BACKGROUND: Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos. RESULTS: We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB) algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes. CONCLUSION: The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through polymerase chain reaction experiments. SpecificDB provides comprehensive information and a user-friendly interface.

In 3G WCDMA, orthogonal variable-spreading-factor (OVSF) codes are valuable and scarce resources. Some single-code and multicode assignment algorithms have been proposed to support as many users as possible. Most of the algorithms suffer from a "code-set fragmentation" problem, which definitely increases the call blocking probability (CBP) of a system. In order to resolve this issue, code-exchange and reassignment policies is applied, but system complexity is also increased. In this paper, we propose a queue-aided best-fit LRU (QBLRU) code assignment scheme to improve system utilization and to obtain lower CBP than that of dynamic optimal reassignment schemes. Simulation results show that the QBLRU scheme has the lowest CBP and the highest utilization and it is an efficient OVSF code assignment scheme.

Quality of service (QoS) is an imperative feature by must newly emerging applications. The first step to provide QoS is to distinguish packets into different data flows, called packet classification. There are many algorithms in multi-dimensional packet classification. Among those algorithms, we can see the tradeoffs between lookup speeds, memory consumption, and update time. In this paper, we proposed a fast algorithm for two-dimensional lookup in tuple space to deal with conflict-free filters. It can achieve O(log w) lookup time while maintaining O(nlog w) memory consumption.

The deployment of the hybrid fiber/coax (HFC) network has becomes ubiquitous to provide broadband services to the home. Due to the asymmetric natural of HFC network - the downstream bandwidth is substantially much larger than that of the upstream; therefore the upstream channel is critical to allocating and scheduling. In this paper, we propose a novel contention period control algorithm that incorporates bandwidth prediction capability in HFC networks to improve the utilization and throughput of the upstream bandwidth. Through simulations, we show that in all the cases studied in the paper, our adaptive method performs better than the MCNS DOCSIS.

The efficiency of radio channel utilization in wideband CDMA (WCDMA) is studied in this paper. The channel allocation in the WCDMA wireless links can be transformed into the orthogonal variable spreading factor (OVSF) code assignment to the connection requests. Code reassigning process is estimated to achieve an average of 20% gain of system throughput. Nevertheless, the disruption to the mobile users and the complexity of the wireless system are growing due to the code reassignment process; the amount of reassignment is expected to be as minimal as possible. The design and implementation of the efficient algorithm in minimizing the OVSF code reassignment is presented in this work. The simulation results demonstrate that the proposed algorithm can reduce in average 60% of the reassignment cost compared to that of the heuristic algorithm.

Active networks enable the customization of network functionality without the lengthy standard-mediated committee processes. Most of the works in the literature utilize capsules or active packets as the means to transfer code information across active networks. In this paper, we propose an active network infrastructure based on mobile agent technologies. In our prototype implementation, mobile agents are the building blocks carrying functional customizations, and the active nodes offer software application layers, caled agent servers, to process mobile agent-specific customizations to facilitate network functionality. Both integrated and discrete operational models of network customizations are supported. In addition, for the application-specific protocol development and deployment, an abstract protocol structure and a protocol loading mechanism are presented. Furthermore, we provide an agent management/control mechanism and devise a protocol management/control mechanism. As a result, improved network functionality can be achieved.

Intelligent agents have been shown to be a good approach to addressing the issues of limited capacity and unreliable wireless links in mobile computing. However, before the approach can be commercially viable, a set of management capabilities that support the controls of intelligent agents in a mobile environment need to be in place. Since controls can only be applied after the target agent is located, an effective agent search algorithm is an indispensable part of the management functions. In this paper, we propose a new algorithm, the highest probability first algorithm, for locating the target agent. The approach makes use of the execution time information to reduce cost and network traffic. The execution time of the agent on a server is assumed to be binomial distributed and therefore is more realistic.

A well accepted policing mechanism for ATM networks is the leaky bucket mechanism. The original leaky bucket has been shown to be effective for traffic with a constant bit rate, but reacts poorly to bursty traffic. Although there are some other policing mechanisms in the literature that provide improvements over the original leaky bucket, most of them enforce the negotiated parameters for individual source traffic and do not fully utilize the statistical multiplexing of multiple connections. As a result, the bandwidth utilisation is low. Even though some source policing mechanisms have been proposed for group connections, they either fail to explore statistical multiplexing fully or do not provide a scheme to protect well-behaved sources from malicious ones in the group. We propose a new source policing mechanism, called the token-bank leaky bucket, for group connections in ATM networks. The mechanism explores the statistical multiplexing of multiple connections in the group and allows the unused bandwidth to be effectively shared by the connections that need it. In addition, it sets a limit of excessive data cells a source can send in a cycle in order to protect well-behaved sources against malicious sources. It is shown by simulations to have a lower violation probability and better bandwidth utilization even for small group connections when compared to the original leaky bucket with a similar configuration.

Libra is an object-oriented simulator developed for simulation and fast prototyping of ATM networks. It is designed and implemented to address the diverse issues encountered in the simulation of any large-scale ATM network, namely, modeling of source traffic, network control, switch architecture design, and effective interaction of all these elements in an integrated fashion. The simulator is built on top of an object-oriented platform named Ptolemy. This simulator provides some distinct features that make it suitable for the simulation and analysis of ATM networks.

The multiprotocol transport networking (MPTN) architecture proposed in this paper is a general solution to providing interconnectivity for applications. The MPTN architecture provides a protocol-independent system interface that includes most functions provided by existing transport protocols. As a result, the MPTN architecture decouples higher-layer protocols, application programming interfaces, and applications from protocols at the transport layer and below. Using the MPTN architecture, current and new applications can function unmodified over any transport supported under the MPTN interface. In addition, MPTN transport-layer gateways provide an end-to-end communication facility across a number of networks running different protocols. Therefore, a collection of networks running different protocols can serve as a single logical network.>

Abstract The star graph has a smaller degree and diameter than the well‐known n‐cube, and can be an alternative to the n‐cube for systems with a large number of nodes [2]. In our previous work [11], three different indirect star‐type networks were obtained from the star graph: the indirect star network I, the indirect star network II, and the star‐delta network. However, the indirect star networks I & II are constructed from large switches, and do not perform as well as the indirect cube‐type networks of comparable switch sizes. Also, they are not modular. The star‐delta network is modular, but it employs varying switch sizes for different switching stages, and has a lower performance than the indirect cube‐type networks based on comparable switch sizes. Moreover, the switch sizes for all three indirect star networks grow with the network size. In this work, a new indirect star network, called the μ‐star network, is proposed. Being modular and constructed from (2 × 2) crossbar switches, the new network is an improvement over previously proposed indirect star‐type networks. The μ‐star network is analyzed for its performance and the analytic results are verified through simulations. © 1993 by John Wiley & Sons, Inc.

Existing packet combining schemes, implemented either by hardware or software, developed for hot-spot congestion-control in multiprocessors are not applicable for use in telecommunication systems. The authors propose a hot-spot prevention scheme which exploits the structural characteristics of buffered delta networks to regulate the traffic. This scheme prevents the tree saturation by controlling the flow of the packets into the network and ensures that the hot-spot traffic can be supported with little degradation to the throughput of the uniform traffic, even when more than one hot-spot exists. The scheme retains all the desirable properties, including packet order preserving, of buffered delta networks, and is shown by simulations to be highly effective under either light or heavy hot-spot traffic. Since no a priori knowledge of the traffic patterns is required, the proposed scheme can be applied equally well to buffered delta networks in multiprocessors and telecommunication systems.>

A modular approach is proposed for constructing a converter for two protocols that go through different phases, performing separate functions in each phase. The construction of such a converter consists of three steps: (1) the decomposition of protocols into distinct functions; (2) the construction of functional converters for each pair of functions selected by the converter designer; and (3) the merging of local functions with functional converters to construct the final converter. The final converter not only contains a common subset of functions of the two protocols, but also includes functionalities specified to each protocol.>