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

Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization

Concept embedding-based weighting scheme for biomedical text clustering and visualization

Biomedical text clustering is a text mining technique used to provide better document search, browsing, and retrieval in biomedical and clinical text collections. In this research, the document representation based on the concept embedding along with the proposed weighting scheme is explored. The concept embedding is learned through the neural networks to capture the associations between the concepts. The proposed weighting scheme makes use of the concept associations to build document vectors for clustering. We evaluate two types of concept embedding and new weighting scheme for text clustering and visualization on two different biomedical text collections. The returned results demonstrate that the concept embedding along with the new weighting scheme performs better than the baseline tf–idf for clustering and visualization. Based on the internal clustering evaluation metric-Davies–Bouldin index and the visualization, the concept embedding generated from aggregated word embedding can form well-separated clusters, whereas the intact concept embedding can better identify more clusters of specific diseases and gain better F-measure

Ontology-Based MEDLINE Document Classification

An increasing and overwhelming amount of biomedical information is available in the research literature mainly in the form of free-text. Biologists need tools that automate their information search and deal with the high volume and ambiguity of free-text. Ontologies can help automatic information processing by providing standard concepts and information about the relationships between concepts. The Medical Subject Headings (MeSH) ontology is already available and used by MEDLINE indexers to annotate the conceptual content of biomedical articles. This paper presents a domain-independent method that uses the MeSH ontology inter-concept relationships to extend the existing MeSH-based representation of MEDLINE documents. The extension method is evaluated within a document triage task organized by the Genomics track of the 2005 Text REtrieval Conference (TREC). Our method for extending the representation of documents leads to an improvement of 17% over a non-extended baseline in terms of normalized utility, the metric defined for the task. The SVMlight software is used to classify documents

Mining the Medical and Patent Literature to Support Healthcare and Pharmacovigilance

Recent advancements in healthcare practices and the increasing use of information technology in the medical domain has lead to the rapid generation of free-text data in forms of scientific articles, e-health records, patents, and document inventories. This has urged the development of sophisticated information retrieval and information extraction technologies. A fundamental requirement for the automatic processing of biomedical text is the identification of information carrying units such as the concepts or named entities. In this context, this work focuses on the identification of medical disorders (such as diseases and adverse effects) which denote an important category of concepts in the medical text. Two methodologies were investigated in this regard and they are dictionary-based and machine learning-based approaches. Futhermore, the capabilities of the concept recognition techniques were systematically exploited to build a semantic search platform for the retrieval of e-health records and patents. The system facilitates conventional text search as well as semantic and ontological searches. Performance of the adapted retrieval platform for e-health records and patents was evaluated within open assessment challenges (i.e. TRECMED and TRECCHEM respectively) wherein the system was best rated in comparison to several other competing information retrieval platforms. Finally, from the medico-pharma perspective, a strategy for the identification of adverse drug events from medical case reports was developed. Qualitative evaluation as well as an expert validation of the developed system's performance showed robust results. In conclusion, this thesis presents approaches for efficient information retrieval and information extraction from various biomedical literature sources in the support of healthcare and pharmacovigilance. The applied strategies have potential to enhance the literature-searches performed by biomedical, healthcare, and patent professionals. The applied strategies have potential to enhance the literature-searches performed by biomedical, healthcare, and patent professionals. This can promote the literature-based knowledge discovery, improve the safety and effectiveness of medical practices, and drive the research and development in medical and healthcare arena

A Semantic-Based Method for Extracting Concept Definitions from Scientific Publications: Evaluation in the Autism Phenotype Domain

Background: A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sentences. These approaches have not typically addressed the challenge of extracting more complex knowledge such as biomedical definitions. In our efforts to facilitate knowledge acquisition of rule-based definitions of autism phenotypes, we have developed a novel semantic-based text-mining approach that can automatically identify such definitions within text. Results: Using an existing knowledge base of 156 autism phenotype definitions and an annotated corpus of 26 source articles containing such definitions, we evaluated and compared the average rank of correctly identified rule definition or corresponding rule template using both our semantic-based approach and a standard term-based approach. We examined three separate scenarios: (1) the snippet of text contained a definition already in the knowledge base; (2) the snippet contained an alternative definition for a concept in the knowledge base; and (3) the snippet contained a definition not in the knowledge base. Our semantic-based approach had a higher average rank than the term-based approach for each of the three scenarios (scenario 1: 3.8 vs. 5.0; scenario 2: 2.8 vs. 4.9; and scenario 3: 4.5 vs. 6.2), with each comparison significant at the p-value of 0.05 using the Wilcoxon signed-rank test. Conclusions: Our work shows that leveraging existing domain knowledge in the information extraction of biomedical definitions significantly improves the correct identification of such knowledge within sentences. Our method can thus help researchers rapidly acquire knowledge about biomedical definitions that are specified and evolving within an ever-growing corpus of scientific publications

Ontology-based document representation for biomedical information retrieval

In the current era of fast sequencing of entire genomes, more data is becoming available for analysis. This data analysis, in turn, leads to an increasing amount of scientfic publications. Consequently, biologists spend a considerable part of their time searching the biomedical literature. This avoids expensive experiment duplications in wet labs, and provides inspiration for new hypotheses. Unfortunately, the fast growth of biological information, in the form of free-text, has led to a lack of standard in the naming of biological entities. As a result, different genes are referred to with the same name, or acronym, and different names refer to tlze same gene. The ambiguity of free-text is problematic, as the success of a search often relies on the matching of a query term with a term contained in the document representation. Biomedical ontologies, when available, can help disambiguate the information expressed in free-text: they provide unique terms to represent concepts and therefore counterweiglzt the occurrence of synonyms and polysems in free-text. They also contain information about the relationships between concepts. This information can be used to understand and evaluate semantic similarities between concepts. The largest repository of biomedical research literature in the world, MEDLINE, is an entry point to biomedical information for most biologists (Hersh et al., 2004). The Medical Subject Headings (MeSH) is the controlled vocabulary used in MEDLINE to annotate the conceptual content of biomedical articles. The annotations include information about the importance of MeSH concepts in the article, and their contexts. The MeSH ontology is organized in several hierarchies that indicate the level of specificity of the MeSH concepts. This hierarchical information can be used to generate semantic similarities between concepts. Our inotivation is the inzprovelnent of MEDLINE search, as it is still a central information access point for biologists in spite of the growing availability of full journal articles on the Web. In particular, we focus on the use of the MeSH ontology to represent and retrieve biomedical articles. Although MeSH is widely used by current MELDINE search methods, we show that the information contained in MEDLINE MeSH annotations and tlze MeSH hierarchies is often overlooked. We hypothesize that MeSH-based document representation can ilzzprove MEDLINE information retrieval. Specifically, our hypothesis is that the integration of iliforniatioli about concept relevance (from the MEDLINE annotation), and interconcept similarities (from tlze MeSH hierarchies), will ilzzprove retrieval performance. We evaluate methods using such information to discriminate and compare MeSH concepts. Our methods are evaluated in the context of MEDLINE ad hoc document retrieval and document binary classifications. Our evaluatiolls use standard datasets and metrics recently used at the Genonzics track of the 2005 Text Retrieval Conference workshop

Semantic annotation and summarization of biomedical text

Advancements in the biomedical community are largely documented and published in text format in scientific forums such as conference papers and journals. To address the scalability of utilizing the large volume of text-based information generated by continuing advances in the biomedical field, two complementary areas are studied. The first area is Semantic Annotation, which is a method for providing machineunderstandable information based on domain-specific resources. A novel semantic annotator, CONANN, is implemented for online matching of concepts defined by a biomedical metathesaurus. CONANN uses a multi-level filter based on both information retrieval and shallow natural language processing techniques. CONANN is evaluated against a state-of-the-art biomedical annotator using the performance measures of time (e.g. number of milliseconds per noun phrase) and precision/recall of the resulting concept matches. CONANN shows that annotation can be performed online, rather than offline, without a significant loss of precision and recall as compared to current offline systems. The second area of study is Text Summarization which is used as a way to perform data reduction of clinical trial texts while still describing the main themes of a biomedical document. The text summarization work is unique in that it focuses exclusively on summarizing biomedical full-text sources as opposed to abstracts, and also exclusively uses domain-specific concepts, rather than terms, to identify important information within a biomedical text. Two novel text summarization algorithms are implemented: one using a concept chaining method based on existing work in lexical chaining (BioChain), and the other using concept distribution to match important sentences between a source text and a generated summary (FreqDist). The BioChain and FreqDist summarizers are evaluated using the publicly-available ROUGE summary evaluation tool. ROUGE compares n-gram co-occurrences between a system summary and one or more model summaries. The text summarization evaluation shows that the two approaches outperform nearly all of the existing term-based approaches.Ph.D., Information Science and Technology -- Drexel University, 200

Factors affecting the effectiveness of biomedical document indexing and retrieval based on terminologies

International audienceThe aim of this work is to evaluate a set of indexing and retrieval strategies based on the integration of several biomedical terminologies on the available TREC Genomics collections for an ad hoc information retrieval (IR) task.Materials and methodsWe propose a multi-terminology based concept extraction approach to selecting best concepts from free text by means of voting techniques. We instantiate this general approach on four terminologies (MeSH, SNOMED, ICD-10 and GO). We particularly focus on the effect of integrating terminologies into a biomedical IR process, and the utility of using voting techniques for combining the extracted concepts from each document in order to provide a list of unique concepts.ResultsExperimental studies conducted on the TREC Genomics collections show that our multi-terminology IR approach based on voting techniques are statistically significant compared to the baseline. For example, tested on the 2005 TREC Genomics collection, our multi-terminology based IR approach provides an improvement rate of +6.98% in terms of MAP (mean average precision) (p < 0.05) compared to the baseline. In addition, our experimental results show that document expansion using preferred terms in combination with query expansion using terms from top ranked expanded documents improve the biomedical IR effectiveness.ConclusionWe have evaluated several voting models for combining concepts issued from multiple terminologies. Through this study, we presented many factors affecting the effectiveness of biomedical IR system including term weighting, query expansion, and document expansion models. The appropriate combination of those factors could be useful to improve the IR performance

Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework

This paper describes a pilot query interface that has been constructed to help us explore a "concept-based" approach for searching the Neuroscience Information Framework (NIF). The query interface is concept-based in the sense that the search terms submitted through the interface are selected from a standardized vocabulary of terms (concepts) that are structured in the form of an ontology. The NIF contains three primary resources: the NIF Resource Registry, the NIF Document Archive, and the NIF Database Mediator. These NIF resources are very different in their nature and therefore pose challenges when designing a single interface from which searches can be automatically launched against all three resources simultaneously. The paper first discusses briefly several background issues involving the use of standardized biomedical vocabularies in biomedical information retrieval, and then presents a detailed example that illustrates how the pilot concept-based query interface operates. The paper concludes by discussing certain lessons learned in the development of the current version of the interface