No abstract

Natural language has been the holy grail of query interface designers, but has generally been considered too hard to work with, except in limited specific circumstances. In this paper, we describe the architecture of an interactive natural language query interface for relational databases. Through a carefully limited interaction with the user, we are able to correctly interpret complex natural language queries, in a generic manner across a range of domains. By these means, a logically complex English language sentence is correctly translated into a SQL query, which may include aggregation, nesting, and various types of joins, among other things, and can be evaluated against an RDBMS. We have constructed a system, NaLIR (Natural Language Interface for Relational databases), embodying these ideas. Our experimental assessment, through user studies, demonstrates that NaLIR is good enough to be usable in practice: even naive users are able to specify quite complex ad-hoc queries.

Abstract. In many decision-making applications, the skyline query is frequently used to find a set of dominating data points (called skyline points) in a multidimensional dataset. In a high-dimensional space skyline points no longer offer any interesting insights as there are too many of them. In this paper, we introduce a novel metric, called skyline frequency that compares and ranks the interestingness of data points based on how often they are returned in the skyline when different number of dimensions (i.e., subspaces) are considered. Intuitively, a point with a high skyline frequency is more interesting as it can be dominated on fewer combinations of the dimensions. Thus, the problem becomes one of finding top-k frequent skyline points. But the algorithms thus far proposed for skyline computation typically do not scale well with dimensionality. Moreover, frequent skyline computation requires that skylines be computed for each of an exponential number of subsets of the dimensions. We present efficient approximate algorithms to address these twin difficulties. Our extensive performance study shows that our approximate algorithm can run fast and compute the correct result on large data sets in high-dimensional spaces.

Abstract. This paper describes the overall design and architecture of the Timber XML database system currently being implemented at the University of Michigan. The system is based upon a bulk algebra for manipulating trees, and natively stores XML. New access methods have been developed to evaluate queries in the XML context, and new cost estimation and query optimization techniques have also been developed. We present performance numbers to support some of our design decisions. We believe that the key intellectual contribution of this system is a comprehensive set-at-a-time query processing ability in a native XML store, with all the standard components of relational query processing, including algebraic rewriting and a cost-based optimizer.

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.

Diabetic neuropathy is a common complication of diabetes. While multiple pathways are implicated in the pathophysiology of diabetic neuropathy, there are no specific treatments and no means to predict diabetic neuropathy onset or progression. Here, we identify gene expression signatures related to diabetic neuropathy and develop computational classification models of diabetic neuropathy progression. Microarray experiments were performed on 50 samples of human sural nerves collected during a 52-week clinical trial. A series of bioinformatics analyses identified differentially expressed genes and their networks and biological pathways potentially responsible for the progression of diabetic neuropathy. We identified 532 differentially expressed genes between patient samples with progressing or non-progressing diabetic neuropathy, and found these were functionally enriched in pathways involving inflammatory responses and lipid metabolism. A literature-derived co-citation network of the differentially expressed genes revealed gene subnetworks centred on apolipoprotein E, jun, leptin, serpin peptidase inhibitor E type 1 and peroxisome proliferator-activated receptor gamma. The differentially expressed genes were used to classify a test set of patients with regard to diabetic neuropathy progression. Ridge regression models containing 14 differentially expressed genes correctly classified the progression status of 92% of patients (P < 0.001). To our knowledge, this is the first study to identify transcriptional changes associated with diabetic neuropathy progression in human sural nerve biopsies and describe their potential utility in classifying diabetic neuropathy. Our results identifying the unique gene signature of patients with progressive diabetic neuropathy will facilitate the development of new mechanism-based diagnostics and therapies.

Regular expressions have served as the dominant workhorse of practical information extraction for several years. However, there has been little work on reducing the manual effort involved in building high-quality, complex regular expressions for information extraction tasks. In this paper, we propose Re-LIE, a novel transformation-based algorithm for learning such complex regular expressions. We evaluate the performance of our algorithm on multiple datasets and compare it against the CRF algorithm. We show that ReLIE, in addition to being an order of magnitude faster, outperforms CRF under conditions of limited training data and cross-domain data. Finally, we show how the accuracy of CRF can be improved by using features extracted by ReLIE.

As the world is increasingly networked and digitized, the data we store has more and more frequently been chopped, baked, diced and stewed. In consequence, there is an increasing need to store and manage provenance for each data item stored in a database, describing exactly where it came from, and what manipulations have been applied to it. Storage of the complete provenance of each data item can become prohibitively expensive. In this paper, we identify important properties of provenance that can be used to considerably reduce the amount of storage required. We identify three different techniques: a family of factorization processes and two methods based on inheritance, to decrease the amount of storage required for provenance.We have used the techniques described in this work to significantly reduce the provenance storage costs associated with constructing MiMI [22], a warehouse of data regarding protein interactions, as well as two provenance stores, Karma [31] and PReServ [20], produced through workflow execution. In these real provenance sets, we were able to reduce the size of the provenance by up to a factor of 20. Additionally, we show that this reduced store can be queried efficiently and further that incremental changes can be made inexpensively.