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.

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.

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.

A tensor encoding model of word meaning : theory and application to information retrieval

This project was a step forward in developing and evaluating a novel, mathematical model that can deduce the meaning of words based on their use in language. This model can be applied to a wide range of natural language applications, including the information seeking process most of us undertake on a daily basis.

Postgraduate response to an information retrieval credit course

Information skills instruction for research candidates bas recently been formalised as coursework at the Queensland University of Technology. Feedback solicited from participants suggests that students benefit from such coursework in a number of ways. Their perception of the value of specific content areas to their literature review and thesis presentation is favourable. A small group of students who participated in Interviews identified five ways in which the coursework assisted the research process. As Instructors continue to work with the post·graduate community it would be useful to deepen our understanding of how such instruction is perceived and the benefits which can be derived from it.

A formalization of logical imaging for information retrieval using quantum theory

In this paper we introduce a formalization of Logical Imaging applied to IR in terms of Quantum Theory through the use of an analogy between states of a quantum system and terms in text documents. Our formalization relies upon the Schrodinger Picture, creating an analogy between the dynamics of a physical system and the kinematics of probabilities generated by Logical Imaging. By using Quantum Theory, it is possible to model more precisely contextual information in a seamless and principled fashion within the Logical Imaging process. While further work is needed to empirically validate this, the foundations for doing so are provided.

Revisiting logical imaging for information retrieval

Retrieval with Logical Imaging is derived from belief revision and provides a novel mechanism for estimating the relevance of a document through logical implication (i.e. P(q -> d)). In this poster, we perform the first comprehensive evaluation of Logical Imaging (LI) in Information Retrieval (IR) across several TREC test Collections. When compared against standard baseline models, we show that LI fails to improve performance. This failure can be attributed to a nuance within the model that means non-relevant documents are promoted in the ranking, while relevant documents are demoted. This is an important contribution because it not only contextualizes the effectiveness of LI, but crucially ex- plains why it fails. By addressing this nuance, future LI models could be significantly improved.

On the use of complex numbers in quantum models for information retrieval

Quantum-inspired models have recently attracted increasing attention in Information Retrieval. An intriguing characteristic of the mathematical framework of quantum theory is the presence of complex numbers. However, it is unclear what such numbers could or would actually represent or mean in Information Retrieval. The goal of this paper is to discuss the role of complex numbers within the context of Information Retrieval. First, we introduce how complex numbers are used in quantum probability theory. Then, we examine van Rijsbergen’s proposal of evoking complex valued representations of informations objects. We empirically show that such a representation is unlikely to be effective in practice (confuting its usefulness in Information Retrieval). We then explore alternative proposals which may be more successful at realising the power of complex numbers.

Creation of a new evaluation benchmark for information retrieval targeting patient information needs

Searching for health advice on the web is becoming increasingly common. Because of the great importance of this activity for patients and clinicians and the effect that incorrect information may have on health outcomes, it is critical to present relevant and valuable information to a searcher. Previous evaluation campaigns on health information retrieval (IR) have provided benchmarks that have been widely used to improve health IR and record these improvements. However, in general these benchmarks have targeted the specialised information needs of physicians and other healthcare workers. In this paper, we describe the development of a new collection for evaluation of effectiveness in IR seeking to satisfy the health information needs of patients. Our methodology features a novel way to create statements of patients’ information needs using realistic short queries associated with patient discharge summaries, which provide details of patient disorders. We adopt a scenario where the patient then creates a query to seek information relating to these disorders. Thus, discharge summaries provide us with a means to create contextually driven search statements, since they may include details on the stage of the disease, family history etc. The collection will be used for the first time as part of the ShARe/-CLEF 2013 eHealth Evaluation Lab, which focuses on natural language processing and IR for clinical care.

Combining word semantics within complex Hilbert space for information retrieval

Complex numbers are a fundamental aspect of the mathematical formalism of quantum physics. Quantum-like models developed outside physics often overlooked the role of complex numbers. Specifically, previous models in Information Retrieval (IR) ignored complex numbers. We argue that to advance the use of quantum models of IR, one has to lift the constraint of real-valued representations of the information space, and package more information within the representation by means of complex numbers. As a first attempt, we propose a complex-valued representation for IR, which explicitly uses complex valued Hilbert spaces, and thus where terms, documents and queries are represented as complex-valued vectors. The proposal consists of integrating distributional semantics evidence within the real component of a term vector; whereas, ontological information is encoded in the imaginary component. Our proposal has the merit of lifting the role of complex numbers from a computational byproduct of the model to the very mathematical texture that unifies different levels of semantic information. An empirical instantiation of our proposal is tested in the TREC Medical Record task of retrieving cohorts for clinical studies.

ShARe/CLEF eHealth Evaluation Lab 2013, Task 3: Information retrieval to address patients' questions when reading clinical reports

This paper presents the results of task 3 of the ShARe/CLEF eHealth Evaluation Lab 2013. This evaluation lab focuses on improving access to medical information on the web. The task objective was to investigate the effect of using additional information such as the discharge summaries and external resources such as medical ontologies on the IR effectiveness. The participants were allowed to submit up to seven runs, one mandatory run using no additional information or external resources, and three each using or not using discharge summaries.

Secure coprocessor-based private information retrieval without periodical preprocessing

Early works on Private Information Retrieval (PIR) focused on minimizing the necessary communication overhead. They seemed to achieve this goal but at the expense of query response time. To mitigate this weakness, protocols with secure coprocessors were introduced. They achieve optimal communication complexity and better online processing complexity. Unfortunately, all secure coprocessor-based PIR protocols require heavy periodical preprocessing. In this paper, we propose a new protocol, which is free from the periodical preprocessing while offering the optimal communication complexity and almost optimal online processing complexity. The proposed protocol is proven to be secure.

Crowdsourcing interactions : using crowdsourcing for evaluating interactive information retrieval systems

In the field of information retrieval (IR), researchers and practitioners are often faced with a demand for valid approaches to evaluate the performance of retrieval systems. The Cranfield experiment paradigm has been dominant for the in-vitro evaluation of IR systems. Alternative to this paradigm, laboratory-based user studies have been widely used to evaluate interactive information retrieval (IIR) systems, and at the same time investigate users’ information searching behaviours. Major drawbacks of laboratory-based user studies for evaluating IIR systems include the high monetary and temporal costs involved in setting up and running those experiments, the lack of heterogeneity amongst the user population and the limited scale of the experiments, which usually involve a relatively restricted set of users. In this paper, we propose an alternative experimental methodology to laboratory-based user studies. Our novel experimental methodology uses a crowdsourcing platform as a means of engaging study participants. Through crowdsourcing, our experimental methodology can capture user interactions and searching behaviours at a lower cost, with more data, and within a shorter period than traditional laboratory-based user studies, and therefore can be used to assess the performances of IIR systems. In this article, we show the characteristic differences of our approach with respect to traditional IIR experimental and evaluation procedures. We also perform a use case study comparing crowdsourcing-based evaluation with laboratory-based evaluation of IIR systems, which can serve as a tutorial for setting up crowdsourcing-based IIR evaluations.

Understanding negation and family history to improve clinical information retrieval

We present a study to understand the effect that negated terms (e.g., "no fever") and family history (e.g., "family history of diabetes") have on searching clinical records. Our analysis is aimed at devising the most effective means of handling negation and family history. In doing so, we explicitly represent a clinical record according to its different content types: negated, family history and normal content; the retrieval model weights each of these separately. Empirical evaluation shows that overall the presence of negation harms retrieval effectiveness while family history has little effect. We show negation is best handled by weighting negated content (rather than the common practise of removing or replacing it). However, we also show that many queries benefit from the inclusion of negated content and that negation is optimally handled on a per-query basis. Additional evaluation shows that adaptive handing of negated and family history content can have significant benefits.

Relevation! : an open source system for information retrieval relevance assessment

Relevation! is a system for performing relevance judgements for information retrieval evaluation. Relevation! is web-based, fully configurable and expandable; it allows researchers to effectively collect assessments and additional qualitative data. The system is easily deployed allowing assessors to smoothly perform their relevance judging tasks, even remotely. Relevation! is available as an open source project at: http://ielab.github.io/relevation.