A Gene Regulatory Network links pairs of genes through an edge if they physically or functionally interact. "Reverse engineering" a gene regulatory network means to infer the edges between genes from the ava...
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ISBN:
(纸本)9780769542652
A Gene Regulatory Network links pairs of genes through an edge if they physically or functionally interact. "Reverse engineering" a gene regulatory network means to infer the edges between genes from the available experimental data. Transcriptional responses (i.e. gene expression profiles obtained through microarray experiments) are often used to reverse-engineer a network of genes. Reverse-engineering consists in analyzing transcriptional responses to a set of treatments and adding an edge between genes if their expressions show a coordinated behavior on a subset of the treatments, according to some underlying model of gene regulation. Mammalian cells contain tens of thousands of genes, and it is necessary to analyze hundreds of transcriptional responses in order to have acceptable statistical evidence of interactions between genes. there currently exist several ready-to-use software packages able to infer gene networks, but few can be used to infer large-size networks from thousands of transcriptional responses as the dimension of the problem leads to high computational costs and memory requirements. We propose to exploit parallel computing techniques to overcome this problem. In this work, we designed and developed a parallel computing algorithm to reverse engineer large-scale gene regulatory networks from tens of thousands of gene expression profiles. the algorithm is based on computing pair-wise Mutual Information between each *** successfully tested it to infer the Mus Musculus (mouse) gene regulatory network in liver from 312 expression profiles collected from a public Internet repository. Each profile measures the expression of 45,101 genes (more specifically, transcripts). We analyzed all of the possible gene-pairs for a total amount of about 109 identifying about 6 · 107 edges. We used a hierarchical clustering algorithm to discover communities within the gene network, and found a modular structure that highlights genes involved in the same biolog
the proceedings contain 5 papers. the topics discussed include: towards a simple service compiler;run-time correlation engine for system monitoring and testing;self-organized server farms for energy savings;an industr...
ISBN:
(纸本)9781605586120
the proceedings contain 5 papers. the topics discussed include: towards a simple service compiler;run-time correlation engine for system monitoring and testing;self-organized server farms for energy savings;an industry survey of autonomic infrastructure;and Resilient Workload Manager: taming bursty workload of scaling Internet applications.
the proceedings contain 53 papers. the topics discussed include: social context: supporting interaction awareness in ubiquitous environments;multi-layered friendship modeling for location-based mobile social networks;...
ISBN:
(纸本)9789639799592
the proceedings contain 53 papers. the topics discussed include: social context: supporting interaction awareness in ubiquitous environments;multi-layered friendship modeling for location-based mobile social networks;security for pervasive medical sensor networks;hash-based sequential aggregate and forward secure signature for unattended wireless sensor networks;on real-time capacity of event-driven data-gathering sensor network;adaptive wireless services for augmented environments;temporal addressing for mobile context-aware communication;trajectory enabled service support platform for mobile users' behavior pattern mining;mining emerging patterns for recognizing activities of multiple users in pervasive computing;understanding and minimizing identity exposure in ubiquitous computing environments;and mining emerging patterns for recognizing activities of multiple users in pervasive computing.
the proceedings contain 42 papers. the topics discussed include: European standards and perspectives for e-voting in Bulgaria;a formula driven incremental construction of web service compositions;evaluating a framewor...
ISBN:
(纸本)9789898111999
the proceedings contain 42 papers. the topics discussed include: European standards and perspectives for e-voting in Bulgaria;a formula driven incremental construction of web service compositions;evaluating a framework for the development and deployment of evolving applications as a software maintenance tool;modeling the evolution of software engineering trends - a bottom up approach;resolving traceability issues in product derivation for software product lines;detecting regulatory vulnerability in functional requirements specifications;model transformation using adaptive systems;a self-adaptive architecture for autonomic systems developed with ASSL;aggregated accounting of memory usage in java;model driven testing with time augmented Markov chain usage models - computations and test case generation algorithms for time augmented Markov chain usage models;and refactoring of C/C++ preprocessor constructs at the model level.
In this paper, we apply a Quantum Inspired Evolutionary Algorithm (QIEA) to the problem of optimally selecting k sensors from a set of m sensors placed for parameter estimation. the computational complexity of finding...
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ISBN:
(纸本)9780889868526
In this paper, we apply a Quantum Inspired Evolutionary Algorithm (QIEA) to the problem of optimally selecting k sensors from a set of m sensors placed for parameter estimation. the computational complexity of finding an optimal subset of sensor through exhaustive search can grow exponentially withthe numbers (m and k) of sensors. the QIEA can be viewed as a probabilistic evolutionary algorithm and thus it is plausible to expect a reasonably good performance in solving combinatorial optimization problems. We implemented a QIEA for solving the sensor selection problem and tested its performance through extensive computational experiments. We found that the performance of proposed QIEA-based sensor selection algorithm is better than well known sensor selection algorithms.
An Attack Graph capable of disclosing causal relationships between multiple vulnerabilities has become a desirable tool for administrators to analyze and locate potential risks to protect critical networked resources ...
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the proceedings contain 37 papers. the topics discussed include: infinite-state verification: from transition systems to markov chains;analyzing large sparse markov chains of kronecker products;an introduction to Mont...
the proceedings contain 37 papers. the topics discussed include: infinite-state verification: from transition systems to markov chains;analyzing large sparse markov chains of kronecker products;an introduction to Monte Carlo methods and rare event simulation;nondeterministic labeled markov processes: bisimulations and logical characterization;simulation-based CTMC model checking: an empirical evaluation;on the impact of modeling choices for distributed information spread;a heuristic approach for fitting MAPs to moments and joint moments;faster maximum likelihood estimation algorithms for markovian arrival processes;timermeter: quantifying properties of software timers for system analysis;a performance model of zoned disk drives with I/O request reordering;design space exploration for java processors with cross-profiling;and exploiting restricted transitions in quasi-birth-and-death processes.
the most common algorithms for signal selective position determination of radio signal emitters are based on selective estimation of a specified parameter such as direction of arrival (DOA) or time of arrival (TOA) of...
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ISBN:
(纸本)9788674663943
the most common algorithms for signal selective position determination of radio signal emitters are based on selective estimation of a specified parameter such as direction of arrival (DOA) or time of arrival (TOA) of the signal. the estimated parameters are then used to determine the transmitter's location. these positioning methods are known as two-step methods. A general problem in these positioning methods is how to ensure that parameters estimated in the different base station correspond to the same signal emitters. In this paper, we propose a one-step subspace-based algorithm for signal selective direct position determination of cyclostationary signals. this proposed algorithm for signal selective direct positioning determination of cyclostationary signals is based on frequency domain and it does not require any knowledge of the optimal time lag parameter which appear in the similar algorithms in time domain. the performance of the proposed algorithm is illustrated by the results of simulations.
Data produced in scientific and industrial applications is growing exponentially but most resource middleware systems lack of appropriate support for data and metadata management. In particular easy and intuitive retr...
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ISBN:
(纸本)9783642141218
Data produced in scientific and industrial applications is growing exponentially but most resource middleware systems lack of appropriate support for data and metadata management. In particular easy and intuitive retrieval of data for later use is a serious problem. In this context the paper proposes a pragmatic approach for data management of distributed data with focus on appropriate means for data organization improving data retrieval. the paper presents the key concepts and architecture of a dedicated data management system for sharing data located on heterogeneous storage resources. the different specifics of storage systems such as data object names, data locations, and data access methods are abstracted to allow transparent data access. Moreover, the system provides means for data structuring and organization by supporting custom data models and annotation of individual metadata on data objects. Current development status of the system is illustrated by presenting an integration withthe UNICORE Rich Client which has been validated in the context of the AeroGrid project.
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