TY - JOUR T1 - Automatically Identifying and Annotating Mouse Embryo Gene Expression Patterns JF - Bioinformatics Y1 - 2011 A1 - Liangxiu Han A1 - van Hemert, Jano A1 - Richard Baldock KW - classification KW - e-Science AB - Motivation: Deciphering the regulatory and developmental mechanisms for multicellular organisms requires detailed knowledge of gene interactions and gene expressions. The availability of large datasets with both spatial and ontological annotation of the spatio-temporal patterns of gene-expression in mouse embryo provides a powerful resource to discover the biological function of embryo organisation. Ontological annotation of gene expressions consists of labelling images with terms from the anatomy ontology for mouse development. If the spatial genes of an anatomical component are expressed in an image, the image is then tagged with a term of that anatomical component. The current annotation is done manually by domain experts, which is both time consuming and costly. In addition, the level of detail is variable and inevitably, errors arise from the tedious nature of the task. In this paper, we present a new method to automatically identify and annotate gene expression patterns in the mouse embryo with anatomical terms. Results: The method takes images from in situ hybridisation studies and the ontology for the developing mouse embryo, it then combines machine learning and image processing techniques to produce classifiers that automatically identify and annotate gene expression patterns in these images.We evaluate our method on image data from the EURExpress-II study where we use it to automatically classify nine anatomical terms: humerus, handplate, fibula, tibia, femur, ribs, petrous part, scapula and head mesenchyme. The accuracy of our method lies between 70–80% with few exceptions. Conclusions: We show that other known methods have lower classification performance than ours. We have investigated the images misclassified by our method and found several cases where the original annotation was not correct. This shows our method is robust against this kind of noise. Availability: The annotation result and the experimental dataset in the paper can be freely accessed at http://www2.docm.mmu.ac.uk/STAFF/L.Han/geneannotation/ Contact: l.han@mmu.ac.uk, j.vanhemert@ed.ac.uk and Richard.Baldock@hgu.mrc.ac.uk VL - 27 UR - http://bioinformatics.oxfordjournals.org/content/early/2011/02/25/bioinformatics.btr105.abstract ER - TY - JOUR T1 - A Generic Parallel Processing Model for Facilitating Data Mining and Integration JF - Parallel Computing Y1 - 2011 A1 - Liangxiu Han A1 - Chee Sun Liew A1 - van Hemert, Jano A1 - Malcolm Atkinson KW - Data Mining and Data Integration (DMI) KW - Life Sciences KW - OGSA-DAI KW - Parallelism KW - Pipeline Streaming KW - workflow AB - To facilitate Data Mining and Integration (DMI) processes in a generic way, we investigate a parallel pipeline streaming model. We model a DMI task as a streaming data-flow graph: a directed acyclic graph (DAG) of Processing Elements PEs. The composition mechanism links PEs via data streams, which may be in memory, buffered via disks or inter-computer data-flows. This makes it possible to build arbitrary DAGs with pipelining and both data and task parallelisms, which provides room for performance enhancement. We have applied this approach to a real DMI case in the Life Sciences and implemented a prototype. To demonstrate feasibility of the modelled DMI task and assess the efficiency of the prototype, we have also built a performance evaluation model. The experimental evaluation results show that a linear speedup has been achieved with the increase of the number of distributed computing nodes in this case study. PB - Elsevier VL - 37 IS - 3 ER - TY - JOUR T1 - Performance database: capturing data for optimizing distributed streaming workflows JF - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Y1 - 2011 A1 - Chee Sun Liew A1 - Atkinson, Malcolm P. A1 - Radoslaw Ostrowski A1 - Murray Cole A1 - van Hemert, Jano I. A1 - Liangxiu Han KW - measurement framework KW - performance data KW - streaming workflows AB - The performance database (PDB) stores performance-related data gathered during workflow enactment. We argue that by carefully understanding and manipulating this data, we can improve efficiency when enacting workflows. This paper describes the rationale behind the PDB, and proposes a systematic way to implement it. The prototype is built as part of the Advanced Data Mining and Integration Research for Europe project. We use workflows from real-world experiments to demonstrate the usage of PDB. VL - 369 IS - 1949 ER - TY - CHAP T1 - Exploiting P2P and Grid Computing Technologies for Resource Sharing to support High Performance Distributed System T2 - Handbook of Research on P2P and Grid Systems for Service-Oriented Computing: Models, Methodologies and Applications Y1 - 2010 A1 - Liangxiu Han ED - Nick Antonopoulos ED - Georgios Exarchakos ED - Maozhen Li ED - Antonio Liottac JF - Handbook of Research on P2P and Grid Systems for Service-Oriented Computing: Models, Methodologies and Applications PB - IGI Global publishing VL - 1 ER - TY - Generic T1 - Federated Enactment of Workflow Patterns T2 - Lecture Notes in Computer Science Y1 - 2010 A1 - Yaikhom, Gagarine A1 - Liew, Chee A1 - Liangxiu Han A1 - van Hemert, Jano A1 - Malcolm Atkinson A1 - Krause, Amy ED - D’Ambra, Pasqua ED - Guarracino, Mario ED - Talia, Domenico AB - In this paper we address two research questions concerning workflows: 1) how do we abstract and catalogue recurring workflow patterns?; and 2) how do we facilitate optimisation of the mapping from workflow patterns to actual resources at runtime? Our aim here is to explore techniques that are applicable to large-scale workflow compositions, where the resources could change dynamically during the lifetime of an application. We achieve this by introducing a registry-based mechanism where pattern abstractions are catalogued and stored. In conjunction with an enactment engine, which communicates with this registry, concrete computational implementations and resources are assigned to these patterns, conditional to the execution parameters. Using a data mining application from the life sciences, we demonstrate this new approach. JF - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 6271 UR - http://dx.doi.org/10.1007/978-3-642-15277-1_31 N1 - 10.1007/978-3-642-15277-1_31 ER - TY - CONF T1 - Towards Optimising Distributed Data Streaming Graphs using Parallel Streams T2 - Data Intensive Distributed Computing (DIDC'10), in conjunction with the 19th International Symposium on High Performance Distributed Computing Y1 - 2010 A1 - Chee Sun Liew A1 - Atkinson, Malcolm P. A1 - van Hemert, Jano A1 - Liangxiu Han KW - Data-intensive Computing KW - Distributed Computing KW - Optimisation KW - Parallel Stream KW - Scientific Workflows AB - Modern scientific collaborations have opened up the opportunity of solving complex problems that involve multi- disciplinary expertise and large-scale computational experiments. These experiments usually involve large amounts of data that are located in distributed data repositories running various software systems, and managed by different organisations. A common strategy to make the experiments more manageable is executing the processing steps as a workflow. In this paper, we look into the implementation of fine-grained data-flow between computational elements in a scientific workflow as streams. We model the distributed computation as a directed acyclic graph where the nodes represent the processing elements that incrementally implement specific subtasks. The processing elements are connected in a pipelined streaming manner, which allows task executions to overlap. We further optimise the execution by splitting pipelines across processes and by introducing extra parallel streams. We identify performance metrics and design a measurement tool to evaluate each enactment. We conducted ex- periments to evaluate our optimisation strategies with a real world problem in the Life Sciences—EURExpress-II. The paper presents our distributed data-handling model, the optimisation and instrumentation strategies and the evaluation experiments. We demonstrate linear speed up and argue that this use of data-streaming to enable both overlapped pipeline and parallelised enactment is a generally applicable optimisation strategy. JF - Data Intensive Distributed Computing (DIDC'10), in conjunction with the 19th International Symposium on High Performance Distributed Computing PB - ACM CY - Chicago, Illinois UR - http://www.cct.lsu.edu/~kosar/didc10/index.php ER - TY - CONF T1 - Automating Gene Expression Annotation for Mouse Embryo T2 - Lecture Notes in Computer Science (Advanced Data Mining and Applications, 5th International Conference) Y1 - 2009 A1 - Liangxiu Han A1 - van Hemert, Jano A1 - Richard Baldock A1 - Atkinson, Malcolm P. ED - Ronghuai Huang ED - Qiang Yang ED - Jian Pei ED - et al JF - Lecture Notes in Computer Science (Advanced Data Mining and Applications, 5th International Conference) PB - Springer VL - LNAI 5678 ER - TY - CONF T1 - A Distributed Architecture for Data Mining and Integration T2 - Data-Aware Distributed Computing (DADC'09), in conjunction with the 18th International Symposium on High Performance Distributed Computing Y1 - 2009 A1 - Atkinson, Malcolm P. A1 - van Hemert, Jano A1 - Liangxiu Han A1 - Ally Hume A1 - Chee Sun Liew AB - This paper presents the rationale for a new architecture to support a significant increase in the scale of data integration and data mining. It proposes the composition into one framework of (1) data mining and (2) data access and integration. We name the combined activity “DMI”. It supports enactment of DMI processes across heterogeneous and distributed data resources and data mining services. It posits that a useful division can be made between the facilities established to support the definition of DMI processes and the computational infrastructure provided to enact DMI processes. Communication between those two divisions is restricted to requests submitted to gateway services in a canonical DMI language. Larger-scale processes are enabled by incremental refinement of DMI-process definitions often by recomposition of lower-level definitions. Autonomous types and descriptions which will support detection of inconsistencies and semi-automatic insertion of adaptations.These architectural ideas are being evaluated in a feasibility study that involves an application scenario and representatives of the community. JF - Data-Aware Distributed Computing (DADC'09), in conjunction with the 18th International Symposium on High Performance Distributed Computing PB - ACM ER - TY - JOUR T1 - The performance model of dynamic Virtual Organization (VO) formations within grid computing context JF - Chaos, Solitons & Fractals Y1 - 2009 A1 - Liangxiu Han KW - complex network KW - graph theory KW - grid computing KW - virtual organization formation PB - Elsevier Science VL - 40 IS - 4 N1 - In press ER - TY - CONF T1 - Using architectural simulation models to aid the design of data intensive application T2 - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009) Y1 - 2009 A1 - Javier Fernández A1 - Liangxiu Han A1 - Alberto Nuñez A1 - Jesus Carretero A1 - van Hemert, Jano JF - The Third International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2009) PB - IEEE Computer Society CY - Sliema, Malta ER - TY - CONF T1 - Using Simulation for Decision Support: Lessons Learned from FireGrid T2 - Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009) Y1 - 2009 A1 - Gerhard Wickler A1 - George Beckett A1 - Liangxiu Han A1 - Sung Han Koo A1 - Stephen Potter A1 - Gavin Pringle A1 - Austin Tate ED - J. Landgren, U. Nulden ED - B. Van de Walle JF - Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009) CY - Gothenburg, Sweden ER - TY - CONF T1 - An Architecture for an Integrated Fire Emergency Response System for the Built Environment T2 - 9th Symposium of the International Association for Fire Safety Science (IAFSS) Y1 - 2008 A1 - Rochan Upadhyay A1 - Galvin Pringle A1 - George Beckett A1 - Stephen Potter A1 - Liangxiu Han A1 - Stephen Welch A1 - Asif Usmani A1 - Jose Torero KW - emergency response system KW - FireGrid KW - system architecture KW - technology integration AB - FireGrid is a modern concept that aims to leverage a number of modern technologies to aid fire emergency response. In this paper we provide a brief introduction to the FireGrid project. A number of different technologies such as wireless sensor networks, grid-enabled High Performance Computing (HPC) implementation of fire models, and artificial intelligence tools need to be integrated to build up a modern fire emergency response system. We propose a system architecture that provides the framework for integration of the various technologies. We describe the components of the generic FireGrid system architecture in detail. Finally we present a small-scale demonstration experiment which has been completed to highlight the concept and application of the FireGrid system to an actual fire. Although our proposed system architecture provides a versatile framework for integration, a number of new and interesting research problems need to be solved before actual deployment of the system. We outline some of the challenges involved which require significant interdisciplinary collaborations. JF - 9th Symposium of the International Association for Fire Safety Science (IAFSS) PB - IAFSS CY - Karlsruhe, GERMANY ER - TY - CONF T1 - A novel visual discriminator on network traffic pattern T2 - The Second International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2008) Y1 - 2008 A1 - Liangxiu Han A1 - J. Hemert AB - The wavelet transform has been shown to be a powerful tool for characterising network traffic. However, the resulting decomposition of a wavelet transform typically forms a high-dimension space. This is obviously problematic on compact representations, visualizations, and modelling approaches that are based on these high-dimensional data. In this study, we show how data projection techniques can represent the high-dimensional wavelet decomposition in a low dimensional space to facilitate visual analysis. A low-dimensional representation can significantly reduce the model complexity. Hence, features in the data can be presented with a small number of parameters. We demonstrate these projections in the context of network traffic pattern analysis. The experimental results show that the proposed method can effectively discriminate between different application flows, such as FTP and P2P. JF - The Second International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2008) PB - IEEE Computer Society CY - Valencia, Spain ER - TY - JOUR T1 - The Self-adaptation to dynamic failures for efficient Virtual Organization formation in Grid computing context JF - Chaos, Solitons and Fractals Y1 - 2008 A1 - Liangxiu Han KW - complex network system KW - failure recovery KW - graph theory KW - grid computing KW - virtual organization formation AB - Grid computing aims to enable “resource sharing and coordinated problem solving in dynamic, multi-institutional Virtual Organizations (VOs)”. However, due to the nature of heterogeneous and dynamic resources, dynamic failures in the distributed grid environment usually occur more than in traditional computation platforms, which cause failed VO formations. In this paper, we develop a novel self-adaptive mechanism to dynamic failures during VO formations. Such a self-adaptive scheme allows an individual and member of VOs to automatically find other available or replaceable one once a failure happens and therefore makes systems automatically recover from dynamic failures. We define dynamic failure situations of a system by using two standard indicators: Mean Time between Failures (MTBF) and Mean Time to Recover (MTTR). We model both MTBF and MTTR as Poisson distributions. We investigate and analyze the efficiency of the proposed self-adaptation mechanism to dynamic failures by comparing the success probability of VO formations before and after adopting it in three different cases: 1) different failure situations; 2) different organizational structures and scales; 3) different task complexities. The experimental results show that the proposed scheme can automatically adapt to dynamic failures and effectively improve the dynamic VO formation performance in the event of node failures, which provide a valuable addition to the field. PB - Elsevier Science ER - TY - JOUR T1 - Semantic-Supported and Agent-Based Decentralized Grid Resource Discovery JF - Future Generation Computer Systems Y1 - 2008 A1 - Liangxiu Han A1 - Dave Berry KW - grid resource discovery, decentralization, agent, semantic similarity, ontology AB - One of open issues in grid computing is efficient resource discovery. In this paper, we propose a novel semantic-supported and agent-based decentralized grid resource discovery mechanism. Without overhead of negotiation, the algorithm allows individual resource agents to semantically interact with neighbour agents based on local knowledge and dynamically form a resource service chain to complete a task. The algorithm ensures resource agent’s ability to cooperate and coordinate on neighbour knowledge requisition for flexible problem solving. The developed algorithm is evaluated by investigating the relationship between the success probability of resource discovery and semantic similarity under different factors. The experiments show the algorithm could flexibly and dynamically discover resources and therefore provide a valuable addition to the field. PB - ScienceDirect VL - 24 IS - 8 ER - TY - CONF T1 - Towards a Grid-Enabled Simulation Framework for Nano-CMOS Electronics T2 - 3rd IEEE International Conference on eScience and Grid Computing Y1 - 2007 A1 - Liangxiu Han A1 - Asen Asenov A1 - Dave Berry A1 - Campbell Millar A1 - Gareth Roy A1 - Scott Roy A1 - Richard Sinnott A1 - Gordon Stewart AB - The electronics design industry is facing major challenges as transistors continue to decrease in size. The next generation of devices will be so small that the position of individual atoms will affect their behaviour. This will cause the transistors on a chip to have highly variable characteristics, which in turn will impact circuit and system design tools. The EPSRC project “Meeting the Design Challenges of Nano-CMOS Electronics” (Nano-CMOS) has been funded to explore this area. In this paper, we describe the distributed data-management and computing framework under development within Nano-CMOS. A key aspect of this framework is the need for robust and reliable security mechanisms that support distributed electronics design groups who wish to collaborate by sharing designs, simulations, workflows, datasets and computation resources. This paper presents the system design, and an early prototype of the project which hasbeen useful in helping us to understand the benefits of such a grid infrastructure. In particular, we also present two typical use cases: user authentication, and execution of large-scale device simulations. JF - 3rd IEEE International Conference on eScience and Grid Computing PB - IEEE Computer Society CY - Bangalore, India ER - TY - CONF T1 - Cross-Layer Peer-to-Peer Traffic Identification and Optimization Based on Active Networking T2 - 7th International Working Conference on Active and Programmable Networks Y1 - 2005 A1 - Dedinski, I. A1 - De Meer, H. A1 - Liangxiu Han A1 - Mathy, L. A1 - Pezaros, D. A1 - P. , Sventek, J. S. A1 - Xiaoying, Z. JF - 7th International Working Conference on Active and Programmable Networks CY - Sophia Antipolis, French Riviera, La Cote d'Azur, France, November 21-23, 2005. ER - TY - JOUR T1 - The Research of Relationship between Self-similar of TCP and Network Performance JF - Journal on communications Y1 - 2004 A1 - yan Liu A1 - Liangxiu Han VL - 25 IS - 4 ER - TY - JOUR T1 - The DWMM network traffic model JF - Journal of Communication Y1 - 2003 A1 - Cong Suo A1 - Liangxiu Han VL - 24 IS - 5 ER - TY - JOUR T1 - Application of the methodology combined formal method with Object-Oriented technology in E-commerce JF - Journal of Computer Engineering Y1 - 2002 A1 - Liangxiu Han VL - 29 IS - z1 ER - TY - JOUR T1 - A network traffic model based on the cascade process JF - Journal of Mini-Micro Computer System Y1 - 2002 A1 - Liangxiu Han A1 - yan Liu A1 - Zhiwei Cen VL - 23 IS - 12 ER - TY - JOUR T1 - A new multifractal network traffic model JF - Journal of Chaos, solitons & fractals Y1 - 2002 A1 - Liangxiu Han A1 - Zhiwei Ceng A1 - Chuanshan Gao PB - Elsevier Science VL - 13 IS - 7 ER - TY - JOUR T1 - The characterizing network traffic based on the wavelet technique JF - Journal of Mini-Micro Computer System Y1 - 2001 A1 - Liangxiu Han A1 - Cong Suo VL - 22 IS - 9 ER - TY - CONF T1 - A new multifractal traffic model based on the wavelet transform T2 - ISCA 14th International Conference on Parallel and Distributed Computing systems Y1 - 2001 A1 - Chuanshan Gao A1 - Liangxiu Han JF - ISCA 14th International Conference on Parallel and Distributed Computing systems CY - Texas, USA ER - TY - JOUR T1 - Neural network applied to the prediction of the failure stress for pressurized cylinders containing defects JF - International Journal of Pressure Vessels and Piping Y1 - 1999 A1 - Lianghao Han A1 - Liangxiu Han A1 - zengdian Liu PB - Elsevier VL - 76 IS - 4 ER - TY - JOUR T1 - Questions considered in object-oriented software quality metrics based on Java environment JF - Journal of East China University of Science and Technology Y1 - 1999 A1 - Liangxiu Han PB - East China University of Science and Technology ER - TY - JOUR T1 - On Zero-symmetric BZ-algebras JF - Journal of East China University of Science and Technology Y1 - 1997 A1 - Wang, Y. A1 - Liangxiu Han PB - East China University of Science and Technology VL - 23 IS - 6 ER -