Currently, most approaches to retrieving textual materials from scientific databases depend on a lexical match between words in users’ requests and those in or assigned to documents in a database. Because of the tremendous diversity in the words people use to describe the same document, lexical methods are necessarily incomplete and imprecise. Using the singular value decomposition (SVD), one can take advantage of the implicit higher-order structure in the association of terms with documents by determining the SVD of large sparse term by document matrices. Terms and documents represented by 200–300 of the largest singular vectors are then matched against user queries. We call this retrieval method latent semantic indexing (LSI) because the subspace represents important associative relationships between terms and documents that are not evident in individual documents. LSI is a completely automatic yet intelligent indexing method, widely applicable, and a promising way to improve users’ access to many kinds of textual materials, or to documents and services for which textual descriptions are available. A survey of the computational requirements for managing LSI-encoded databases as well as current and future applications of LSI is presented.

The evolution of digital libraries and the Internet has dramatically transformed the processing, storage, and retrieval of information. Efforts to digitize text, images, video, and audio now consume a substantial portion of both academic and industrial activity. Even when there is no shortage of textual materials on a particular topic, procedures for indexing or extracting the knowledge or conceptual information contained in them can be lacking. Recently developed information retrieval technologies are based on the concept of a vector space. Data are modeled as a matrix, and a user's query of the database is represented as a vector. Relevant documents in the database are then identified via simple vector operations. Orthogonal factorizations of the matrix provide mechanisms for handling uncertainty in the database itself. The purpose of this paper is to show how such fundamental mathematical concepts from linear algebra can be used to manage and index large text collections.

Motivation: A major challenge in the interpretation of high-throughput genomic data is understanding the functional associations between genes. Previously, several approaches have been described to extract gene relationships from various biological databases using term-matching methods. However, more flexible automated methods are needed to identify functional relationships (both explicit and implicit) between genes from the biomedical literature. In this study, we explored the utility of Latent Semantic Indexing (LSI), a vector space model for information retrieval, to automatically identify conceptual gene relationships from titles and abstracts in MEDLINE citations. Results: We found that LSI identified gene-to-gene and keyword-to-gene relationships with high average precision. In addition, LSI identified implicit gene relationships based on word usage patterns in the gene abstract documents. Finally, we demonstrate here that pairwise distances derived from the vector angles of gene abstract documents can be effectively used to functionally group genes by hierarchical clustering. Our results provide proof-of-principle that LSI is a robust automated method to elucidate both known (explicit) and unknown (implicit) gene relationships from the biomedical literature. These features make LSI particularly useful for the analysis of novel associations discovered in genomic experiments. Availability: The 50-gene document collection used in this study can be interactively queried at http://shad.cs.utk.edu/sgo/sgo.html Contact:rhomayouni@utmem.edu Supplementary information:http://shad.cs.utk.edu/sgo/pubs.html