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37
Curated databases
 PODS'08
, 2008
"... Curated databases are databases that are populated and updated with a great deal of human effort. Most reference works that one traditionally found on the reference shelves of libraries – dictionaries, encyclopedias, gazetteers etc. – are now curated databases. Since it is now easy to publish databa ..."
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Cited by 64 (11 self)
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Curated databases are databases that are populated and updated with a great deal of human effort. Most reference works that one traditionally found on the reference shelves of libraries – dictionaries, encyclopedias, gazetteers etc. – are now curated databases. Since it is now easy to publish databases on the web, there has been an explosion in the number of new curated databases used in scientific research. The value of curated databases lies in the organization and the quality of the data they contain. Like the paper reference works they have replaced, they usually represent the efforts of a dedicated group of people to produce a definitive description of some subject area. Curated databases present a number of challenges for database research. The topics of annotation, provenance, and citation are central, because curated databases are heavily crossreferenced with, and include data from, other databases, and much of the work of a curator is annotating existing data. Evolution of structure is important because these databases often evolve from semistructured representations, and because they have to accommodate new scientific discoveries. Much of the work in these areas is in its infancy, but it is beginning to provide suggest new research for both theory and practice. We discuss some of this research and emphasize the need to find appropriate models of the processes associated with curated databases.
From dirt to shovels: Fully automatic tool generation from ad hoc data
 In POPL
, 2008
"... An ad hoc data source is any semistructured data source for which useful data analysis and transformation tools are not readily available. Such data must be queried, transformed and displayed by systems administrators, computational biologists, financial analysts and hosts of others on a regular bas ..."
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Cited by 33 (10 self)
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An ad hoc data source is any semistructured data source for which useful data analysis and transformation tools are not readily available. Such data must be queried, transformed and displayed by systems administrators, computational biologists, financial analysts and hosts of others on a regular basis. In this paper, we demonstrate that it is possible to generate a suite of useful data processing tools, including a semistructured query engine, several format converters, a statistical analyzer and data visualization routines directly from the ad hoc data itself, without any human intervention. The key technical contribution of the work is a multiphase algorithm that automatically infers the structure of an ad hoc data source and produces a format specification in the PADS data description language. Programmers wishing to implement custom data analysis tools can use such descriptions to generate printing and parsing libraries for the data. Alternatively, our software infrastructure will push these descriptions through the PADS compiler and automatically generate fully functional tools. We evaluate the performance of our inference algorithm, showing it scales linearly in the size of the training data — completing in seconds, as opposed to the hours or days it takes to write a description by hand. We also evaluate the correctness of the algorithm, demonstrating that generating accurate descriptions often requires less than 5 % of the available data. 1.
Learning Deterministic Regular Expressions for the Inference of Schemas from XML Data
, 2008
"... Inferring an appropriate DTD or XML Schema Definition (XSD) for a given collection of XML documents essentially reduces to learning deterministic regular expressions from sets of positive example words. Unfortunately, there is no algorithm capable of learning the complete class of deterministic regu ..."
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Cited by 24 (5 self)
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Inferring an appropriate DTD or XML Schema Definition (XSD) for a given collection of XML documents essentially reduces to learning deterministic regular expressions from sets of positive example words. Unfortunately, there is no algorithm capable of learning the complete class of deterministic regular expressions from positive examples only, as we will show. The regular expressions occurring in practical DTDs and XSDs, however, are such that every alphabet symbol occurs only a small number of times. As such, in practice it suffices to learn the subclass of regular expressions in which each alphabet symbol occurs at most k times, for some small k. We refer to such expressions as koccurrence regular expressions (kOREs for short). Motivated by this observation, we provide a probabilistic algorithm that learns kOREs for increasing values of k, and selects the one that best describes the sample based on a Minimum Description Length argument. The effectiveness of the method is empirically validated both on real world and synthetic data. Furthermore, the method is shown to be conservative over the simpler classes of expressions considered in previous work.
SUCCINCTNESS OF THE COMPLEMENT AND INTERSECTION OF REGULAR EXPRESSIONS
, 2008
"... We study the succinctness of the complement and intersection of regular expressions. In particular, we show that when constructing a regular expression defining the complement of a given regular expression, a double exponential size increase cannot be avoided. Similarly, when constructing a regular ..."
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Cited by 17 (5 self)
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We study the succinctness of the complement and intersection of regular expressions. In particular, we show that when constructing a regular expression defining the complement of a given regular expression, a double exponential size increase cannot be avoided. Similarly, when constructing a regular expression defining the intersection of a fixed and an arbitrary number of regular expressions, an exponential and double exponential size increase, respectively, can in worstcase not be avoided. All mentioned lower bounds improve the existing ones by one exponential and are tight in the sense that the target expression can be constructed in the corresponding time class, i.e., exponential or double exponential time. As a byproduct, we generalize a theorem by Ehrenfeucht and Zeiger stating that there is a class of DFAs which are exponentially more succinct than regular expressions, to a fixed fourletter alphabet. When the given regular expressions are oneunambiguous, as for instance required by the XML Schema specification, the complement can be computed in polynomial time whereas the bounds concerning intersection continue to hold. For the subclass of singleoccurrence regular expressions, we prove a tight exponential lower bound for intersection.
Simplifying XML Schema: Effortless Handling of Nondeterministic Regular Expressions
, 2009
"... Whether beloved or despised, XML Schema is momentarily the only industrially accepted schema language for XML and is unlikely to become obsolete any time soon. Nevertheless, many nontransparent restrictions unnecessarily complicate the design of XSDs. For instance, complex content models in XML Sche ..."
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Cited by 12 (8 self)
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Whether beloved or despised, XML Schema is momentarily the only industrially accepted schema language for XML and is unlikely to become obsolete any time soon. Nevertheless, many nontransparent restrictions unnecessarily complicate the design of XSDs. For instance, complex content models in XML Schema are constrained by the infamous unique particle attribution (UPA) constraint. In formal language theoretic terms, this constraint restricts content models to deterministic regular expressions. As the latter constitute a semantic notion and no simple corresponding syntactical characterization is known, it is very difficult for nonexpert users to understand exactly when and why content models do or do not violate UPA. In the present paper, we therefore investigate solutions to relieve users from the burden of UPA by automatically transforming nondeterministic expressions into concise deterministic ones defining the same language or constituting good approximations. The presented techniques facilitate XSD construction by reducing the design task at hand more towards the complexity of the modeling task. In addition, our algorithms can serve as a plugin for
Simple off the shelf abstractions for XML Schema
"... Although the advent of XML Schema [25] has rendered DTDs obsolete, research on practical XML optimization is mostly biased towards DTDs and tends to largely ignore XSDs (some notable exceptions nonwithstanding). One ..."
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Cited by 12 (6 self)
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Although the advent of XML Schema [25] has rendered DTDs obsolete, research on practical XML optimization is mostly biased towards DTDs and tends to largely ignore XSDs (some notable exceptions nonwithstanding). One
3.23 Finding Optimal Probabilistic Generators for XML Collections Pierre Senellart (Telecom Paris Tech, FR) License Creative Commons BYNCND 3.0 Unported license © Pierre Senellart Joint work of Abiteboul
 in Proc. ICDT
, 2012
"... We study the problem of, given a corpus of XML documents and its schema, finding an optimal (generative) probabilistic model, where optimality here means maximizing the likelihood of the particular corpus to be generated. Focusing first on the structure of documents, we present an efficient algorith ..."
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Cited by 9 (6 self)
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We study the problem of, given a corpus of XML documents and its schema, finding an optimal (generative) probabilistic model, where optimality here means maximizing the likelihood of the particular corpus to be generated. Focusing first on the structure of documents, we present an efficient algorithm for finding the best generative probabilistic model, in the absence of constraints. We further study the problem in the presence of integrity constraints, namely key, inclusion, and domain constraints. We study in this case two different kinds of generators. First, we consider a continuationtest generator that performs, while generating documents, tests of schema satisfiability; these tests prevent from generating a document violating the constraints but, as we will see, they are computationally expensive. We also study a restart generator that may generate an invalid document and, when this is the case, restarts and tries again. Finally, we consider the injection of data values into the structure, to obtain a full XML document. We study different approaches for generating these values.
Simplifying XML Schema: SingleType Approximations of Regular Tree Languages
, 2010
"... XML Schema Definitions (XSDs) can be adequately abstracted by the singletype regular tree languages. It is wellknown, that these form a strict subclass of the robust class of regular unranked tree languages. Sadly, in this respect, XSDs are not closed under the basic operations of union and set dif ..."
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Cited by 9 (3 self)
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XML Schema Definitions (XSDs) can be adequately abstracted by the singletype regular tree languages. It is wellknown, that these form a strict subclass of the robust class of regular unranked tree languages. Sadly, in this respect, XSDs are not closed under the basic operations of union and set difference, complicating important tasks in schema integration and evolution. The purpose of this paper is to investigate how the union and difference of two XSDs can be approximated within the framework of singletype regular tree languages. We consider both optimal lower and upper approximations. We also address the more general question of how to approximate an arbitrary regular tree language by an XSD and consider the complexity of associated decision problems.
Probabilistic XML: Models and complexity
, 2011
"... Abstract. Uncertainty in data naturally arises in various applications, such as data integration and Web information extraction. Probabilistic XML is one of the concepts that have been proposed to model and manage various kinds of uncertain data. In essence, a probabilistic XML document is a compact ..."
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Cited by 7 (7 self)
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Abstract. Uncertainty in data naturally arises in various applications, such as data integration and Web information extraction. Probabilistic XML is one of the concepts that have been proposed to model and manage various kinds of uncertain data. In essence, a probabilistic XML document is a compact representation of a probability distribution over ordinary XML documents. Various models of probabilistic XML provide different languages, with various degrees of expressiveness, for such compact representations. Beyond representation, probabilistic XML systems are expected to support data management in a way that properly reflects the uncertainty. For instance, query evaluation entails probabilistic inference, and update operations need to properly change the entire probability space. Efficiently and effectively accomplishing datamanagement tasks in that manner is a major technical challenge. This chapter reviews the literature on probabilistic XML. Specifically, this chapter discusses the probabilistic XML models that have been proposed, and the complexity of query evaluation therein. Also discussed are other datamanagement tasks like updates and compression, as well as systemic and implementation aspects. 1
Generating, sampling and counting subclasses of regular tree languages
"... To experimentally validate learning and approximation algorithms for XML Schema Definitions (XSDs), we need algorithms to generate uniformly at random a corpus of XSDs as well as a similarity measure to compare how close the generated XSD resembles the target schema. In this paper, we provide the fo ..."
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Cited by 7 (0 self)
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To experimentally validate learning and approximation algorithms for XML Schema Definitions (XSDs), we need algorithms to generate uniformly at random a corpus of XSDs as well as a similarity measure to compare how close the generated XSD resembles the target schema. In this paper, we provide the formal foundation for such a testbed. We adopt similarity measures based on counting the number of common and different trees in the two languages, and we develop the necessary machinery for computing them. We use the formalism of extended DTDs (EDTDs) to represent the unranked regular tree languages. In particular, we obtain an efficient algorithm to count the number of trees up to a certain size in an unambiguous EDTD. The latter class of unambiguous EDTDs encompasses the more familiar classes of singletype, restrained competition and bottomup deterministic EDTDs. The singletype EDTDs correspond precisely to the core of XML Schema, while the others are strictly more expressive. We also show how constraints on the shape of allowed trees can be incorporated. As we make use of a translation into a wellknown formalism for combinatorial specifications, we get for free a sampling procedure to draw members of any unambiguous EDTD. When dropping the restriction to unambiguous EDTDs, i.e. taking the full class of EDTDs into account, we show that the counting problem becomes #Pcomplete and provide an approximation algorithm. Finally, we discuss uniform generation of We acknowledge the financial support of the Future and