to be inadequate to meet current increasingly management requirement of SLM. Due to the stochastic service request rate, the random inherent failure and load surge of IT devices during service operating stage of large scaled IT system, service level objective (SLO) maintenance issue has become a realistic and important issue in dynamic SLM. This paper proposes a closed-loop feedback control mechanism to adaptively maintain SLO that service provider (SP) guaranteed at service operation stage. The mechanism can automatically tune the capacity of IT infrastructure according to service performance dispersion and reduce SLO violations. Considering that the tuning operations also affect service performance, fuzzy control is applied to alleviate the negative effect caused by tuning operations. In the dynamic SLM system that is applied with this mechanism compared with the traditional threshold-based solution, it is proved that the amount of SLO violations obviously decreases, the reliability of the service system increases relatively, and the resource utilization of IT infrastructure is optimized.
References |
Related Articles |
Metrics
|
|
Equivalence of stability criteria for time-delay
systems
Haiyun AN, Hongjie JIA, Yuan ZENG, Wei WEI,
Front. Electr. Electron. Eng.. 2010, 5 (2): 207-217.
https://doi.org/10.1007/s11460-010-0013-2
During the past few decades, there have been a number of new delay-dependent stability criteria based on linear matrix inequalities published in the literature. These criteria, to some extent, can reduce the conservativeness. In fact, some criteria are equivalence. In this paper, we aim to theoretically establish equivalence of two stability criteria. One was obtained by Sun et al. [Sun et al. In: Proceedings of IEEE Power & Energy Society General Meeting. 2009, 1–7] and the other was given by Xu et al. [Xu et al. IEEE Transactions on Automatic Control, 2005, 50(3): 384–387]. Also, we theoretically establish equivalence of the robust stability criterion presented by Jia et al. [Jia et al. Automation of Electric Power Systems, 2010, 34(3): 6–11] and the one given by Xu et al. (2005).
References |
Related Articles |
Metrics
|
18 articles
|