Semantic and context-based retrieval of digital cultural objects [Published in Chinese]

Cultural objects are increasingly generated and stored in digital form, yet effective methods for their indexing and retrieval still remain an important area of research. The main problem arises from the disconnection between the content-based indexing approach used by computer scientists and the description-based approach used by information scientists. There is also a lack of representational schemes that allow the alignment of the semantics and context with keywords and low-level features that can be automatically extracted from the content of these cultural objects. This paper presents an integrated approach to address these problems, taking advantage of both computer science and information science approaches. We firstly discuss the requirements from a number of perspectives: users, content providers, content managers and technical systems. We then present an overview of our system architecture and describe various techniques which underlie the major components of the system. These include: automatic object category detection; user-driven tagging; metadata transform and augmentation, and an expression language for digital cultural objects. In addition, we discuss our experience on testing and evaluating some existing collections, analyse the difficulties encountered and propose ways to address these problems.

Taxonomy and diagnostics of fruit fly infesting Opiine Braconids in Australia and the South Pacific

Opiine wasps (Hymenoptera: Braconidae: Opiinae) are parasitoids of dacine fruit flies (Diptera: Tephritidae: Dacinae), the primary horticultural pests of Australia and the South Pacific. Effective use of opiines for biological control of fruit flies is limited by poor taxonomy and identification difficulties. To overcome these problems, this thesis had two aims: (i) to carry out traditional taxonomic research on the fruit fly infesting opine braconids of Australia and the South Pacific; and (ii) to transfer the results of the taxonomic research into user friendly diagnostic tools. Curated wasp material was borrowed from all major Australian museum collections holding specimens. This was supplemented by a large body of material gathered as part of a major fruit fly project in Papua New Guinea: nearly 4000 specimens were examined and identified. Each wasp species was illustrated using traditional scientific drawings, full colour photomicroscopy and scanning electron microscopy. An electronic identification key was developed using Lucid software and diagnostic images were loaded on the web-based Pest and Diseases Image Library (PaDIL). A taxonomic synopsis and distribution and host records for each of the 15 species of dacine-parasitising opiine braconids found in the South Pacific is presented. Biosteres illusorius Fischer (1971) was formally transferred to the genus Fopius and a new species, Fopius ferrari Carmichael and Wharton (2005), was described. Other species dealt with were Diachasmimorpha hageni (Fullaway, 1952), D. kraussii (Fullaway, 1951), D. longicaudata (Ashmead, 1905), D. tryoni (Cameron, 1911), Fopius arisanus (Sonan, 1932), F. deeralensis (Fullaway, 1950), F. schlingeri Wharton (1999), Opius froggatti Fullaway (195), Psyttalia fijiensis (Fullaway, 1936), P. muesebecki (Fischer, 1963), P. novaguineensis (Szépliget, 1900i) and Utetes perkinsi (Fullaway, 1950). This taxonomic component of the thesis has been formally published in the scientific literature. An interactive diagnostics package (“OpiineID”) was developed, the centre of which is a Lucid based multi-access key. Because the diagnostics package is computer based, without the space limitations of the journal publication, there is no pictorial limit in OpiineID and so it is comprehensively illustrated with SEM photographs, full colour photographs, line drawings and fully rendered illustrations. The identification key is only one small component of OpiineID and the key is supported by fact sheets with morphological descriptions, host associations, geographical information and images. Each species contained within the OpiineID package has also been uploaded onto the PaDIL website (www.padil.gov.au). Because the identification of fruit fly parasitoids is largely of concern to fruit fly workers, rather than braconid specialists, this thesis deals directly with an area of growing importance to many areas of pure and applied biology; the nexus between taxonomy and diagnostics. The Discussion chapter focuses on this area, particularly the opportunities offered by new communication and information tools as new ways delivering the outputs of taxonomic science.

Improvement to Chinese information retrieval by incorporating word segmentation and query expansion

The increasing diversity of the Internet has created a vast number of multilingual resources on the Web. A huge number of these documents are written in various languages other than English. Consequently, the demand for searching in non-English languages is growing exponentially. It is desirable that a search engine can search for information over collections of documents in other languages. This research investigates the techniques for developing high-quality Chinese information retrieval systems. A distinctive feature of Chinese text is that a Chinese document is a sequence of Chinese characters with no space or boundary between Chinese words. This feature makes Chinese information retrieval more difficult since a retrieved document which contains the query term as a sequence of Chinese characters may not be really relevant to the query since the query term (as a sequence Chinese characters) may not be a valid Chinese word in that documents. On the other hand, a document that is actually relevant may not be retrieved because it does not contain the query sequence but contains other relevant words. In this research, we propose two approaches to deal with the problems. In the first approach, we propose a hybrid Chinese information retrieval model by incorporating word-based techniques with the traditional character-based techniques. The aim of this approach is to investigate the influence of Chinese segmentation on the performance of Chinese information retrieval. Two ranking methods are proposed to rank retrieved documents based on the relevancy to the query calculated by combining character-based ranking and word-based ranking. Our experimental results show that Chinese segmentation can improve the performance of Chinese information retrieval, but the improvement is not significant if it incorporates only Chinese segmentation with the traditional character-based approach. In the second approach, we propose a novel query expansion method which applies text mining techniques in order to find the most relevant words to extend the query. Unlike most existing query expansion methods, which generally select the highly frequent indexing terms from the retrieved documents to expand the query. In our approach, we utilize text mining techniques to find patterns from the retrieved documents that highly correlate with the query term and then use the relevant words in the patterns to expand the original query. This research project develops and implements a Chinese information retrieval system for evaluating the proposed approaches. There are two stages in the experiments. The first stage is to investigate if high accuracy segmentation can make an improvement to Chinese information retrieval. In the second stage, a text mining based query expansion approach is implemented and a further experiment has been done to compare its performance with the standard Rocchio approach with the proposed text mining based query expansion method. The NTCIR5 Chinese collections are used in the experiments. The experiment results show that by incorporating the text mining based query expansion with the hybrid model, significant improvement has been achieved in both precision and recall assessments.

Efficient and accurate retrieval of business process models through indexing

Recent years have seen an increased uptake of business process management technology in industries. This has resulted in organizations trying to manage large collections of business process models. One of the challenges facing these organizations concerns the retrieval of models from large business process model repositories. For example, in some cases new process models may be derived from existing models, thus finding these models and adapting them may be more effective than developing them from scratch. As process model repositories may be large, query evaluation may be time consuming. Hence, we investigate the use of indexes to speed up this evaluation process. Experiments are conducted to demonstrate that our proposal achieves a significant reduction in query evaluation time.

Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.

Clustering with random indexing K-tree and XML structure

This paper describes the approach taken to the clustering task at INEX 2009 by a group at the Queensland University of Technology. The Random Indexing (RI) K-tree has been used with a representation that is based on the semantic markup available in the INEX 2009 Wikipedia collection. The RI K-tree is a scalable approach to clustering large document collections. This approach has produced quality clustering when evaluated using two different methodologies.

Managing process model collections with AProMoRe

As organizations reach higher levels of Business Process Management maturity, they tend to collect numerous business process models. Such models may be linked with each other or mutually overlap, supersede one another and evolve over time. Moreover, they may be represented at different abstraction levels depending on the target audience and modeling purpose, and may be available in multiple languages (e.g. due to company mergers). Thus, it is common that organizations struggle with keeping track of their process models. This demonstration introduces AProMoRe (Advanced Process Model Repository) which aims to facilitate the management of (large) process model collections.

QUT Digital Repository: Integrating the University’s IR with other digital collections

Queensland University of Technology’s Institutional Repository, QUT ePrints (http://eprints.qut.edu.au/), was established in 2003. With the help of an institutional mandate (endorsed in 2004) the repository now holds over 11,000 open access publications. The repository’s success is celebrated within the University and acknowledged nationally and internationally. QUT ePrints was built on GNU EPrints open source repository software (currently running v.3.1.3) and was originally configured to accommodate open access versions of the traditional range of research publications (journal articles, conference papers, books, book chapters and working papers). However, in 2009, the repository’s scope, content and systems were broadened and the ‘QUT Digital repository’ is now a service encompassing a range of digital collections, services and systems. For a work to be accepted in to the institutional repository, at least one of the authors/creators must have a current affiliation with QUT. However, the success of QUT ePrints in terms of its capacity to increase the visibility and accessibility of our researchers' scholarly works resulted in requests to accept digital collections of works which were out of scope. To address this need, a number of parallel digital collections have been developed. These collections include, OZcase, a collection of legal research materials and ‘The Sugar Industry Collection’; a digitsed collection of books and articles on sugar cane production and processing. Additionally, the Library has responded to requests from academics for a service to support the publication of new, and existing, peer reviewed open access journals. A project is currently underway to help a group of senior QUT academics publish a new international peer reviewed journal. The QUT Digital Repository website will be a portal for access to a range of resources to support copyright management. It is likely that it will provide an access point for the institution’s data repository. The data repository, provisionally named the ‘QUT Data Commons’, is currently a work-in-progress. The metadata for some QUT datasets will also be harvested by and discoverable via ‘Research Data Australia’, the dataset discovery service managed by the Australian National Data Service (ANDS). QUT Digital repository will integrate a range of technologies and services related to scholarly communication. This paper will discuss the development of the QUT Digital Repository, its strategic functions, the stakeholders involved and lessons learned.

Fast and accurate phonetic spoken term detection

For the first time in human history, large volumes of spoken audio are being broadcast, made available on the internet, archived, and monitored for surveillance every day. New technologies are urgently required to unlock these vast and powerful stores of information. Spoken Term Detection (STD) systems provide access to speech collections by detecting individual occurrences of specified search terms. The aim of this work is to develop improved STD solutions based on phonetic indexing. In particular, this work aims to develop phonetic STD systems for applications that require open-vocabulary search, fast indexing and search speeds, and accurate term detection. Within this scope, novel contributions are made within two research themes, that is, accommodating phone recognition errors and, secondly, modelling uncertainty with probabilistic scores. A state-of-the-art Dynamic Match Lattice Spotting (DMLS) system is used to address the problem of accommodating phone recognition errors with approximate phone sequence matching. Extensive experimentation on the use of DMLS is carried out and a number of novel enhancements are developed that provide for faster indexing, faster search, and improved accuracy. Firstly, a novel comparison of methods for deriving a phone error cost model is presented to improve STD accuracy, resulting in up to a 33% improvement in the Figure of Merit. A method is also presented for drastically increasing the speed of DMLS search by at least an order of magnitude with no loss in search accuracy. An investigation is then presented of the effects of increasing indexing speed for DMLS, by using simpler modelling during phone decoding, with results highlighting the trade-off between indexing speed, search speed and search accuracy. The Figure of Merit is further improved by up to 25% using a novel proposal to utilise word-level language modelling during DMLS indexing. Analysis shows that this use of language modelling can, however, be unhelpful or even disadvantageous for terms with a very low language model probability. The DMLS approach to STD involves generating an index of phone sequences using phone recognition. An alternative approach to phonetic STD is also investigated that instead indexes probabilistic acoustic scores in the form of a posterior-feature matrix. A state-of-the-art system is described and its use for STD is explored through several experiments on spontaneous conversational telephone speech. A novel technique and framework is proposed for discriminatively training such a system to directly maximise the Figure of Merit. This results in a 13% improvement in the Figure of Merit on held-out data. The framework is also found to be particularly useful for index compression in conjunction with the proposed optimisation technique, providing for a substantial index compression factor in addition to an overall gain in the Figure of Merit. These contributions significantly advance the state-of-the-art in phonetic STD, by improving the utility of such systems in a wide range of applications.

Raman spectroscopic study of the mineral thorikosite Pb3(OH)(SbO3,AsO3)Cl2 : a mineral of archaeological significance

The mineral thorikosite Pb3(OH)(SbO3,AsO3)Cl2 is named after the ancient city of Thorikos, in the region of Attica, where the ancient mine sites dating back to the bronze ages are found. Raman spectra of the antimonate bearing mineral thorikosite Pb3(OH)(SbO3,AsO3)Cl2 were studied, and related to the structure of the mineral. Two intense Raman peaks are observed at 596 and 730 cm-1 and are assigned to the Sb3+O3 and As3+O3 stretching vibrations. A peak at 1085 cm-1 is assigned to the Sb3+OH deformation mode. Raman band at 325 cm-1 is assigned to an OAsO bending vibration of the As3+O3 units and the bands at 269 and 275 cm-1 are attributed to the OSbO bending modes of the Sb3+O3 units. The intense Raman bands at 112 and 133 cm-1 are associated with PbCl stretching modes. Minerals such as nealite and thorikosite are minerals of archaeological significance. Yet no spectroscopic studies of these minerals have been undertaken.

Discovering characteristics of stochastic collections of process models

Process models in organizational collections are typically modeled by the same team and using the same conventions. As such, these models share many characteristic features like size range, type and frequency of errors. In most cases merely small samples of these collections are available due to e.g. the sensitive information they contain. Because of their sizes, these samples may not provide an accurate representation of the characteristics of the originating collection. This paper deals with the problem of constructing collections of process models, in the form of Petri nets, from small samples of a collection for accurate estimations of the characteristics of this collection. Given a small sample of process models drawn from a real-life collection, we mine a set of generation parameters that we use to generate arbitrary-large collections that feature the same characteristics of the original collection. In this way we can estimate the characteristics of the original collection on the generated collections.We extensively evaluate the quality of our technique on various sample datasets drawn from both research and industry.

Urban Informatics Research and Insights for Libraries, Cultural Industries and Innovation Systems

Over less than a decade, we have witnessed a seismic shift in the way knowledge is produced and exchanged. This is opening up new opportunities for civic and community engagement, entrepreneurial behaviour, sustainability initiatives and creative practices. It also has the potential to create fresh challenges in areas of privacy, cyber-security and misuse of data and personal information. The field of urban informatics focuses on the use and impacts of digital media technology in urban environments. Urban informatics is a dynamic and cross-disciplinary area of inquiry that encapsulates social media, ubiquitous computing, mobile applications and location-based services. Its insights suggest the emergence of a new economic force with the potential for driving innovation, wealth and prosperity through technological advances, digital media and online networks that affect patterns of both social and economic development. Urban informatics explores the intersections between people, place and technology, and their implications for creativity, innovation and engagement. This paper examines how the key learnings from this field can be used to position creative and cultural institutions such as galleries, libraries, archives and museums (GLAM) to take advantage of the opportunities presented by these changing social and technological developments. This paper introduces the underlying principles, concepts and research areas of urban informatics, against the backdrop of modern knowledge economies. Both theoretical ideas and empirical examples are covered in this paper. The first part discusses three challenges: a. People, and the challenge of creativity: The paper explores the opportunities and challenges of urban informatics that can lead to the design and development of new tools, methods and applications fostering participation, the democratisation of knowledge, and new creative practices. b. Technology, and the challenge of innovation: The paper examines how urban informatics can be applied to support user-led innovation with a view to promoting entrepreneurial ideas and creative industries. c. Place, and the challenge of engagement: The paper discusses the potential to establish place-based applications of urban informatics, using the example of library spaces designed to deliver community and civic engagement strategies. The discussion of these challenges is illustrated by a review of projects as examples drawn from diverse fields such as urban computing, locative media, community activism, and sustainability initiatives. The second part of the paper introduces an empirically grounded case study that responds to these three challenges: The Edge, the Queensland Government’s Digital Culture Centre which is an initiative of the State Library of Queensland to explore the nexus of technology and culture in an urban environment. The paper not only explores the new role of libraries in the knowledge economy, but also how the application of urban informatics in prototype engagement spaces such as The Edge can provide transferable insights that can inform the design and development of responsive and inclusive new library spaces elsewhere. To set the scene and background, the paper begins by drawing the bigger picture and outlining some key characteristics of the knowledge economy and the role that the creative and cultural industries play in it, grasping new opportunities that can contribute to the prosperity of Australia.

Raman spectroscopy of the multi-anion mineral mallestigite Pb3Sb5+(SO4)(AsO4)(OH)6•3H2O – a mineral of archaeological significance

Some minerals are formed which show poorly defined X-ray diffraction patterns. Vibrational spectroscopy offers one of the few methods for the assessment of the structure of the oxyanions in such minerals. Among this group of minerals is mallestigite with formula Pb3Sb5+(SO4)(AsO4)(OH)6•3H2O. The objective of this research is to determine the molecular structure of the mineral mallestigite using vibrational spectroscopy. Raman and infrared bands are attributed to the AsO43- , SO42- and water stretching vibrations. Mallestigite is a mineral formed in ancient waste dumps such as occurs at Mallestiger, Carinthia, Austria and as such is a mineral of archaeological significance.