Online Information in the Health Sciences

Features information retrieval system for health sciences. BRS information retrieval system; Full text biomedical databases; BIOSIS Information Transfer System

Fusion Techniques in Biomedical Information Retrieval

For difficult cases clinicians usually use their experience and also the information found in textbooks to determine a diagnosis. Computer tools can help them supply the relevant information now that much medical knowledge is available in digital form. A biomedical search system such as developed in the Khresmoi project (that this chapter partially reuses) has the goal to fulfil information needs of physicians. This chapter concentrates on information needs for medical cases that contain a large variety of data, from free text, structured data to images. Fusion techniques will be compared to combine the various information sources to supply cases similar to an example case given. This can supply physicians with answers to problems similar to the one they are analyzing and can help in diagnosis and treatment planning

Proof of concept: concept-based biomedical information retrieval

In this thesis we investigate the possibility to integrate domain-specific knowledge into biomedical information retrieval (IR). Recent decades have shown a fast growing interest in biomedical research, reflected by an exponential growth in scientific literature. An important problem for biomedical IR is dealing with the complex and inconsistent terminology encountered in biomedical publications. Dealing with the terminology problem requires domain knowledge stored in terminological resources: controlled indexing vocabularies and thesauri. The integration of this knowledge in modern word-based information retrieval is, however, far from trivial.\ud \ud The first research theme investigates heuristics for obtaining word-based representations from biomedical text for robust word-based retrieval. We investigated the effect of choices in document preprocessing heuristics on retrieval effectiveness. Document preprocessing heuristics such as stop word removal, stemming, and breakpoint identification and normalization were shown to strongly affect retrieval performance.\ud An effective combination of heurisitics was identified to obtain a word-based representation from text for the remainder of this thesis.\ud \ud The second research theme deals with concept-based retrieval. We compared a word-based to a concept-based representation and determined to what extent a manual concept-based representation can be automatically obatined from text. Retrieval based on only concepts was demonstrated to be significantly less effective than word-based retrieval. This deteriorated performance could be explained by errors in the classification process, limitations of the concept vocabularies and limited exhaustiveness of the concept-based document representations. Retrieval based on a combination of word-based and automatically obtained concept-based query representations did significantly improve word-only retrieval. \ud \ud In the third and last research theme we propose a cross-lingual framework for monolingual biomedical IR. In this framework, the integration of a concept-based representation is viewed as a cross-lingual matching problem involving a word-based and concept-based representation language. This framework gives us the opportunity to adopt a large set of established cross-lingual information retrieval methods and techniques for this domain. Experiments with basic term-to-term translation models demonstrate that this approach can significantly improve word-based retrieval.\ud \ud Directions for future work are using these concepts for communication between user and retrieval system, extending upon the translation models and extending CLIR-enhanced concept-based retrieval outside the biomedical domain

Method and data evaluation at NASA endocrine laboratory

The biomedical data of the astronauts on Skylab 3 were analyzed to evaluate the univariate statistical methods for comparing endocrine series experiments in relation to other medical experiments. It was found that an information storage and retrieval system was needed to facilitate statistical analyses

The Influence of Basic Tokenization on Biomedical Document Retrieval

Tokenization is a fundamental preprocessing step in Information Retrieval systems in which text is turned into index terms. This paper quantifies and compares the influence of various simple tokenization techniques on document retrieval effectiveness in two domains: biomedicine and news. As expected, biomedical retrieval is more sensitive to small changes in the tokenization method. The tokenization strategy can make the difference between a mediocre and well performing IR system, especially in the biomedical domain

Shangri-La: a medical case-based retrieval tool

Large amounts of medical visual data are produced in hospitals daily and made available continuously via publications in the scientific literature, representing the medical knowledge. However, it is not always easy to find the desired information and in clinical routine the time to fulfil an information need is often very limited. Information retrieval systems are a useful tool to provide access to these documents/images in the biomedical literature related to information needs of medical professionals. Shangri–La is a medical retrieval system that can potentially help clinicians to make decisions on difficult cases. It retrieves articles from the biomedical literature when querying a case description and attached images. The system is based on a multimodal retrieval approach with a focus on the integration of visual information connected to text. The approach includes a query–adaptive multimodal fusion criterion that analyses if visual features are suitable to be fused with text for the retrieval. Furthermore, image modality information is integrated in the retrieval step. The approach is evaluated using the ImageCLEFmed 2013 medical retrieval benchmark and can thus be compared to other approaches. Results show that the final approach outperforms the best multimodal approach submitted to ImageCLEFmed 2013