Supplementary Information : Hogan, Holland, Holloway, Petit and Read : Read Classification for Next Generation Sequencing, ESANN 2013, April 2013

This item provides supplementary materials for the paper mentioned in the title, specifically a range of organisms used in the study. The full abstract for the main paper is as follows: Next Generation Sequencing (NGS) technologies have revolutionised molecular biology, allowing clinical sequencing to become a matter of routine. NGS data sets consist of short sequence reads obtained from the machine, given context and meaning through downstream assembly and annotation. For these techniques to operate successfully, the collected reads must be consistent with the assumed species or species group, and not corrupted in some way. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans,with some strains exhibiting antibiotic resistance. In this paper, we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from alternative pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

Procuring OSM : base-line models of off-site manufacture business processes in Australia

A pressing cost issue facing construction is the procurement of off-site pre-manufactured assemblies. In order to encourage Australian adoption of off-site manufacture (OSM), a new approach to underlying processes is required. The advent of object oriented digital models for construction design assumes intelligent use of data. However, the construction production system relies on traditional methods and data sources and is expected to benefit from the application of well-established business process management techniques. The integration of the old and new data sources allows for the development of business process models which, by capturing typical construction processes involving OSM, provides insights into such processes. This integrative approach is the foundation of research into the use of OSM to increase construction productivity in Australia. The purpose of this study is to develop business process models capturing the procurement, resources and information flow of construction projects. For each stage of the construction value chain, a number of sub-processes are identified. Business Process Modelling Notation (BPMN), a mainstream business process modelling standard, is used to create base-line generic construction process models. These models identify OSM decision-making points that could provide cost reductions in procurement workflow and management systems. This paper reports on phase one of an on-going research aiming to develop a proto-type workflow application that can provide semi-automated support to construction processes involving OSM and assist in decision-making in the adoption of OSM thus contributing to a sustainable built environment.

V1-inspired features induce a weighted margin in SVMs

Image representations derived from simplified models of the primary visual cortex (V1), such as HOG and SIFT, elicit good performance in a myriad of visual classification tasks including object recognition/detection, pedestrian detection and facial expression classification. A central question in the vision, learning and neuroscience communities regards why these architectures perform so well. In this paper, we offer a unique perspective to this question by subsuming the role of V1-inspired features directly within a linear support vector machine (SVM). We demonstrate that a specific class of such features in conjunction with a linear SVM can be reinterpreted as inducing a weighted margin on the Kronecker basis expansion of an image. This new viewpoint on the role of V1-inspired features allows us to answer fundamental questions on the uniqueness and redundancies of these features, and offer substantial improvements in terms of computational and storage efficiency.

Fourier Lucas-Kanade Algorithm

In this paper we propose a framework for both gradient descent image and object alignment in the Fourier domain. Our method centers upon the classical Lucas & Kanade (LK) algorithm where we represent the source and template/model in the complex 2D Fourier domain rather than in the spatial 2D domain. We refer to our approach as the Fourier LK (FLK) algorithm. The FLK formulation is advantageous when one pre-processes the source image and template/model with a bank of filters (e.g. oriented edges, Gabor, etc.) as: (i) it can handle substantial illumination variations, (ii) the inefficient pre-processing filter bank step can be subsumed within the FLK algorithm as a sparse diagonal weighting matrix, (iii) unlike traditional LK the computational cost is invariant to the number of filters and as a result far more efficient, and (iv) this approach can be extended to the inverse compositional form of the LK algorithm where nearly all steps (including Fourier transform and filter bank pre-processing) can be pre-computed leading to an extremely efficient and robust approach to gradient descent image matching. Further, these computational savings translate to non-rigid object alignment tasks that are considered extensions of the LK algorithm such as those found in Active Appearance Models (AAMs).

Towards a secure human-and-computer mutual authentication protocol

We blend research from human-computer interface (HCI) design with computational based crypto- graphic provable security. We explore the notion of practice-oriented provable security (POPS), moving the focus to a higher level of abstraction (POPS+) for use in providing provable security for security ceremonies involving humans. In doing so we high- light some challenges and paradigm shifts required to achieve meaningful provable security for a protocol which includes a human. We move the focus of security ceremonies from being protocols in their context of use, to the protocols being cryptographic building blocks in a higher level protocol (the security cere- mony), which POPS can be applied to. In order to illustrate the need for our approach, we analyse both a protocol proven secure in theory, and a similar proto- col implemented by a �nancial institution, from both HCI and cryptographic perspectives.

Design and modeling of collaboration architecture for security

Threats against computer networks evolve very fast and require more and more complex measures. We argue that teams respectively groups with a common purpose for intrusion detection and prevention improve the measures against rapid propagating attacks similar to the concept of teams solving complex tasks known from field of work sociology. Collaboration in this sense is not easy task especially for heterarchical environments. We propose CIMD (collaborative intrusion and malware detection) as a security overlay framework to enable cooperative intrusion detection approaches. Objectives and associated interests are used to create detection groups for exchange of security-related data. In this work, we contribute a tree-oriented data model for device representation in the scope of security. We introduce an algorithm for the formation of detection groups, show realization strategies for the system and conduct vulnerability analysis. We evaluate the benefit of CIMD by simulation and probabilistic analysis.

Goodbye TAIS and thanks for all the information

The Therapeutic Advice and Information Service was funded by the National Prescribing Service to provide a national drug information service for health professionals working in the community. For ten years the service achieved high levels of client satisfaction, and reached its contracted target of 6000 enquiries about medicines per year, however the service ceased on 30 June 2010.

Ontology-based feature modeling for construction information extraction from a building information model

A building information model (BIM) provides a rich representation of a building's design. However, there are many challenges in getting construction-specific information from a BIM, limiting the usability of BIM for construction and other downstream processes. This paper describes a novel approach that utilizes ontology-based feature modeling, automatic feature extraction based on ifcXML, and query processing to extract information relevant to construction practitioners from a given BIM. The feature ontology generically represents construction-specific information that is useful for a broad range of construction management functions. The software prototype uses the ontology to transform the designer-focused BIM into a construction-specific feature-based model (FBM). The formal query methods operate on the FBM to further help construction users to quickly extract the necessary information from a BIM. Our tests demonstrate that this approach provides a richer representation of construction-specific information compared to existing BIM tools.

Querying a building information model for construction-specific spatial information

The design and construction community has shown increasing interest in adopting building information models (BIMs). The richness of information provided by BIMs has the potential to streamline the design and construction processes by enabling enhanced communication, coordination, automation and analysis. However, there are many challenges in extracting construction-specific information out of BIMs. In most cases, construction practitioners have to manually identify the required information, which is inefficient and prone to error, particularly for complex, large-scale projects. This paper describes the process and methods we have formalized to partially automate the extraction and querying of construction-specific information from a BIM. We describe methods for analyzing a BIM to query for spatial information that is relevant for construction practitioners, and that is typically represented implicitly in a BIM. Our approach integrates ifcXML data and other spatial data to develop a richer model for construction users. We employ custom 2D topological XQuery predicates to answer a variety of spatial queries. The validation results demonstrate that this approach provides a richer representation of construction-specific information compared to existing BIM tools.

Crowdsourcing information systems : definition, typology and design

Crowdsourcing has become a popular approach for capitalizing on the potential of large and open crowds of people external to the organization. While crowdsourcing as a phenomenon is studied in a variety of fields, research mostly focuses on isolated aspects and little is known about the integrated design of crowdsourcing efforts. We introduce a socio-technical systems perspective on crowdsourcing, which provides a deeper understanding of the components and relationships in crowdsourcing systems. By considering the function of crowdsourcing systems within their organizational context, we develop a typology of four distinct system archetypes. We analyze the characteristics of each type and derive a number of design requirements for the respective system components. The paper lays a foundation for IS-based crowdsourcing research, channels related academic work, and helps guiding the study and design of crowdsourcing information systems.

Open source information retrieval : a report on the SIGIR 2012 workshop

On August 16, 2012 the SIGIR 2012 Workshop on Open Source Information Retrieval was held as part of the SIGIR 2012 conference in Portland, Oregon, USA. There were 2 invited talks, one from industry and one from academia. There were 6 full papers and 6 short papers presented as well as demonstrations of 4 open source tools. Finally there was a lively discussion on future directions for the open source Information Retrieval community. This contribution discusses the events of the workshop and outlines future directions for the community.

An innovative information gathering and data analysis platform for railway level crossing safety data

This paper describes an innovative platform that facilitates the collection of objective safety data around occurrences at railway level crossings using data sources including forward-facing video, telemetry from trains and geo-referenced asset and survey data. This platform is being developed with support by the Australian rail industry and the Cooperative Research Centre for Rail Innovation. The paper provides a description of the underlying accident causation model, the development methodology and refinement process as well as a description of the data collection platform. The paper concludes with a brief discussion of benefits this project is expected to provide the Australian rail industry.

Approaches to access control under uncertainty

The ultimate goal of an access control system is to allocate each user the precise level of access they need to complete their job - no more and no less. This proves to be challenging in an organisational setting. On one hand employees need enough access to the organisation’s resources in order to perform their jobs and on the other hand more access will bring about an increasing risk of misuse - either intentionally, where an employee uses the access for personal benefit, or unintentionally, through carelessness or being socially engineered to give access to an adversary. This thesis investigates issues of existing approaches to access control in allocating optimal level of access to users and proposes solutions in the form of new access control models. These issues are most evident when uncertainty surrounding users’ access needs, incentive to misuse and accountability are considered, hence the title of the thesis. We first analyse access control in environments where the administrator is unable to identify the users who may need access to resources. To resolve this uncertainty an administrative model with delegation support is proposed. Further, a detailed technical enforcement mechanism is introduced to ensure delegated resources cannot be misused. Then we explicitly consider that users are self-interested and capable of misusing resources if they choose to. We propose a novel game theoretic access control model to reason about and influence the factors that may affect users’ incentive to misuse. Next we study access control in environments where neither users’ access needs can be predicted nor they can be held accountable for misuse. It is shown that by allocating budget to users, a virtual currency through which they can pay for the resources they deem necessary, the need for a precise pre-allocation of permissions can be relaxed. The budget also imposes an upper-bound on users’ ability to misuse. A generalised budget allocation function is proposed and it is shown that given the context information the optimal level of budget for users can always be numerically determined. Finally, Role Based Access Control (RBAC) model is analysed under the explicit assumption of administrators’ uncertainty about self-interested users’ access needs and their incentives to misuse. A novel Budget-oriented Role Based Access Control (B-RBAC) model is proposed. The new model introduces the notion of users’ behaviour into RBAC and provides means to influence users’ incentives. It is shown how RBAC policy can be used to individualise the cost of access to resources and also to determine users’ budget. The implementation overheads of B-RBAC is examined and several low-cost sub-models are proposed.

Link discovery for Chinese/English cross-language web information retrieval

Nowadays people heavily rely on the Internet for information and knowledge. Wikipedia is an online multilingual encyclopaedia that contains a very large number of detailed articles covering most written languages. It is often considered to be a treasury of human knowledge. It includes extensive hypertext links between documents of the same language for easy navigation. However, the pages in different languages are rarely cross-linked except for direct equivalent pages on the same subject in different languages. This could pose serious difficulties to users seeking information or knowledge from different lingual sources, or where there is no equivalent page in one language or another. In this thesis, a new information retrieval task—cross-lingual link discovery (CLLD) is proposed to tackle the problem of the lack of cross-lingual anchored links in a knowledge base such as Wikipedia. In contrast to traditional information retrieval tasks, cross language link discovery algorithms actively recommend a set of meaningful anchors in a source document and establish links to documents in an alternative language. In other words, cross-lingual link discovery is a way of automatically finding hypertext links between documents in different languages, which is particularly helpful for knowledge discovery in different language domains. This study is specifically focused on Chinese / English link discovery (C/ELD). Chinese / English link discovery is a special case of cross-lingual link discovery task. It involves tasks including natural language processing (NLP), cross-lingual information retrieval (CLIR) and cross-lingual link discovery. To justify the effectiveness of CLLD, a standard evaluation framework is also proposed. The evaluation framework includes topics, document collections, a gold standard dataset, evaluation metrics, and toolkits for run pooling, link assessment and system evaluation. With the evaluation framework, performance of CLLD approaches and systems can be quantified. This thesis contributes to the research on natural language processing and cross-lingual information retrieval in CLLD: 1) a new simple, but effective Chinese segmentation method, n-gram mutual information, is presented for determining the boundaries of Chinese text; 2) a voting mechanism of name entity translation is demonstrated for achieving a high precision of English / Chinese machine translation; 3) a link mining approach that mines the existing link structure for anchor probabilities achieves encouraging results in suggesting cross-lingual Chinese / English links in Wikipedia. This approach was examined in the experiments for better, automatic generation of cross-lingual links that were carried out as part of the study. The overall major contribution of this thesis is the provision of a standard evaluation framework for cross-lingual link discovery research. It is important in CLLD evaluation to have this framework which helps in benchmarking the performance of various CLLD systems and in identifying good CLLD realisation approaches. The evaluation methods and the evaluation framework described in this thesis have been utilised to quantify the system performance in the NTCIR-9 Crosslink task which is the first information retrieval track of this kind.