Decentralized and adaptive sensor data routing

Wireless sensor network (WSN) has been attracting research efforts due to the rapidly increasing applications in military and civilian fields. An important issue in wireless sensor network is how to send information in an efficient and adaptive way. Information can be directly sent back to the base station or through a sequence of intermediate nodes. In the later case, it becomes the problem of routing. Current routing protocols can be categorized into two groups, namely table-drive (proactive) routing protocols and source-initiated on-demand (reactive) routing. For ad hoc wireless sensor network, routing protocols must deal with some unique constraints such as energy conservation, low bandwidth, high error rate and unpredictable topology, of which wired network might not possess. Thus, a routing protocol, which is energy efficient, self-adaptive and error tolerant is highly demanded. A new peer to peer (P2P) routing notion based on the theory of cellular automata has been put forward to solve this problem. We proposed two different models, namely Spin Glass (Physics) inspired model and Multi-fractal (Chemistry) inspired model. Our new routing models are distributed in computation and self-adaptive to topological disturbance. All these merits can not only save significant amount of communication and computation cost but also well adapt to the highly volatile environment of ad hoc WSN. With the cellular automata Cantor modeling tool, we implemented two dynamic link libraries (DLL) in C++ and the corresponding graphic display procedures in Tcl/tk. Results of each model’s routing ability are discussed and hopefully it will lead to new peer to peer algorithms, which can combine the advantages of current models

Adaptive remote visualization system with optimized network performance for large scale scientific data

This dissertation discusses algorithmic and implementation aspects of an automatically configurable remote visualization system, which optimally decomposes and adaptively maps the visualization pipeline to a wide-area network. The first node typically serves as a data server that generates or stores raw data sets and a remote client resides on the last node equipped with a display device ranging from a personal desktop to a powerwall. Intermediate nodes can be located anywhere on the network and often include workstations, clusters, or custom rendering engines. We employ a regression model-based network daemon to estimate the effective bandwidth and minimal delay of a transport path using active traffic measurement. Data processing time is predicted for various visualization algorithms using block partition and statistical technique. Based on the link measurements, node characteristics, and module properties, we strategically organize visualization pipeline modules such as filtering, geometry generation, rendering, and display into groups, and dynamically assign them to appropriate network nodes to achieve minimal total delay for post-processing or maximal frame rate for streaming applications. We propose polynomial-time algorithms using the dynamic programming method to compute the optimal solutions for the problems of pipeline decomposition and network mapping under different constraints. A parallel based remote visualization system, which comprises a logical group of autonomous nodes that cooperate to enable sharing, selection, and aggregation of various types of resources distributed over a network, is implemented and deployed at geographically distributed nodes for experimental testing. Our system is capable of handling a complete spectrum of remote visualization tasks expertly including post processing, computational steering and wireless sensor network monitoring. Visualization functionalities such as isosurface, ray casting, streamline, linear integral convolution (LIC) are supported in our system. The proposed decomposition and mapping scheme is generic and can be applied to other network-oriented computation applications whose computing components form a linear arrangement

Efficient and Fair Bandwidth Scheduling in Cloud Environments

Hundreds of thousands of servers from data centers are operated to provide users with pay-as-yougo infrastructure as a service, platform as a service, and software as a service. Many different types of virtual machine (VM) instances hosted on these servers oftentimes need to efficiently communicate with data movement under current bandwidth capacity. This motivates providers to seek for a bandwidth scheduler to satisfy objectives, namely assuring the minimum bandwidth per VM for the guaranteed deadline and eliminating network congestion as much as possible. Based on some rigorous mathematical models, we formulated a cloud-based bandwidth scheduling algorithm which enables dynamic and fair bandwidth management by categorizing the total bandwidth into several categories and adjusting the allocated bandwidth limit per VM for both upstream and downstream traffics in real time. The simulation showed that paradigm was able to utilize the total assigned bandwidth more efficiently compared to algorithms such as bandwidth efficiency persistence proportional sharing (PPS), PPS, and PS at the network level

A Distributed System for Parallel Simulations

We presented the technologies and algorithms to build a web-based visualization and steering system to monitor the dynamics of remote parallel simulations executed on a Linux Cluster. The polynomial time based algorithm to optimally utilize distributed computing resources over a network to achieve maximum frame-rate was also proposed. Keeping up with the advancements in modern web technologies, we have developed an Ajax-based web frontend which allows users to remotely access and control ongoing computations via a web browser facilitated by visual feedbacks in real-time. Experimental results are also given from sample runs mapped to distributed computing nodes and initiated by users at different geographical locations. Our preliminary results on frame-rates illustrated that system performance was affected by network conditions of the chosen mapping loop including available network bandwidth and computing capacities. The underlying programming framework of our system supports mixed-programming mode and is flexible to integrate most serial or parallel simulation code written in different programming languages such as Fortran, C and Java

A stable iterative method for refining discriminative gene clusters

<p>Abstract</p> <p>Background</p> <p>Microarray technology is often used to identify the genes that are differentially expressed between two biological conditions. On the other hand, since microarray datasets contain a small number of samples and a large number of genes, it is usually desirable to identify small gene subsets with distinct pattern between sample classes. Such gene subsets are highly discriminative in phenotype classification because of their tightly coupling features. Unfortunately, such identified classifiers usually tend to have poor generalization properties on the test samples due to overfitting problem.</p> <p>Results</p> <p>We propose a novel approach combining both supervised learning with unsupervised learning techniques to generate increasingly discriminative gene clusters in an iterative manner. Our experiments on both simulated and real datasets show that our method can produce a series of robust gene clusters with good classification performance compared with existing approaches.</p> <p>Conclusion</p> <p>This backward approach for refining a series of highly discriminative gene clusters for classification purpose proves to be very consistent and stable when applied to various types of training samples.</p

Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference

<p>Abstract</p> <p>Background</p> <p>Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality.</p> <p>Results</p> <p>Microarray experiments were performed in a γ-proteobacterium <it>Shewanella oneidensis</it>. Pair-wise comparison of three experimental conditions was obtained either with two labeled cDNA samples co-hybridized to the same array, or by employing <it>Shewanella </it>genomic DNA as a standard reference. Various data processing techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that data quality was significantly improved by imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses.</p> <p>Conclusion</p> <p>These findings demonstrate that data processing significantly influences data quality, which provides an explanation for the conflicting evaluation in the literature. This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference.</p

Optimizing Network Performance of Computing Pipelines in Distributed Environments

Supporting high performance computing pipelines over wide-area networks is critical to enabling large-scale distributed scientific applications that require fast responses for interactive operations or smooth flows for data streaming. We construct analytical cost models for computing modules, network nodes, and communication links to estimate the computing times on nodes and the data transport times over connections. Based on these time estimates, we present the Efficient Linear Pipeline Configuration method based on dynamic programming that partitions the pipeline modules into groups and strategically maps them onto a set of selected computing nodes in a network to achieve minimum end-to-end delay or maximum frame rate. We implemented this method and evaluated its effectiveness with experiments on a large set of simulated application pipelines and computing networks. The experimental results show that the proposed method outperforms the Streamline and Greedy algorithms. These results, together with polynomial computational complexity, make our method a potential scalable solution for large practical deployments

Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays

Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories (2, 3, 5, 7, 9, 20, 24-26). While some reported that experimental results of microarrays using genomic DNA reference conformed nicely to those obtained by cDNA: cDNA co-hybridization method, others acquired poor results. We hypothesized that these conflicting reports could be resolved by biostatistical analyses. To test it, microarray experiments were performed in a 4 proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either by direct cDNA: cDNA co-hybridization, or by indirect calculation through a Shewanella genomic DNA reference. Several major biostatistical techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses significantly improved the data quality. These findings could potentially serve as guidelines for microarray data analysis using genomic DNA as reference

System Design and Algorithmic Development for Computational Steering in Distributed Environments

Supporting visualization pipelines over wide-area networks is critical to enabling large-scale scientific applications that require visual feedback to interactively steer online computations. We propose a remote computational steering system that employs analytical models to estimate the cost of computing and communication components and optimizes the overall system performance in distributed environments with heterogeneous resources. We formulate and categorize the visualization pipeline configuration problems for maximum frame rate into three classes according to the constraints on node reuse or resource sharing, namely no, contiguous, and arbitrary reuse. We prove all three problems to be NP-complete and present heuristic approaches based on a dynamic programming strategy. The superior performance of the proposed solution is demonstrated with extensive simulation results in comparison with existing algorithms and is further evidenced by experimental results collected on a prototype implementation deployed over the Internet