Edge-weighting of gene expression graphs

In recent years, considerable research efforts have been directed to micro-array technologies and their role in providing simultaneous information on expression profiles for thousands of genes. These data, when subjected to clustering and classification procedures, can assist in identifying patterns and providing insight on biological processes. To understand the properties of complex gene expression datasets, graphical representations can be used. Intuitively, the data can be represented in terms of a bipartite graph, with weighted edges corresponding to gene-sample node couples in the dataset. Biologically meaningful subgraphs can be sought, but performance can be influenced both by the search algorithm, and, by the graph-weighting scheme and both merit rigorous investigation. In this paper, we focus on edge-weighting schemes for bipartite graphical representation of gene expression. Two novel methods are presented: the first is based on empirical evidence; the second on a geometric distribution. The schemes are compared for several real datasets, assessing efficiency of performance based on four essential properties: robustness to noise and missing values, discrimination, parameter influence on scheme efficiency and reusability. Recommendations and limitations are briefly discussed. Keywords: Edge-weighting; weighted graphs; gene expression; bi-clustering

Shortest path and vehicle trajectory aided map-matching for low frequency GPS data

Map-matching algorithms that utilise road segment connectivity along with other data (i.e.position, speed and heading) in the process of map-matching are normally suitable for high frequency (1 Hz or higher) positioning data from GPS. While applying such map-matching algorithms to low frequency data (such as data from a fleet of private cars, buses or light duty vehicles or smartphones), the performance of these algorithms reduces to in the region of 70% in terms of correct link identification, especially in urban and sub-urban road networks. This level of performance may be insufficient for some real-time Intelligent Transport System (ITS) applications and services such as estimating link travel time and speed from low frequency GPS data. Therefore, this paper develops a new weight-based shortest path and vehicle trajectory aided map-matching (stMM) algorithm that enhances the map-matching of low frequency positioning data on a road map. The well-known A* search algorithm is employed to derive the shortest path between two points while taking into account both link connectivity and turn restrictions at junctions. In the developed stMM algorithm, two additional weights related to the shortest path and vehicle trajectory are considered: one shortest path-based weight is related to the distance along the shortest path and the distance along the vehicle trajectory, while the other is associated with the heading difference of the vehicle trajectory. The developed stMM algorithm is tested using a series of real-world datasets of varying frequencies (i.e. 1 s, 5 s, 30 s, 60 s sampling intervals). A high-accuracy integrated navigation system (a high-grade inertial navigation system and a carrier-phase GPS receiver) is used to measure the accuracy of the developed algorithm. The results suggest that the algorithm identifies 98.9% of the links correctly for every 30 s GPS data. Omitting the information from the shortest path and vehicle trajectory, the accuracy of the algorithm reduces to about 73% in terms of correct link identification. The algorithm can process on average 50 positioning fixes per second making it suitable for real-time ITS applications and services.

Improved cryptanalysis of the Common Scrambling Algorithm Stream Cipher

This paper provides a fresh analysis of the widely-used Common Scrambling Algorithm Stream Cipher (CSA-SC). Firstly, a new representation of CSA-SC with a state size of only 89 bits is given, a significant reduction from the 103 bit state of a previous CSA-SC representation. Analysis of this 89-bit representation demonstrates that the basis of a previous guess-and-determine attack is flawed. Correcting this flaw increases the complexity of that attack so that it is worse than exhaustive key search. Although that attack is not feasible, the reduced state size of our representation makes it obvious that CSA-SC is vulnerable to several generic attacks, for which feasible parameters are given.

Fast searching algorithm for candidate satellite-node set in NLMG

The Node-based Local Mesh Generation (NLMG) algorithm, which is free of mesh inconsistency, is one of core algorithms in the Node-based Local Finite Element Method (NLFEM) to achieve the seamless link between mesh generation and stiffness matrix calculation, and the seamless link helps to improve the parallel efficiency of FEM. Furthermore, the key to ensure the efficiency and reliability of NLMG is to determine the candidate satellite-node set of a central node quickly and accurately. This paper develops a Fast Local Search Method based on Uniform Bucket (FLSMUB) and a Fast Local Search Method based on Multilayer Bucket (FLSMMB), and applies them successfully to the decisive problems, i.e. presenting the candidate satellite-node set of any central node in NLMG algorithm. Using FLSMUB or FLSMMB, the NLMG algorithm becomes a practical tool to reduce the parallel computation cost of FEM. Parallel numerical experiments validate that either FLSMUB or FLSMMB is fast, reliable and efficient for their suitable problems and that they are especially effective for computing the large-scale parallel problems.

Enhancing an Incremental Clustering Algorithm for Web Page Collections

With the size and state of the Internet today, a good quality approach to organizing this mass of information is of great importance. Clustering web pages into groups of similar documents is one approach, but relies heavily on good feature extraction and document representation as well as a good clustering approach and algorithm. Due to the changing nature of the Internet, resulting in a dynamic dataset, an incremental approach is preferred. In this work we propose an enhanced incremental clustering approach to develop a better clustering algorithm that can help to better organize the information available on the Internet in an incremental fashion. Experiments show that the enhanced algorithm outperforms the original histogram based algorithm by up to 7.5%.

A hybrid genetic algorithm for the optimal constrained web service selection problem in web service composition

Web service composition is an important problem in web service based systems. It is about how to build a new value-added web service using existing web services. A web service may have many implementations, all of which have the same functionality, but may have different QoS values. Thus, a significant research problem in web service composition is how to select a web service implementation for each of the web services such that the composite web service gives the best overall performance. This is so-called optimal web service selection problem. There may be mutual constraints between some web service implementations. Sometimes when an implementation is selected for one web service, a particular implementation for another web service must be selected. This is so called dependency constraint. Sometimes when an implementation for one web service is selected, a set of implementations for another web service must be excluded in the web service composition. This is so called conflict constraint. Thus, the optimal web service selection is a typical constrained ombinatorial optimization problem from the computational point of view. This paper proposes a new hybrid genetic algorithm for the optimal web service selection problem. The hybrid genetic algorithm has been implemented and evaluated. The evaluation results have shown that the hybrid genetic algorithm outperforms other two existing genetic algorithms when the number of web services and the number of constraints are large.

Partitioning composite web services for decentralized execution using a genetic algorithm

Composite web services comprise several component web services. When a composite web service is executed centrally, a single web service engine is responsible for coordinating the execution of the components, which may create a bottleneck and degrade the overall throughput of the composite service when there are a large number of service requests. Potentially this problem can be handled by decentralizing execution of the composite web service, but this raises the issue of how to partition a composite service into groups of component services such that each group can be orchestrated by its own execution engine while ensuring acceptable overall throughput of the composite service. Here we present a novel penalty-based genetic algorithm to solve the composite web service partitioning problem. Empirical results show that our new algorithm outperforms existing heuristic-based solutions.

QoS-oriented sesource allocation and scheduling of multiple composite web services in a hybrid cloud using a random-key genetic algorithm

In cloud computing resource allocation and scheduling of multiple composite web services is an important challenge. This is especially so in a hybrid cloud where there may be some free resources available from private clouds but some fee-paying resources from public clouds. Meeting this challenge involves two classical computational problems. One is assigning resources to each of the tasks in the composite web service. The other is scheduling the allocated resources when each resource may be used by more than one task and may be needed at different points of time. In addition, we must consider Quality-of-Service issues, such as execution time and running costs. Existing approaches to resource allocation and scheduling in public clouds and grid computing are not applicable to this new problem. This paper presents a random-key genetic algorithm that solves new resource allocation and scheduling problem. Experimental results demonstrate the effectiveness and scalability of the algorithm.

Dynamic coast control of train movement with genetic algorithm

The railway service is now the major transportation means in most of the countries around the world. With the increasing population and expanding commercial and industrial activities, a high quality of railway service is the most desirable. Train service usually varies with the population activities throughout a day and train coordination and service regulation are then expected to meet the daily passengers' demand. Dwell time control at stations and fixed coasting point in an inter-station run are the current practices to regulate train service in most metro railway systems. However, a flexible and efficient train control and operation is not always possible. To minimize energy consumption of train operation and make certain compromises on the train schedule, coast control is an economical approach to balance run-time and energy consumption in railway operation if time is not an important issue, particularly at off-peak hours. The capability to identify the starting point for coasting according to the current traffic conditions provides the necessary flexibility for train operation. This paper presents an application of genetic algorithms (GA) to search for the appropriate coasting point(s) and investigates the possible improvement on fitness of genes. Single and multiple coasting point control with simple GA are developed to attain the solutions and their corresponding train movement is examined. Further, a hierarchical genetic algorithm (HGA) is introduced here to identify the number of coasting points required according to the traffic conditions, and Minimum-Allele-Reserve-Keeper (MARK) is adopted as a genetic operator to achieve fitter solutions.

Railway junction conflict resolution by genetic algorithm

In general, simple and traditional methods are applied to resolve traffic conflicts at railway junctions. They are, however, either inefficient or computationally demanding. A simple genetic algorithm is presented to enable a search for a near optimal resolution to be carried out while meeting the constraints on generation evolution and minimising the search time.

Coasting control of train operation by genetic algorithm

Balancing between the provision of high quality of service and running within a tight budget is one of the biggest challenges for most metro railway operators around the world. Conventionally, one possible approach for the operator to adjust the time schedule is to alter the stop time at stations, if other system constraints, such as traction equipment characteristic, are not taken into account. Yet it is not an effective, flexible and economical method because the run-time of a train simply cannot be extended without limitation, and a balance between run-time and energy consumption has to be maintained. Modification or installation of a new signalling system not only increases the capital cost, but also affects the normal train service. Therefore, in order to procure a more effective, flexible and economical means to improve the quality of service, optimisation of train performance by coasting point identification has become more attractive and popular. However, identifying the necessary starting points for coasting under the constraints of current service conditions is no simple task because train movement is attributed by a large number of factors, most of which are non-linear and inter-dependent. This paper presents an application of genetic algorithms (GA) to search for the appropriate coasting points and investigates the possible improvement on computation time and fitness of genes.

A synthesizable hardware evolutionary algorithm design for unmanned aerial system real-time path planning

The main objective of this paper is to detail the development of a feasible hardware design based on Evolutionary Algorithms (EAs) to determine flight path planning for Unmanned Aerial Vehicles (UAVs) navigating terrain with obstacle boundaries. The design architecture includes the hardware implementation of Light Detection And Ranging (LiDAR) terrain and EA population memories within the hardware, as well as the EA search and evaluation algorithms used in the optimizing stage of path planning. A synthesisable Very-high-speed integrated circuit Hardware Description Language (VHDL) implementation of the design was developed, for realisation on a Field Programmable Gate Array (FPGA) platform. Simulation results show significant speedup compared with an equivalent software implementation written in C++, suggesting that the present approach is well suited for UAV real-time path planning applications.

Shrinking neighborhood evolution : a novel stochastic algorithm for numerical optimization

Focusing on the conditions that an optimization problem may comply with, the so-called convergence conditions have been proposed and sequentially a stochastic optimization algorithm named as DSZ algorithm is presented in order to deal with both unconstrained and constrained optimizations. The principle is discussed in the theoretical model of DSZ algorithm, from which we present the practical model of DSZ algorithm. Practical model efficiency is demonstrated by the comparison with the similar algorithms such as Enhanced simulated annealing (ESA), Monte Carlo simulated annealing (MCS), Sniffer Global Optimization (SGO), Directed Tabu Search (DTS), and Genetic Algorithm (GA), using a set of well-known unconstrained and constrained optimization test cases. Meanwhile, further attention goes to the strategies how to optimize the high-dimensional unconstrained problem using DSZ algorithm.