3731147
A Multi-tiered Model for Performance Analysis of Storage Area Network
3813961
Using MMQ Model for Performance Simulation of Storage Area Network
The infrastructures of SANs are complex, and the implementations/designs of SANs are varied. So finding a proper modeling method to analysis and simulate SAN performance in a systemic/consistent way is very important for the work efficiency of SAN designers and performance tuners. This paper proposes a methodology of using a multi-tier multiserver queue (MMQ) network system to model a SAN system, which can be generalized to different SAN instances neatly, and be used for both performance analysis and simulation. Besides the main idea and high-level MMQ model, the application of this method is illustrated by constructing a software simulator, which is also designed and implemented in a systemic and reusable style. The simulation validation shows that maximum error range is less than 10%. So we can consider this method a sound solution for the quick performance design comparison and analysis of SAN.
2190827
Chosen-Plaintext Cryptanalysis of a Clipped-Neural-Network-Based Chaotic Cipher
At ISNN'04, a novel symmetric cipher was proposed, by combining a chaotic signal and a clipped neural network (CNN) for encryption. The present paper analyzes the security of this chaotic cipher against chosen-plaintext attacks, and points out that this cipher can be broken by a chosen-plaintext attack. Experimental analyses are given to support the feasibility of the proposed attack.
14960694
Comparative analysis of gene sets in the gene ontology space under the multiple hypothesis testing framework
The gene ontology (GO) resource can be used as a powerful tool to uncover the properties shared among, and specific to, a list of genes produced by high-throughput functional genomics studies, such as microarray studies. In the comparative analysis of several gene lists, researchers maybe interested in knowing which GO terms are enriched in one list of genes but relatively depleted in another. Statistical tests such as Fisher's exact test or Chi-square test can be performed to search for such GO terms. However, because multiple GO terms are tested simultaneously, individual p-values from individual tests do not serve as good indicators for picking GO terms. Furthermore, these multiple tests are highly correlated, usual multiple testing procedures that work under an independence assumption are not applicable. In this paper we introduce a procedure, based on false discovery rate (FDR), to treat this correlated multiple testing problem. This procedure calculates a moderately conserved estimator of q-value for every GO term. We identify the GO terms with q-values that satisfy a desired level as the significant GO terms. This procedure has been implemented into the GoSurfer software. GoSurfer is a windows based graphical data mining tool. It is freely available at http://www.gosurfer.org.
10820274
Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data
MOTIVATION
Analysis of high-throughput proteomic/genomic data, in particular, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) data and microarray data, has led to a multitude of techniques aimed at identifying potential biomarkers. Most of the statistical techniques for comparing two groups are based on qualitative measures such as P-value. A quantitative way such as interval estimation for the contrasts of two groups is more appealing.


RESULTS
We have devised a simultaneous confidence bands method capable of detecting potential biomarkers, while controlling for overall confidence coverage level, in high-dimensional datasets that discriminate two treatment groups using a permutation scheme. For example, for the SELDI-TOF MS data, we deal with the entire spectrum simultaneously and construct (1 - alpha) confidence bands for the mean differences between groups. Furthermore, peaks were identified based on the maximal differences between the groups as determined by the confidence bands. The analysis method herein described gives both qualitative (P-value) and quantitative data (magnitude of difference). The Clinical Proteomics Programs Databank's ovarian cancer dataset and data from in-house samples containing known spiked-in proteins were analyzed. We were able to identify potential biomarkers similar to those described in previous analysis of the ovarian cancer data, however, while these markers are highly significant between cancer and normal groups, our analysis indicated the absolute difference between the two groups was minimal. In addition, we found additional markers than those previously described with greater differences in average intensities. The proposed confidence bands method successfully detected the spiked-in peaks, as well as, secondary peaks generated by adducts and double-charged species. We also illustrate our method utilizing paired gene expression data from a prostate cancer microarray experiment by constructing confidence bands for the fold changes between cancer and normal samples.


AVAILABILITY
R-package, 'seie.zip' (license: GNU GPL), is publiclly available at http://research2.dfci.harvard.edu/dfci/MS_spike-in_data/
8267935
Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets
The purpose of this paper is to discuss how to model and analyze signaling pathways by using Petri net. Firstly, we propose a modeling method based on Petri net by paying attention to the molecular interactions and mechanisms. Then, we introduce a new notion "activation transduction component" in order to describe an enzymic activation process of reactions in signaling pathways and shows its correspondence to a so-called elementary T-invariant in the Petri net models. Further, we design an algorithm to effectively find basic enzymic activation processes by obtaining a series of elementary T-invariants in the Petri net models. Finally, we demonstrate how our method is practically used in modeling and analyzing signaling pathway mediated by thrombopoietin as an example.
14325657
An approach to reducing the labeling cost of Markov random fields within an infinite label space
This work proposes a novel idea, called SOIL, for reducing the computational complexity of the maximum a posteriori optimization problem using Markov random fields (MRFs). The local characteristics of MRFs are employed so that the searching in a virtually infinite label space is confined in a small finite space. Globally, the number of labels allowed is as many as the number of image sites while locally the optimal label is sampled from a space consisting of the labels assigned to the four-neighbor plus a random one. Neither the prior knowledge about the number of classes nor the estimation phase of the class number is required in this work. The proposed method is applied to the problem of texture segmentation and the result is compared with those obtained from conventional methods.