Schema summarization
Real database systems can often be very complex. A person wishing to access data from an unfamiliar database has the daunting task of understanding its schema before being able to pose a correct query against it. A schema summary can be of great help, providing a succinct overview of the entire schema, and making it possible to explore in depth only the relevant schema components.In this paper we formally define a schema summary and two desirable properties (in addition to minimizing size) of a summary: presenting important schema elements and achieving broad information coverage. We develop algorithms that allow us to automatically generate schema summaries based on these two goals. We further develop an objective metric for assessing the quality of a schema summary using query information. Experimental evaluation using this metric demonstrates that the summaries produced by our algorithms can significantly reduce the amount of user effort required to formulate a query through schema exploration.

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: Efficient discovery of XML data redundancies
abstract: As XML becomes widely used, dealing with redundancies in XML data has become an increasingly important issue. Redundantly stored information can lead not just to a higher data storage cost, but also to increased costs for data transfer and data manipulation. Furthermore, such data redundancies can lead to potential update anomalies, rendering the database inconsistent.One way to avoid data redundancies is to employ good schema design based on known functional dependencies. In fact, several recent studies have focused on defining the notion of XML Functional Dependencies (XML FDs) to capture XML data redundancies. We observe further that XML databases are often "casually designed" and XML FDs may not be determined in advance. Under such circumstances, discovering XML data redundancies (in terms of FDs) from the data itself becomes necessary and is an integral part of the schema refinement process.In this paper, we present the design and implementation of the first system, DiscoverXFD, for effcient discovery of XML data redundancies. It employs a novel XML data structure and introduces a new class of partition based algorithms. DiscoverXFD can not only be used for the previous definitions of XML functional dependencies, but also for a more comprehensive notion we develop in this paper, capable of detecting redundancies involving set elements while maintaining clear semantics. Experimental evaluations using real life and benchmark datasets demonstrate that our system is practical and scales well with increasing data size.

title: Making database systems usable
abstract: Database researchers have striven to improve the capability of a database in terms of both performance and functionality. We assert that the usability of a database is as important as its capability. In this paper, we study why database systems today are so difficult to use. We identify a set of five pain points and propose a research agenda to address these. In particular, we introduce a presentation data model and recommend direct data manipulation with a schema later approach. We also stress the importance of provenance and of consistency across presentation models.

title: Querying structured text in an XML database
abstract: 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: 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: A multimodal learning interface for grounding spoken language in sensory perceptions
abstract: Most speech interfaces are based on natural language processing techniques that use pre-defined symbolic representations of word meanings and process only linguistic information. To understand and use language like their human counterparts in multimodal human-computer interaction, computers need to acquire spoken language and map it to other sensory perceptions. This paper presents a multimodal interface that learns to associate spoken language with perceptual features by being situated in users' everyday environments and sharing user-centric multisensory information. The learning interface is trained in unsupervised mode in which users perform everyday tasks while providing natural language descriptions of their behaviors. We collect acoustic signals in concert with multisensory information from non-speech modalities, such as user's perspective video, gaze positions, head directions and hand movements. The system firstly estimates users' focus of attention from eye and head cues. Attention, as represented by gaze fixation, is used for spotting the target object of user interest. Attention switches are calculated and used to segment an action sequence into action units which are then categorized by mixture hidden Markov models. A multimodal learning algorithm is developed to spot words from continuous speech and then associate them with perceptually grounded meanings extracted from visual perception and action. Successful learning has been demonstrated in the experiments of three natural tasks: "unscrewing a jar", "stapling a letter" and "pouring water".

title: Distributed Top-N Query Processing with Possibly Uncooperative Local Systems
abstract: We consider the problem of processing top-N queries in a distributed environment with possibly uncooperative local database systems. For a given top-N query, the problem is to find the N tuples that satisfy the query the best but not necessarily completely in an efficient manner. Top-N queries are gaining popularity in relational databases and are expected to be very useful for e-commerce applications. Many companies provide the same type of goods and services to the public on the Web, and relational databases may be employed to manage the data. It is not feasible for a user to query a large number of databases. It is therefore desirable to provide a facility where a user query is accepted at some site, suitable tuples from appropriate sites are retrieved and the results are merged and then presented to the user. In this paper, we present a method for constructing the desired facility. Our method consists of two steps. The first step determines which databases are likely to contain the desired tuples for a given query so that the databases can be ranked based on their desirability with respect to the query. Four different techniques are introduced for this step with one requiring no cooperation from local systems. The second step determines how the ranked databases should be searched and what tuples from the searched databases should be returned. A new algorithm is proposed for this purpose. Experimental results are presented to compare different methods and very promising results are obtained using the method that requires no cooperation from local databases.

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: Recent Advances in PC-Linux Systems for Electronic Structure Computations by Optimized Compilers and Numerical Libraries
abstract: One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.

title: A Methodology to Retrieve Text Documents from Multiple Databases
abstract: This paper presents a methodology for finding the n most similar documents across multiple text databases for any given query and for any positive integer n. This methodology consists of two steps. First, the contents of databases are indicated approximately by database representatives. Databases are ranked using their representatives with respect to the given query. We provide a necessary and sufficient condition to rank the databases optimally. In order to satisfy this condition, we provide three estimation methods. One estimation method is intended for short queries; the other two are for all queries. Second, we provide an algorithm, OptDocRetrv, to retrieve documents from the databases according to their rank and in a particular way. We show that if the databases containing the n most similar documents for a given query are ranked ahead of other databases, our methodology will guarantee the retrieval of the n most similar documents for the query. When the number of databases is large, we propose to organize database representatives into a hierarchy and employ a best-search algorithm to search the hierarchy. It is shown that the effectiveness of the best-search algorithm is the same as that of evaluating the user query against all database representatives.