Medical free-text to concept mapping as an information retrieval problem

Concept mapping involves determining relevant concepts from a free-text input, where concepts are defined in an external reference ontology. This is an important process that underpins many applications for clinical information reporting, derivation of phenotypic descriptions, and a number of state-of-the-art medical information retrieval methods. Concept mapping can be cast into an information retrieval (IR) problem: free-text mentions are treated as queries and concepts from a reference ontology as the documents to be indexed and retrieved. This paper presents an empirical investigation applying general-purpose IR techniques for concept mapping in the medical domain. A dataset used for evaluating medical information extraction is adapted to measure the effectiveness of the considered IR approaches. Standard IR approaches used here are contrasted with the effectiveness of two established benchmark methods specifically developed for medical concept mapping. The empirical findings show that the IR approaches are comparable with one benchmark method but well below the best benchmark.

Integrating and evaluating neural word embeddings in information retrieval

Recent advances in neural language models have contributed new methods for learning distributed vector representations of words (also called word embeddings). Two such methods are the continuous bag-of-words model and the skipgram model. These methods have been shown to produce embeddings that capture higher order relationships between words that are highly effective in natural language processing tasks involving the use of word similarity and word analogy. Despite these promising results, there has been little analysis of the use of these word embeddings for retrieval. Motivated by these observations, in this paper, we set out to determine how these word embeddings can be used within a retrieval model and what the benefit might be. To this aim, we use neural word embeddings within the well known translation language model for information retrieval. This language model captures implicit semantic relations between the words in queries and those in relevant documents, thus producing more accurate estimations of document relevance. The word embeddings used to estimate neural language models produce translations that differ from previous translation language model approaches; differences that deliver improvements in retrieval effectiveness. The models are robust to choices made in building word embeddings and, even more so, our results show that embeddings do not even need to be produced from the same corpus being used for retrieval.

A task-oriented approach to search engine usability studies

Usability is a multi-dimensional characteristic of a computer system. This paper focuses on usability as a measurement of interaction between the user and the system. The research employs a task-oriented approach to evaluate the usability of a meta search engine. This engine encourages and accepts queries of unlimited size expressed in natural language. A variety of conventional metrics developed by academic and industrial research, including ISO standards,, are applied to the information retrieval process consisting of sequential tasks. Tasks range from formulating (long) queries to interpreting and retaining search results. Results of the evaluation and analysis of the operation log indicate that obtaining advanced search engine results can be accomplished simultaneously with enhancing the usability of the interactive process. In conclusion, we discuss implications for interactive information retrieval system design and directions for future usability research. © 2008 Academy Publisher.

Towards a visually enhanced medical search engine

This paper presents the prototype of an information retrieval system for medical records that utilises visualisation techniques, namely word clouds and timelines. The system simplifies and assists information seeking tasks within the medical domain. Access to patient medical information can be time consuming as it requires practitioners to review a large number of electronic medical records to find relevant information. Presenting a summary of the content of a medical document by means of a word cloud may permit information seekers to decide upon the relevance of a document to their information need in a simple and time effective manner. We extend this intuition, by mapping word clouds of electronic medical records onto a timeline, to provide temporal information to the user. This allows exploring word clouds in the context of a patient’s medical history. To enhance the presentation of word clouds, we also provide the means for calculating aggregations and differences between patient’s word clouds.

The information systems discipline in Australian universities : a contextual framework

This chapter presents the contextual framework for the second phase of a multi-method, multiple study of the information systems (IS) academic discipline in Australia. The chapter outlines the genesis of a two-phase Australian study, and positions the study as the precursor to a larger Pacific-Asia study. Analysis of existing literature on the state of IS and on relevant theory underpins a series of individual Australian state case studies summarised in this chapter and represented as separate chapters in the book. This chapter outlines the methodological approach employed, with emphasis on the case-study method of the multiple state studies. The process of multiple peer review of the studies is described. Importantly, this chapter summarises and analyses each of the subsequent chapters of this book, emphasising the role of a framework developed to guide much of the data gathering and analysis. This chapter also highlights the process involved in conducting the meta-analysis reported in the final chapter of this book, and summarises some of the main results of the meta-analysis.

Rough set-based reasoning and pattern mining for information filtering

An information filtering (IF) system monitors an incoming document stream to find the documents that match the information needs specified by the user profiles. To learn to use the user profiles effectively is one of the most challenging tasks when developing an IF system. With the document selection criteria better defined based on the users’ needs, filtering large streams of information can be more efficient and effective. To learn the user profiles, term-based approaches have been widely used in the IF community because of their simplicity and directness. Term-based approaches are relatively well established. However, these approaches have problems when dealing with polysemy and synonymy, which often lead to an information overload problem. Recently, pattern-based approaches (or Pattern Taxonomy Models (PTM) [160]) have been proposed for IF by the data mining community. These approaches are better at capturing sematic information and have shown encouraging results for improving the effectiveness of the IF system. On the other hand, pattern discovery from large data streams is not computationally efficient. Also, these approaches had to deal with low frequency pattern issues. The measures used by the data mining technique (for example, “support” and “confidences”) to learn the profile have turned out to be not suitable for filtering. They can lead to a mismatch problem. This thesis uses the rough set-based reasoning (term-based) and pattern mining approach as a unified framework for information filtering to overcome the aforementioned problems. This system consists of two stages - topic filtering and pattern mining stages. The topic filtering stage is intended to minimize information overloading by filtering out the most likely irrelevant information based on the user profiles. A novel user-profiles learning method and a theoretical model of the threshold setting have been developed by using rough set decision theory. The second stage (pattern mining) aims at solving the problem of the information mismatch. This stage is precision-oriented. A new document-ranking function has been derived by exploiting the patterns in the pattern taxonomy. The most likely relevant documents were assigned higher scores by the ranking function. Because there is a relatively small amount of documents left after the first stage, the computational cost is markedly reduced; at the same time, pattern discoveries yield more accurate results. The overall performance of the system was improved significantly. The new two-stage information filtering model has been evaluated by extensive experiments. Tests were based on the well-known IR bench-marking processes, using the latest version of the Reuters dataset, namely, the Reuters Corpus Volume 1 (RCV1). The performance of the new two-stage model was compared with both the term-based and data mining-based IF models. The results demonstrate that the proposed information filtering system outperforms significantly the other IF systems, such as the traditional Rocchio IF model, the state-of-the-art term-based models, including the BM25, Support Vector Machines (SVM), and Pattern Taxonomy Model (PTM).

Recommending best answer in a collaborative question answering system

The World Wide Web has become a medium for people to share information. People use Web-based collaborative tools such as question answering (QA) portals, blogs/forums, email and instant messaging to acquire information and to form online-based communities. In an online QA portal, a user asks a question and other users can provide answers based on their knowledge, with the question usually being answered by many users. It can become overwhelming and/or time/resource consuming for a user to read all of the answers provided for a given question. Thus, there exists a need for a mechanism to rank the provided answers so users can focus on only reading good quality answers. The majority of online QA systems use user feedback to rank users’ answers and the user who asked the question can decide on the best answer. Other users who didn’t participate in answering the question can also vote to determine the best answer. However, ranking the best answer via this collaborative method is time consuming and requires an ongoing continuous involvement of users to provide the needed feedback. The objective of this research is to discover a way to recommend the best answer as part of a ranked list of answers for a posted question automatically, without the need for user feedback. The proposed approach combines both a non-content-based reputation method and a content-based method to solve the problem of recommending the best answer to the user who posted the question. The non-content method assigns a score to each user which reflects the users’ reputation level in using the QA portal system. Each user is assigned two types of non-content-based reputations cores: a local reputation score and a global reputation score. The local reputation score plays an important role in deciding the reputation level of a user for the category in which the question is asked. The global reputation score indicates the prestige of a user across all of the categories in the QA system. Due to the possibility of user cheating, such as awarding the best answer to a friend regardless of the answer quality, a content-based method for determining the quality of a given answer is proposed, alongside the non-content-based reputation method. Answers for a question from different users are compared with an ideal (or expert) answer using traditional Information Retrieval and Natural Language Processing techniques. Each answer provided for a question is assigned a content score according to how well it matched the ideal answer. To evaluate the performance of the proposed methods, each recommended best answer is compared with the best answer determined by one of the most popular link analysis methods, Hyperlink-Induced Topic Search (HITS). The proposed methods are able to yield high accuracy, as shown by correlation scores: Kendall correlation and Spearman correlation. The reputation method outperforms the HITS method in terms of recommending the best answer. The inclusion of the reputation score with the content score improves the overall performance, which is measured through the use of Top-n match scores.

Evidence-based practice : information professionals' experience of information literacy in the workplace

Evidence-based practice is increasingly being recognised as an important issue in a range of professional contexts including education, nursing, occupational therapy and librarianship. Many of these professions have observed a relationship or interface between evidence-based practice and information literacy. Using a phenomenographic approach this research explores variation in the how library and information professionals are experiencing evidence-based practice as part of their professional work. The findings of the research provide a basis for arguing that evidence-based practice represents the professional's enactment of information literacy in the workplace.

Scalability of encryption techniques for electronic health record (EHR) retrieval

Electronic Health Record (EHR) retrieval processes are complex demanding Information Technology (IT) resources exponentially in particular memory usage. Database-as-a-service (DAS) model approach is proposed to meet the scalability factor of EHR retrieval processes. A simulation study using ranged of EHR records with DAS model was presented. The bucket-indexing model incorporated partitioning fields and bloom filters in a Singleton design pattern were used to implement custom database encryption system. It effectively provided faster responses in the range query compared to different types of queries used such as aggregation queries among the DAS, built-in encryption and the plain-text DBMS. The study also presented with constraints around the approach should consider for other practical applications.

A secure telehealth system for ubiquitous health environment

U-Healthcare means that it provides healthcare services "at anytime and anywhere" using wired, wireless and ubiquitous sensor network technologies. As a main field of U-healthcare, Telehealth has been developed as an enhancement of Telemedicine. This system includes two-way interactive web-video communications, sensor technology, and health informatics. With these components, it will assist patients to receive their first initial diagnosis. Futhermore, Telehealth will help doctors diagnose patient's diseases at early stages and recommend treatments to patients. However, this system has a few limitations such as privacy issues, interruption of real-time service and a wrong ordering from remote diagnosis. To deal with those flaws, security procedures such as authorised access should be applied to as an indispensible component in medical environment. As a consequence, Telehealth system with these protection procedures in clinical services will cope with anticipated vulnerabilities of U-Healthcare services and security issues involved.

Impact of the social networking applications for health information management for patients and physicians

Most social network users hold more than one social network account and utilize them in different ways depending on the digital context. For example, friendly chat on Facebook, professional discussion on LinkedIn, and health information exchange on PatientsLikeMe. Thus many web users need to manage many disparate profiles across many distributed online sources. Maintaining these profiles is cumbersome, time consuming, inefficient, and leads to lost opportunity. In this paper we propose a framework for multiple profile management of online social networks and showcase a demonstrator utilising an open source platform. The result of the research enables a user to create and manage an integrated profile and share/synchronise their profiles with their social networks. A number of use cases were created to capture the functional requirements and describe the interactions between users and the online services. An innovative application of this project is in public health informatics. We utilize the prototype to examine how the framework can benefit patients and physicians. The framework can greatly enhance health information management for patients and more importantly offer a more comprehensive personal health overview of patients to physicians.

Retrieval of health advice on the web: AEHRC at ShARe/CLEF eHealth Evaluation Lab Task 3

This paper details the participation of the Australian e- Health Research Centre (AEHRC) in the ShARe/CLEF 2013 eHealth Evaluation Lab { Task 3. This task aims to evaluate the use of information retrieval (IR) systems to aid consumers (e.g. patients and their relatives) in seeking health advice on the Web. Our submissions to the ShARe/CLEF challenge are based on language models generated from the web corpus provided by the organisers. Our baseline system is a standard Dirichlet smoothed language model. We enhance the baseline by identifying and correcting spelling mistakes in queries, as well as expanding acronyms using AEHRC's Medtex medical text analysis platform. We then consider the readability and the authoritativeness of web pages to further enhance the quality of the document ranking. Measures of readability are integrated in the language models used for retrieval via prior probabilities. Prior probabilities are also used to encode authoritativeness information derived from a list of top-100 consumer health websites. Empirical results show that correcting spelling mistakes and expanding acronyms found in queries signi cantly improves the e ectiveness of the language model baseline. Readability priors seem to increase retrieval e ectiveness for graded relevance at early ranks (nDCG@5, but not precision), but no improvements are found at later ranks and when considering binary relevance. The authoritativeness prior does not appear to provide retrieval gains over the baseline: this is likely to be because of the small overlap between websites in the corpus and those in the top-100 consumer-health websites we acquired.

A reputation-enhanced recommender system

Reputation systems are employed to provide users with advice on the quality of items on the Web, based on the aggregated value of user-based ratings. Recommender systems are used online to suggest items to users according to the users, expressed preferences. Yet, recommender systems will endorse an item regardless of its reputation value. In this paper, we report the incorporation of reputation models into recommender systems to enhance the accuracy of recommendations. The proposed method separates the implementation of recommender and reputation systems for generality. Our experiment showed that the proposed method could enhance the accuracy of existing recommender systems.

A tag-based personalized item recommendation system using tensor modeling and topic model approaches

This research falls in the area of enhancing the quality of tag-based item recommendation systems. It aims to achieve this by employing a multi-dimensional user profile approach and by analyzing the semantic aspects of tags. Tag-based recommender systems have two characteristics that need to be carefully studied in order to build a reliable system. Firstly, the multi-dimensional correlation, called as tag assignment , should be appropriately modelled in order to create the user profiles [1]. Secondly, the semantics behind the tags should be considered properly as the flexibility with their design can cause semantic problems such as synonymy and polysemy [2]. This research proposes to address these two challenges for building a tag-based item recommendation system by employing tensor modeling as the multi-dimensional user profile approach, and the topic model as the semantic analysis approach. The first objective is to optimize the tensor model reconstruction and to improve the model performance in generating quality rec-ommendation. A novel Tensor-based Recommendation using Probabilistic Ranking (TRPR) method [3] has been developed. Results show this method to be scalable for large datasets and outperforming the benchmarking methods in terms of accuracy. The memory efficient loop implements the n-mode block-striped (matrix) product for tensor reconstruction as an approximation of the initial tensor. The probabilistic ranking calculates the probabil-ity of users to select candidate items using their tag preference list based on the entries generated from the reconstructed tensor. The second objective is to analyse the tag semantics and utilize the outcome in building the tensor model. This research proposes to investigate the problem using topic model approach to keep the tags nature as the “social vocabulary” [4]. For the tag assignment data, topics can be generated from the occurrences of tags given for an item. However there is only limited amount of tags availa-ble to represent items as collection of topics, since an item might have only been tagged by using several tags. Consequently, the generated topics might not able to represent the items appropriately. Furthermore, given that each tag can belong to any topics with various probability scores, the occurrence of tags cannot simply be mapped by the topics to build the tensor model. A standard weighting technique will not appropriately calculate the value of tagging activity since it will define the context of an item using a tag instead of a topic.