Querying structured text in an XML database
XML databases often contain documents comprising structured text. Therefore, it is important to integrate "information retrieval style" query evaluation, which is well-suited for natural language text, with standard "database style" query evaluation, which handles structured queries efficiently. Relevance scoring is central to information retrieval. In the case of XML, this operation becomes more complex because the data required for scoring could reside not directly in an element itself but also in its descendant elements.In this paper, we propose a bulk-algebra, TIX, and describe how it can be used as a basis for integrating information retrieval techniques into a standard pipelined database query evaluation engine. We develop new evaluation strategies essential to obtaining good performance, including a stack-based TermJoin algorithm for efficiently scoring composite elements. We report results from an extensive experimental evaluation, which show, among other things, that the new TermJoin access method outperforms a direct implementation of the same functionality using standard operators by a large factor.

title: Constraint-based XML query rewriting for data integration
abstract: We study the problem of answering queries through a target schema, given a set of mappings between one or more source schemas and this target schema, and given that the data is at the sources. The schemas can be any combination of relational or XML schemas, and can be independently designed. In addition to the source-to-target mappings, we consider as part of the mapping scenario a set of target constraints specifying additional properties on the target schema. This becomes particularly important when integrating data from multiple data sources with overlapping data and when such constraints can express data merging rules at the target. We define the semantics of query answering in such an integration scenario, and design two novel algorithms, basic query rewrite and query resolution, to implement the semantics. The basic query rewrite algorithm reformulates target queries in terms of the source schemas, based on the mappings. The query resolution algorithm generates additional rewritings that merge related information from multiple sources and assemble a coherent view of the data, by incorporating target constraints. The algorithms are implemented and then evaluated using a comprehensive set of experiments based on both synthetic and real-life data integration scenarios.

title: Semantic Adaptation of Schema Mappings when Schemas Evolve
abstract: Schemas evolve over time to accommodate the changes in the information they represent. Such evolution causes invalidation of various artifacts depending on the schemas, such as schema mappings. In a heterogenous environment, where cooperation among data sources depends essentially upon them, schema mappings must be adapted to reflect schema evolution. In this study, we explore the mapping composition approach for addressing this mapping adaptation problem. We study the semantics of mapping composition in the context of mapping adaptation and compare our approach with the incremental approach of Velegrakis et al [21]. We show that our method is superior in terms of capturing the semantics of both the original mappings and the evolution. We design and implement a mapping adaptation system based on mapping composition as well as additional mapping pruning techniques that significantly speed up the adaptation. We conduct comprehensive experimental analysis and show that the composition approach is practical in various evolution scenarios. The mapping language that we consider is a nested relational extension of the second-order dependencies of Fagin et al . Our work can also be seen as an implementation of the mapping composition operator of the model management framework.

title: Schema-Free XQuery
abstract: The widespread adoption of XML holds out the promise that document structure can be exploited to specify precise database queries. However, the user may have only a limited knowledge of the XML structure, and hence may be unable to produce a correct XQuery, especially in the context of a heterogeneous information collection. The default is to use keyword-based search and we are all too familiar with how difficult it is to obtain precise answers by these means. We seek to address these problems by introducing the notion of Meaningful Lowest Common Ancestor Structure (MLCAS) for finding related nodes within an XML document. By automatically computing MLCAS and expanding ambiguous tag names, we add new functionality to XQuery and enable users to take full advantage of XQuery in querying XML data precisely and efficiently without requiring (perfect) knowledge of the document structure. Such a Schema-Free XQuery is potentially of value not just to casual users with partial knowledge of schema, but also to experts working in a data integration or data evolution context. In such a context, a schema-free query, once written, can be applied universally to multiple data sources that supply similar content under different schemas, and applied "forever" as these schemas evolve. Our experimental evaluation found that it was possible to express a wide variety of queries in a schema-free manner and have them return correct results over a broad diversity of schemas. Furthermore, the evaluation of a schema-free query is not expensive using a novel stack-based algorithm we develop for computing MLCAS: from 1 to 4 times the execution time of an equivalent schema-aware query.

title: Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together
abstract: Protein interaction data exists in a number of repositories. Each repository has its own data format, molecule identifier and supplementary information. Michigan Molecular Interactions (MiMI) assists scientists searching through this overwhelming amount of protein interaction data. MiMI gathers data from well-known protein interaction databases and deep-merges the information. Utilizing an identity function, molecules that may have different identifiers but represent the same real-world object are merged. Thus, MiMI allows the users to retrieve information from many different databases at once, highlighting complementary and contradictory information. To help scientists judge the usefulness of a piece of data, MiMI tracks the provenance of all data. Finally, a simple yet powerful user interface aids users in their queries, and frees them from the onerous task of knowing the data format or learning a query language. MiMI allows scientists to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI is part of the National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: .

title: Effective Integration of Protein Data through Better Data Modeling
abstract: Protein data, from sequence and structure to interaction, is being generated through many diverse methodologies; it is stored and reported in numerous forms and multiple places. The magnitude of the data limits researchers abilities to utilize all information generated. Effective integration of protein data can be accomplished through better data modeling. We demonstrate this through the MIPD project.

title: Determining Text Databases to Search in the Internet
abstract: Text data in the Internet can be partitioned into many databases naturally. Efficient retrieval of desired data can be achieved if we can accurately predict the usefulness of each database, because with such information, we only need to retrieve potentially useful documents from useful databases. In this paper, we propose two new methods for estimating the usefulness of text databases. For a given query, the usefulness of a text database in this paper is defined to be the number of documents in the database that are sufficiently similar to the query. Such a usefulness measure enables naive-users to make informed decision about which databases to search. We also consider the collection fusion problem. Because local databases may employ similarity functions that are different from that used by the global database, the threshold used by a local database to determine whether a document is potentially useful may be different from that used by the global database. We provide techniques that determine the best threshold for a given local database.

title: The Role of Embodied Intention in Early Lexical Acquisition
abstract: We examine the influence of inferring interlocutors' referential intentions from their body movements at the early stage of lexical acquisition. By testing human participants and comparing their performances in different learning conditions, we find that those embodied intentions facilitate both word discovery and word-meaning association. In light of empirical findings, the main part of this article presents a computational model that can identify the sound patterns of individual words from continuous speech, using nonlinguistic contextual information, and employ body movements as deictic references to discover word-meaning associations. To our knowledge, this work is the first model of word learning that not only learns lexical items from raw multisensory signals to closely resemble infant language development from natural environments, but also explores the computational role of social cognitive skills in lexical acquisition.

title: The emergence of links between lexical acquisition and object categorization: a computational study
abstract: Language is about symbols, and those symbols must be grounded in the physical world. Children learn to associate language with sensorimotor experiences during their development. In light of this, we first provide a computational account of how words are mapped to their perceptually grounded meanings. Moreover, the main part of this work proposes and implements a computational model of how word learning influences the formation of object categories to which those words refer. This model simulates the bi-directional relationship between word and object category learning: (1) object categorization provides mental representations of meanings that are mapped to words to form lexical items; (2) linguistic labels help object categorization by providing additional teaching signals; and (3) these two learning processes interplay with each other and form a developmental feedback loop. Compared with the method that performs these two tasks separately, our model shows promising improvements in both word-to-world mapping and perceptual categorization, suggesting a unified view of lexical and category learning in an integrative framework. Most importantly, this work provides a cognitively plausible explanation of the mechanistic nature of early word learning and object learning from co-occurring multisensory data.

title: Efficient and effective metasearch for text databases incorporating linkages among documents
abstract: Linkages among documents have a significant impact on the importance of documents, as it can be argued that important documents are pointed to by many documents or by other important documents. Metasearch engines can be used to facilitate ordinary users for retrieving information from multiple local sources (text databases). There is a search engine associated with each database. In a large-scale metasearch engine, the contents of each local database is represented by a representative. Each user query is evaluated against he set of representatives of all databases in order to determine the appropriate databases (search engines) to search (invoke) In previous word, the linkage information between documents has not been utilized in determining the appropriate databases to search. In this paper, such information is employed to determine the degree of relevance of a document with respect to a given query. Specifically, the importance (rank) of each document as determined by the linkages is integrated in each database representative to facilitate the selection of databases for each given query. We establish a necessary and sufficient condition to rank databases optimally, while incorporating the linkage information. A method is provided to estimate the desired quantities stated in the necessary and sufficient condition. The estimation method runs in time linearly proportional to the number of query terms. Experimental results are provided to demonstrate the high retrieval effectiveness of the method.

title: Numerical Performance and Throughput Benchmark for Electronic Structure Calculations in PC-Linux Systems with New Architectures, Updated Compilers, and Libraries
abstract: A number of recently released numerical libraries including Automatically Tuned Linear Algebra Subroutines (ATLAS) library, Intel Math Kernel Library (MKL), GOTO numerical library, and AMD Core Math Library (ACML) for AMD Opteron processors, are linked against the executables of the Gaussian 98 electronic structure calculation package, which is compiled by updated versions of Fortran compilers such as Intel Fortran compiler (ifc/efc) 7.1 and PGI Fortran compiler (pgf77/pgf90) 5.0. The ifc 7.1 delivers about 3% of improvement on 32-bit machines compared to the former version 6.0. Performance improved from pgf77 3.3 to 5.0 is also around 3% when utilizing the original unmodified optimization options of the compiler enclosed in the software. Nevertheless, if extensive compiler tuning options are used, the speed can be further accelerated to about 25%. The performances of these fully optimized numerical libraries are similar. The double-precision floating-point (FP) instruction sets (SSE2) are also functional on AMD Opteron processors operated in 32-bit compilation, and Intel Fortran compiler has performed better optimization. Hardware-level tuning is able to improve memory bandwidth by adjusting the DRAM timing, and the efficiency in the CL2 mode is further accelerated by 2.6% compared to that of the CL2.5 mode. The FP throughput is measured by simultaneous execution of two identical copies of each of the test jobs. Resultant performance impact suggests that IA64 and AMD64 architectures are able to fulfill significantly higher throughput than the IA32, which is consistent with the SpecFPrate2000 benchmarks.