Exploiting SNOMED CT concepts and relationships for clinical information retrieval : Australian e-Health Research Centre and Queensland University of Technology at the TREC 2012 Medical Track

The Australian e-Health Research Centre and Queensland University of Technology recently participated in the TREC 2012 Medical Records Track. This paper reports on our methods, results and experience using an approach that exploits the concept and inter-concept relationships defined in the SNOMED CT medical ontology. Our concept-based approach is intended to overcome specific challenges in searching medical records, namely vocabulary mismatch and granularity mismatch. Queries and documents are transformed from their term-based originals into medical concepts as defined by the SNOMED CT ontology, this is done to tackle vocabulary mismatch. In addition, we make use of the SNOMED CT parent-child `is-a' relationships between concepts to weight documents that contained concept subsumed by the query concepts; this is done to tackle the problem of granularity mismatch. Finally, we experiment with other SNOMED CT relationships besides the is-a relationship to weight concepts related to query concepts. Results show our concept-based approach performed significantly above the median in all four performance metrics. Further improvements are achieved by the incorporation of weighting subsumed concepts, overall leading to improvement above the median of 28% infAP, 10% infNDCG, 12% R-prec and 7% Prec@10. The incorporation of other relations besides is-a demonstrated mixed results, more research is required to determined which SNOMED CT relationships are best employed when weighting related concepts.

Defining and describing what we do : doctrinal legal research

The practitioner lawyer of the past had little need to reflect on process. The doctrinal research methodology developed intuitively within the common law — a research method at the core of practice. There was no need to justify or classify it within a broader research framework. Modern academic lawyers are facing a different situation. At a time when competition for limited research funds is becoming more intense, and in which interdisciplinary work is highly valued and non-lawyers are involved in the assessment of grant applications, lawyer-applicants who engage in doctrinal research need to be able to explain their methodology more clearly. Doctrinal scholars need to be more open and articulate about their methods. These methods may be different in different contexts. This paper examines the doctrinal method used in legal research and its place in recent research dialogue. Some commentators are of the view that the doctrinal method is simply scholarship rather than a separate research methodology. Richard Posner even suggests that law is ‘not a field with a distinct methodology, but an amalgam of applied logic, rhetoric, economics and familiarity with a specialized vocabulary and a particular body of texts, practices, and institutions ...’.1 Therefore, academic lawyers are beginning to realise that the doctrinal research methodology needs clarification for those outside the legal profession and that a discussion about the standing and place of doctrinal research compared to other methodologies is required.

Learning personalized tag ontology from user tagging information

The cross-sections of the Social Web and the Semantic Web has put folksonomy in the spot light for its potential in overcoming knowledge acquisition bottleneck and providing insight for "wisdom of the crowds". Folksonomy which comes as the results of collaborative tagging activities has provided insight into user's understanding about Web resources which might be useful for searching and organizing purposes. However, collaborative tagging vocabulary poses some challenges since tags are freely chosen by users and may exhibit synonymy and polysemy problem. In order to overcome these challenges and boost the potential of folksonomy as emergence semantics we propose to consolidate the diverse vocabulary into a consolidated entities and concepts. We propose to extract a tag ontology by ontology learning process to represent the semantics of a tagging community. This paper presents a novel approach to learn the ontology based on the widely used lexical database WordNet. We present personalization strategies to disambiguate the semantics of tags by combining the opinion of WordNet lexicographers and users’ tagging behavior together. We provide empirical evaluations by using the semantic information contained in the ontology in a tag recommendation experiment. The results show that by using the semantic relationships on the ontology the accuracy of the tag recommender has been improved.

Personalization in tag ontology learning for recommendation making

Due to the explosive growth of the Web, the domain of Web personalization has gained great momentum both in the research and commercial areas. One of the most popular web personalization systems is recommender systems. In recommender systems choosing user information that can be used to profile users is very crucial for user profiling. In Web 2.0, one facility that can help users organize Web resources of their interest is user tagging systems. Exploring user tagging behavior provides a promising way for understanding users’ information needs since tags are given directly by users. However, free and relatively uncontrolled vocabulary makes the user self-defined tags lack of standardization and semantic ambiguity. Also, the relationships among tags need to be explored since there are rich relationships among tags which could provide valuable information for us to better understand users. In this paper, we propose a novel approach for learning tag ontology based on the widely used lexical database WordNet for capturing the semantics and the structural relationships of tags. We present personalization strategies to disambiguate the semantics of tags by combining the opinion of WordNet lexicographers and users’ tagging behavior together. To personalize further, clustering of users is performed to generate a more accurate ontology for a particular group of users. In order to evaluate the usefulness of the tag ontology, we use the tag ontology in a pilot tag recommendation experiment for improving the recommendation performance by exploiting the semantic information in the tag ontology. The initial result shows that the personalized information has improved the accuracy of the tag recommendation.

Spatio temporal feature evaluation for action recognition

Spatio-Temporal interest points are the most popular feature representation in the field of action recognition. A variety of methods have been proposed to detect and describe local patches in video with several techniques reporting state of the art performance for action recognition. However, the reported results are obtained under different experimental settings with different datasets, making it difficult to compare the various approaches. As a result of this, we seek to comprehensively evaluate state of the art spatio- temporal features under a common evaluation framework with popular benchmark datasets (KTH, Weizmann) and more challenging datasets such as Hollywood2. The purpose of this work is to provide guidance for researchers, when selecting features for different applications with different environmental conditions. In this work we evaluate four popular descriptors (HOG, HOF, HOG/HOF, HOG3D) using a popular bag of visual features representation, and Support Vector Machines (SVM)for classification. Moreover, we provide an in-depth analysis of local feature descriptors and optimize the codebook sizes for different datasets with different descriptors. In this paper, we demonstrate that motion based features offer better performance than those that rely solely on spatial information, while features that combine both types of data are more consistent across a variety of conditions, but typically require a larger codebook for optimal performance.

Graph-based concept weighting for medical information retrieval

This paper presents a graph-based method to weight medical concepts in documents for the purposes of information retrieval. Medical concepts are extracted from free-text documents using a state-of-the-art technique that maps n-grams to concepts from the SNOMED CT medical ontology. In our graph-based concept representation, concepts are vertices in a graph built from a document, edges represent associations between concepts. This representation naturally captures dependencies between concepts, an important requirement for interpreting medical text, and a feature lacking in bag-of-words representations. We apply existing graph-based term weighting methods to weight medical concepts. Using concepts rather than terms addresses vocabulary mismatch as well as encapsulates terms belonging to a single medical entity into a single concept. In addition, we further extend previous graph-based approaches by injecting domain knowledge that estimates the importance of a concept within the global medical domain. Retrieval experiments on the TREC Medical Records collection show our method outperforms both term and concept baselines. More generally, this work provides a means of integrating background knowledge contained in medical ontologies into data-driven information retrieval approaches.

Of repetition and of song

Allyson Reynolds, for many years now, has been a keen student of nature. Nature’s forms have always been important to her work, but it would be wrong to see Reynolds as simply transcribing directly from the natural world. For this artist, nature and the natural world represents an elusive invitation and so Reynolds doesn’t so much paint from nature, although resemblance and imitation are clearly evident, as work to render visually and emotionally tangible this invitation. And for a viewer this is no small thing as the invitation is to become attuned and connect with nature as it exists in ourselves, that is to see as nature. Reynolds’ is inviting us as viewers to connect and participate with the nature of nature that is evident in ourselves through the act of perceiving. Reynolds’ work can do this because it is a work born of deep evocation. The sensibility from which it emerges or is transacted is poetic, intensely so, but more than that it works to make of viewing an act of poetry, through a celebration of seeing. Reynolds evocation is born of a deep feeling towards and contemplation of the natural world - it is as though the world lives in her and is now a seamless part of her creative vocabulary. In such personal work there is a profoundly felt and revealed sense of the intimate and like true intimacy it revels in both its dark and quiet, as well as its playful and light, aspects. What is special about Reynolds’ visual poetry is that it able to render this intimacy so accessible. It is an accessibility that is available for the viewer who is able to not only look but also surrender to that looking, accepting and working with the flow of thoughts and associations it occasions...

Personalized recommender systems integrating tags and item taxonomy

The social tags in Web 2.0 are becoming another important information source to profile users' interests and preferences to make personalized recommendations. To solve the problem of low information sharing caused by the free-style vocabulary of tags and the long tails of the distribution of tags and items, this paper proposes an approach to integrate the social tags given by users and the item taxonomy with standard vocabulary and hierarchical structure provided by experts to make personalized recommendations. The experimental results show that the proposed approach can effectively improve the information sharing and recommendation accuracy.

The effects of linguistic factors on student performance on economics multiple choice questions

This paper proposes a framework to analyse performance on multiple choice questions with the focus on linguistic factors. Item Response Theory (IRT) is deployed to estimate ability and question difficulty levels. A logistic regression model is used to detect Differential Item Functioning questions. Probit models testify relationships between performance and linguistic factors controlling the effects of question construction and students’ background. Empirical results have important implications. The lexical density of stems affects performance. The use of non-Economics specialised vocabulary has differing impacts on the performance of students with different language backgrounds. The IRT-based ability and difficulty help explain performance variations.

Basic cognitive experiences and definitions in the Longman Dictionary of Contemporary English

This study applies theories of cognitive linguistics to the compilation of English learners’ dictionaries. Specifically, it employs the concepts of basic level categories and image schemas, two basic cognitive experiences, to examine the ‘definition proper’ of English dictionaries for foreign learners. In the study, the definition proper refers to the constituent part of a reference work that provides an explanation of the meanings of a word, phrase or term. This rationalization mainly consists of defining vocabulary, sense division and arrangement, as well as the means of defining (i.e. paraphrase, true definition, functional definition, and pictorial illustration). The aim of the study is to suggest ways of aligning the consultation and learning of definitions with dictionary users’ cognitive experiences. For this purpose, an analysis of the definition proper of the fourth edition of the Longman Dictionary of Contemporary English (LDOCE4) from the perspective of basic cognitive experiences has been undertaken. The study found that, generally, the lexicographic practices of LDOCE4 are consistent with theories of cognitive linguistics. However, there exist shortcomings that result from disregarding basic cognitive experiences.

Supporting children's language and literacy skills : the effectiveness of shared book reading intervention strategies with parents

Parents are encouraged to read with their children from an early age because shared book reading helps children to develop their language and early literacy skills. A pragmatic Randomised Controlled Trial (RCT) research design was adopted to investigate the influence of two forms of a shared reading intervention (Dialogic Reading and Dialogic Reading with the addition of Print Referencing) on children’s language and literacy skills. Dialogic reading is a validated shared reading intervention that has been shown to improve children’s oral language skills prior to formal schooling (Whitehurst & Lonigan, 1998). Print referencing is another form of shared reading intervention that has the potential to have effects on children’s print knowledge as they begin school (Justice & Ezell, 2002). However, training parents to use print referencing strategies at home has not been researched extensively although research findings indicate its effectiveness when used by teachers in the early years of school. Eighty parents of Preparatory year children from three Catholic schools in low income areas in the outer suburbs of a metropolitan city were trained to deliver specific shared reading strategies in an eight-week home intervention. Parents read eight books to their children across the period of the intervention. Each book was requested to be read at least three times a week. There were 42 boys and 38 girls ranging in age from 4.92 years to 6.25 years (M=5.53, SD=0.33) in the sample. The families were randomly assigned to three groups: Dialogic Reading (DR); Dialogic Reading with the addition of Print Referencing (DR + PR); and a Control group. Six measures were used to assess children’s language skills at pre and post, and follow-up (three months after the intervention). These measures assessed oral language (receptive and expressive vocabulary), phonological awareness skills (rhyme, word completion), alphabet knowledge, and concepts about print. Results of the intervention showed that there were significant differences from pre to post between the two intervention groups and the control group on three measures: expressive vocabulary, rhyme, and concepts about print. The shared reading strategies delivered by parents of the dialogic reading, and dialogic reading with the addition of print referencing, showed promising results to develop children’s oral language skills in terms of expressive vocabulary and rhyme, as well as understanding of the concepts about print. At follow-up, when the children entered Year 1, the two intervention groups (DR and DR + PR) group had significantly maintained their knowledge of concepts about prints when compared with the control group. Overall, the findings from this intervention study did not show that dialogic reading with the addition of print referencing had stronger effects on children’s early literacy skills than dialogic reading alone. The research also explored if pre-existing family factors impacted on the outcomes of the intervention from pre to post. The relationships between maternal education and home reading practices prior to intervention and child outcomes at post were considered. However, there were no significant effects of maternal education and home literacy activities on child outcomes at post. Additionally, there were no significant effects for the level of compliance of parents with the intervention program in terms of regular weekly reading to children during the intervention period on child outcomes at post. These non-significant findings are attributed to the lack of variability in the recruited sample. Parents participating in the intervention had high levels of education, although they were recruited from schools in low socio-economic areas; parents were already highly engaged in home literacy activities at recruitment; and the parents were highly compliant in reading regularly to their child during the intervention. Findings of the current study did show that training in shared reading strategies enhanced children’s early language and literacy skills. Both dialogic reading and dialogic reading with the addition of print referencing improved children’s expressive vocabulary, rhyme, and concepts about print at post intervention. Further research is needed to identify how, and if, print referencing strategies used by parents at home can be effective over and above the use of dialogic reading strategies. In this research, limitations of sample size and the nature of the intervention to use print referencing strategies at home may have restricted the opportunities for this research study to find more effects on children’s emergent literacy skills or for the effectiveness of combining dialogic reading with print referencing strategies. However, these results did indicate that there was value in teaching parents to implement shared reading strategies at home in order to improve early literacy skills as children begin formal schooling.

An ontology-based method for sparsity problem in tag recommendation

Tags or personal metadata for annotating web resources have been widely adopted in Web 2.0 sites. However, as tags are freely chosen by users, the vocabularies are diverse, ambiguous and sometimes only meaningful to individuals. Tag recommenders may assist users during tagging process. Its objective is to suggest relevant tags to use as well as to help consolidating vocabulary in the systems. In this paper we discuss our approach for providing personalized tag recommendation by making use of existing domain ontology generated from folksonomy. Specifically we evaluated the approach in sparse situation. The evaluation shows that the proposed ontology-based method has improved the accuracy of tag recommendation in this situation.

Survey and Mapping Infrastructure Regulation 2004- Comments Relating to a 10-Year Review

Democratic governments raise taxes and charges and spend revenue on delivering peace, order and good government. The delivery process begins with a legislature as that can provide a framework of legally enforceable rules enacted according to the government’s constitution. These rules confer rights and obligations that allow particular people to carry on particular functions at particular places and times. Metadata standards as applied to public records contain information about the functioning of government as distinct from the non-government sector of society. Metadata standards apply to database construction. Data entry, storage, maintenance, interrogation and retrieval depend on a controlled vocabulary needed to enable accurate retrieval of suitably catalogued records in a global information environment. Queensland’s socioeconomic progress now depends in part on technical efficiency in database construction to address queries about who does what, where and when; under what legally enforceable authority; and how the evidence of those facts is recorded. The Survey and Mapping Infrastructure Act 2003 (Qld) addresses technical aspects of where questions – typically the officially recognised name of a place and a description of its boundaries. The current 10-year review of the Survey and Mapping Regulation 2004 provides a valuable opportunity to consider whether the Regulation makes sense in the context of a number of later laws concerned with management of Public Sector Information (PSI) as well as policies for ICT hardware and software procurement. Removing ambiguities about how official place names are to be regarded on a whole-of-government basis can achieve some short term goals. Longer-term goals depend on a more holistic approach to information management – and current aspirations for more open government and community engagement are unlikely to occur without such a longer-term vision.

Middle schooling and scientific literacy : bringing the students to science

This study is about young adolescents' engagement in learning science. The middle years of schooling are critical in the development of students' interest and engagement with learning. Successful school experiences enhance dispositions towards a career related to those experiences. Poor experiences lead to negative attitudes and rejection of certain career pathways. At a time when students are becoming more aware, more independent and focused on peer relationships and social status, the high school environment in some circumstances offers more a content-centred curriculum that is less personally relevant to their lives than the social melee surrounding them. Science education can further exacerbate the situation by presenting abstract concepts that have limited contextual relevance and a seemingly difficult vocabulary that further alienates adolescents from the curriculum. In an attempt to reverse a perceived growing disinterest by students to science (Goodrum, Druhan & Abbs, 2011), a study was initiated based on a student-centred unit designed to enhance and sustain adolescent engagement in science. The premise of the study was that adolescent students are more responsive toward learning if they are given an appropriate learning environment that helps connect their learning with life beyond the school. The purpose of this study was to examine the experiences of young adolescents with the aim of transforming school learning in science into meaningful experiences that connected with their lives. Two areas were specifically canvassed and subsumed within the study to strengthen the design base. One area that of the middle schooling ideology, offered specific pedagogical approaches and a philosophical framework that could provide opportunities for reform. The other area, the construct of scientific literacy (OECD, 2007) as defined by Holbrook and Rannikmae, (2009) appeared to provide a sense of purpose for students to aim toward and value for becoming active citizens. The study reported here is a self-reflection of a teacher/researcher exploring practice and challenging existing approaches to the teaching of science in the middle years of schooling. The case study approach (Yin, 2003) was adopted to guide the design of the study. Over a 6-month period, the researcher, an experienced secondary-science teacher, designed, implemented and documented a range of student-centred pedagogical practices with a Year-7 secondary science class. Data for this case study included video recordings, journals, interviews and surveys of students. Both quantitative and qualitative data sources were employed in a partially mixed methods research approach (Leech & Onwuegbuzie, 2009) dominated by qualitative data with the concurrent collection of quantitative data to corroborate interpretations as a means of analysing and developing a model of the dynamic learning environment. The findings from the case study identified five propositions that became the basis for a model of a student-centred learning environment that was able to sustain student participation and thus engagement in science. The study suggested that adolescent student engagement can be promoted and sustained by providing a classroom climate that encourages and strengthens social interaction. Engagement in science can be enhanced by presenting developmentally appropriate challenges that require rigorous exploration of contextually relevant learning environments; supporting students to develop connections with a curriculum that aligns with their own experiences. By setting an environment empathetic to adolescent needs and understandings, students were able to actively explore phenomena collaboratively through developmentally appropriate experiences. A significant outcome of this study was the transformative experiences of an insider, the teacher as researcher, whose reflections provide an authentic model for reforming pedagogy. The model and theory presented became an adjunct to my repertoire for science teaching in the middle years of schooling. The study was rewarding in that it helped address a void in my understanding of middle years of schooling by prompting me to re-think the notion of adolescence in the context of the science classroom. This study is timely given the report "The Status and Quality of Year 11 and 12 Science in Australian Schools" (Goodrum, Druhan & Abbs, 2011) and national curricular changes that are being proposed for science (ACARA, 2009).

Acquiring search expertise : learning experiences and threshold concepts

Expert searchers engage with information as information brokers, researchers, reference librarians, information architects, faculty who teach advanced search, and in a variety of other information-intensive professions. Their experiences are characterized by a profound understanding of information concepts and skills and they have an agile ability to apply this knowledge to interacting with and having an impact on the information environment. This study explored the learning experiences of searchers to understand the acquisition of search expertise. The research question was: What can be learned about becoming an expert searcher from the learning experiences of proficient novice searchers and highly experienced searchers? The key objectives were: (1) to explore the existence of threshold concepts in search expertise; (2) to improve our understanding of how search expertise is acquired and how novice searchers, intent on becoming experts, can learn to search in more expertlike ways. The participant sample drew from two population groups: (1) highly experienced searchers with a minimum of 20 years of relevant professional experience, including LIS faculty who teach advanced search, information brokers, and search engine developers (11 subjects); and (2) MLIS students who had completed coursework in information retrieval and online searching and demonstrated exceptional ability (9 subjects). Using these two groups allowed a nuanced understanding of the experience of learning to search in expertlike ways, with data from those who search at a very high level as well as those who may be actively developing expertise. The study used semi-structured interviews, search tasks with think-aloud narratives, and talk-after protocols. Searches were screen-captured with simultaneous audio-recording of the think-aloud narrative. Data were coded and analyzed using NVivo9 and manually. Grounded theory allowed categories and themes to emerge from the data. Categories represented conceptual knowledge and attributes of expert searchers. In accord with grounded theory method, once theoretical saturation was achieved, during the final stage of analysis the data were viewed through lenses of existing theoretical frameworks. For this study, threshold concept theory (Meyer & Land, 2003) was used to explore which concepts might be threshold concepts. Threshold concepts have been used to explore transformative learning portals in subjects ranging from economics to mathematics. A threshold concept has five defining characteristics: transformative (causing a shift in perception), irreversible (unlikely to be forgotten), integrative (unifying separate concepts), troublesome (initially counter-intuitive), and may be bounded. Themes that emerged provided evidence of four concepts which had the characteristics of threshold concepts. These were: information environment: the total information environment is perceived and understood; information structures: content, index structures, and retrieval algorithms are understood; information vocabularies: fluency in search behaviors related to language, including natural language, controlled vocabulary, and finesse using proximity, truncation, and other language-based tools. The fourth threshold concept was concept fusion, the integration of the other three threshold concepts and further defined by three properties: visioning (anticipating next moves), being light on one's 'search feet' (dancing property), and profound ontological shift (identity as searcher). In addition to the threshold concepts, findings were reported that were not concept-based, including praxes and traits of expert searchers. A model of search expertise is proposed with the four threshold concepts at its core that also integrates the traits and praxes elicited from the study, attributes which are likewise long recognized in LIS research as present in professional searchers. The research provides a deeper understanding of the transformative learning experiences involved in the acquisition of search expertise. It adds to our understanding of search expertise in the context of today's information environment and has implications for teaching advanced search, for research more broadly within library and information science, and for methodologies used to explore threshold concepts.