Query Expansion is commonly used in Information Retrieval to overcome vocabulary mismatch issues, such as synonymy between the original query terms and a relevant document. In general, query expansion experiments exhibit mixed results. Overall TREC Genomics Track results are also mixed; however, results from the top performing systems provide strong evidence supporting the need for expansion. In this paper, we examine the conditions necessary for optimal query expansion performance with respect to two system design issues: IR framework and knowledge source used for expansion. We present a query expansion framework that improves Okapi baseline passage MAP performance by 185%. Using this framework, we compare and contrast the effectiveness of a variety of biomedical knowledge sources used by TREC 2006 Genomics Track participants for expansion. Based on the outcome of these experiments, we discuss the success factors required for effective query expansion with respect to various sources of term expansion, such as corpus-based cooccurrence statistics, pseudo-relevance feedback methods, and domain-specific and domain-independent ontologies and databases. Our results show that choice of document ranking algorithm is the most important factor affecting retrieval performance on this dataset. In addition, when an appropriate ranking algorithm is used, we find that query expansion with domain-specific knowledge sources provides an equally substantive gain in performance over a baseline system.Keywords Passage retrieval for genomic queries Á Knowledge based query expansion Á Corpus based query expansion Á Pseudo relevance feedback Á Concept-based normalisation passage ranking Á TREC

Document clustering has many important applications in the area of data mining and information retrieval. Many existing document clustering techniques use the ''bag-of-words'' model to represent the content of a document. However, this representation is only effective for grouping related documents when these documents share a large proportion of lexically equivalent terms. In other words, instances of synonymy between related documents are ignored, which can reduce the effectiveness of applications using a standard full-text document representation. To address this problem, we present a new approach for clustering scientific documents, based on the utilization of citation contexts. A citation context is essentially the text surrounding the reference markers used to refer to other scientific works. We hypothesize that citation contexts will provide relevant synonymous and related vocabulary which will help increase the effectiveness of the bag-ofwords representation. In this paper, we investigate the power of these citation-specific word features, and compare them with the original document's textual representation in a document clustering task on two collections of labeled scientific journal papers from two distinct domains: High Energy Physics and Genomics. We also compare these text-based clustering techniques with a link-based clustering algorithm which determines the similarity between documents based on the number of co-citations, that is in-links represented by citing documents and out-links represented by cited documents. Our experimental results indicate that the use of citation contexts, when combined with the vocabulary in the full-text of the document, is a promising alternative means of capturing critical topics covered by journal articles. More specifically, this document representation strategy when used by the clustering algorithm investigated in this paper, outperforms both the full-text clustering approach and the link-based clustering technique on both scientific journal datasets.

In this paper we describe a type of data fusion involving the combination of evidence derived from multiple document representations. Our aim is to investigate if a composite representation can improve the online detection of novel events in a stream of broadcast news stories. This classification process otherwise known as first story detection FSD (or in the Topic Detection and Tracking pilot study as online new event detection [1]), is one of three main classification tasks defined by the TDT initiative. Our composite document representation consists of a semantic representation (based on the lexical chains derived from a text) and a syntactic representation (using proper nouns). Using the TDT1 evaluation methodology, we evaluate a number of document representation combinations using these document classifiers.

In this paper, we explore the effects of data fusion on First Story Detection [1] in a broadcast news domain. The data fusion element of this experiment involves the combination of evidence derived from two distinct representations of document content in a single cluster run. Our composite document representation consists of a concept representation (based on the lexical chains derived from a text) and free text representation (using traditional keyword index terms). Using the TDT1 evaluation methodology we evaluate a number of document representation strategies and propose reasons why our data fusion experiment shows performance improvements in the TDT domain.