Towards semantic search and inference in electronic medical records : an approach using concept-based information retrieval

For more than a decade research in the field of context aware computing has aimed to find ways to exploit situational information that can be detected by mobile computing and sensor technologies. The goal is to provide people with new and improved applications, enhanced functionality and better use experience (Dey, 2001). Early applications focused on representing or computing on physical parameters, such as showing your location and the location of people or things around you. Such applications might show where the next bus is, which of your friends is in the vicinity and so on. With the advent of social networking software and microblogging sites such as Facebook and Twitter, recommender systems and so on context-aware computing is moving towards mining the social web in order to provide better representations and understanding of context, including social context. In this paper we begin by recapping different theoretical framings of context. We then discuss the problem of context- aware computing from a design perspective.

Semantics-based web service discovery using information retrieval techniques

This paper demonstrates an experimental study that examines the accuracy of various information retrieval techniques for Web service discovery. The main goal of this research is to evaluate algorithms for semantic web service discovery. The evaluation is comprehensively benchmarked using more than 1,700 real-world WSDL documents from INEX 2010 Web Service Discovery Track dataset. For automatic search, we successfully use Latent Semantic Analysis and BM25 to perform Web service discovery. Moreover, we provide linking analysis which automatically links possible atomic Web services to meet the complex requirements of users. Our fusion engine recommends a final result to users. Our experiments show that linking analysis can improve the overall performance of Web service discovery. We also find that keyword-based search can quickly return results but it has limitation of understanding users’ goals.

A quantum information retrieval approach to memory

As computers approach the physical limits of information storable in memory, new methods will be needed to further improve information storage and retrieval. We propose a quantum inspired vector based approach, which offers a contextually dependent mapping from the subsymbolic to the symbolic representations of information. If implemented computationally, this approach would provide exceptionally high density of information storage, without the traditionally required physical increase in storage capacity. The approach is inspired by the structure of human memory and incorporates elements of Gardenfors’ Conceptual Space approach and Humphreys et al.’s matrix model of memory.

Towards semantic search and inference in electronic medical records : an approach using concept-based information retrieval

Background This paper presents a novel approach to searching electronic medical records that is based on concept matching rather than keyword matching. Aim The concept-based approach is intended to overcome specific challenges we identified in searching medical records. Method Queries and documents were transformed from their term-based originals into medical concepts as defined by the SNOMED-CT ontology. Results Evaluation on a real-world collection of medical records showed our concept-based approach outperformed a keyword baseline by 25% in Mean Average Precision. Conclusion The concept-based approach provides a framework for further development of inference based search systems for dealing with medical data.

Efficient safety information retrieval on construction sites: a preliminary methodology

IT-supported field data management benefits on-site construction management by improving accessibility to the information and promoting efficient communication between project team members. However, most of on-site safety inspections still heavily rely on subjective judgment and manual reporting processes and thus observers’ experiences often determine the quality of risk identification and control. This study aims to develop a methodology to efficiently retrieve safety-related information so that the safety inspectors can easily access to the relevant site safety information for safer decision making. The proposed methodology consists of three stages: (1) development of a comprehensive safety database which contains information of risk factors, accident types, impact of accidents and safety regulations; (2) identification of relationships among different risk factors based on statistical analysis methods; and (3) user-specified information retrieval using data mining techniques for safety management. This paper presents an overall methodology and preliminary results of the first stage research conducted with 101 accident investigation reports.

AEHRC & QUT at TREC 2011 Medical Track : a concept-based information retrieval approach

The Australian e-Health Research Centre and Queensland University of Technology recently participated in the TREC 2011 Medical Records Track. This paper reports on our methods, results and experience using a concept-based information retrieval approach. Our concept-based approach is intended to overcome specific challenges we identify in searching medical records. Queries and documents are transformed from their term-based originals into medical concepts as de ned by the SNOMED-CT ontology. Results show our concept-based approach performed above the median in all three performance metrics: bref (+12%), R-prec (+18%) and Prec@10 (+6%).

Exploiting medical hierarchies for concept-based information retrieval

Search technologies are critical to enable clinical sta to rapidly and e ectively access patient information contained in free-text medical records. Medical search is challenging as terms in the query are often general but those in rel- evant documents are very speci c, leading to granularity mismatch. In this paper we propose to tackle granularity mismatch by exploiting subsumption relationships de ned in formal medical domain knowledge resources. In symbolic reasoning, a subsumption (or `is-a') relationship is a parent-child rela- tionship where one concept is a subset of another concept. Subsumed concepts are included in the retrieval function. In addition, we investigate a number of initial methods for combining weights of query concepts and those of subsumed concepts. Subsumption relationships were found to provide strong indication of relevant information; their inclusion in retrieval functions yields performance improvements. This result motivates the development of formal models of rela- tionships between medical concepts for retrieval purposes.

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.

Efficient safety information retrieval on construction sites : a preliminary methodology

IT-supported field data management benefits on-site construction management by improving accessibility to the information and promoting efficient communication between project team members. However, most of on-site safety inspections still heavily rely on subjective judgment and manual reporting processes and thus observers’ experiences often determine the quality of risk identification and control. This study aims to develop a methodology to efficiently retrieve safety-related information so that the safety inspectors can easily access to the relevant site safety information for safer decision making. The proposed methodology consists of three stages: (1) development of a comprehensive safety database which contains information of risk factors, accident types, impact of accidents and safety regulations; (2) identification of relationships among different risk factors based on statistical analysis methods; and (3) user-specified information retrieval using data mining techniques for safety management. This paper presents an overall methodology and preliminary results of the first stage research conducted with 101 accident investigation reports.

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.

An evaluation of corpus-driven measures of medical concept similarity for information retrieval

Measures of semantic similarity between medical concepts are central to a number of techniques in medical informatics, including query expansion in medical information retrieval. Previous work has mainly considered thesaurus-based path measures of semantic similarity and has not compared different corpus-driven approaches in depth. We evaluate the effectiveness of eight common corpus-driven measures in capturing semantic relatedness and compare these against human judged concept pairs assessed by medical professionals. Our results show that certain corpus-driven measures correlate strongly (approx 0.8) with human judgements. An important finding is that performance was significantly affected by the choice of corpus used in priming the measure, i.e., used as evidence from which corpus-driven similarities are drawn. This paper provides guidelines for the implementation of semantic similarity measures for medical informatics and concludes with implications for medical information retrieval.

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.