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WellStructured Transition Systems Everywhere!
 THEORETICAL COMPUTER SCIENCE
, 1998
"... Wellstructured transition systems (WSTS's) are a general class of infinite state systems for which decidability results rely on the existence of a wellquasiordering between states that is compatible with the transitions. In this article, we provide an extensive treatment of the WSTS idea and ..."
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Cited by 194 (9 self)
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Wellstructured transition systems (WSTS's) are a general class of infinite state systems for which decidability results rely on the existence of a wellquasiordering between states that is compatible with the transitions. In this article, we provide an extensive treatment of the WSTS idea and show several new results. Our improved definitions allow many examples of classical systems to be seen as instances of WSTS's.
Visibly pushdown languages
, 2004
"... Abstract. We study congruences on words in order to characterize the class of visibly pushdown languages (Vpl), a subclass of contextfree languages. For any language L, we define a natural congruence on words that resembles the syntactic congruence for regular languages, such that this congruence i ..."
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Cited by 134 (15 self)
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Abstract. We study congruences on words in order to characterize the class of visibly pushdown languages (Vpl), a subclass of contextfree languages. For any language L, we define a natural congruence on words that resembles the syntactic congruence for regular languages, such that this congruence is of finite index if, and only if, L is a Vpl. We then study the problem of finding canonical minimal deterministic automata for Vpls. Though Vpls in general do not have unique minimal automata, we consider a subclass of VPAs called kmodule singleentry VPAs that correspond to programs with recursive procedures without input parameters, and show that the class of wellmatched Vpls do indeed have unique minimal kmodule singleentry automata. We also give a polynomial time algorithm that minimizes such kmodule singleentry VPAs. 1 Introduction The class of visibly pushdown languages (Vpl), introduced in [1], is a subclassof contextfree languages accepted by pushdown automata in which the input letter determines the type of operation permitted on the stack. Visibly pushdown languages are closed under all boolean operations, and problems such as inclusion, that are undecidable for contextfree languages, are decidable for Vpl. Vpls are relevant to several applications that use contextfree languages suchas the modelchecking of software programs using their pushdown models [13]. Recent work has shown applications in other contexts: in modeling semanticsof effects in processing XML streams [4], in game semantics for programming languages [5], and in identifying larger classes of pushdown specifications thatadmit decidable problems for infinite games on pushdown graphs [6].
Adding nesting structure to words
 In Developments in Language Theory, LNCS 4036
, 2006
"... We propose the model of nested words for representation of data with both a linear ordering and a hierarchically nested matching of items. Examples of data with such dual linearhierarchical structure include executions of structured programs, annotated linguistic data, and HTML/XML documents. Neste ..."
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Cited by 74 (11 self)
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We propose the model of nested words for representation of data with both a linear ordering and a hierarchically nested matching of items. Examples of data with such dual linearhierarchical structure include executions of structured programs, annotated linguistic data, and HTML/XML documents. Nested words generalize both words and ordered trees, and allow both word and tree operations. We define nested word automata—finitestate acceptors for nested words, and show that the resulting class of regular languages of nested words has all the appealing theoretical properties that the classical regular word languages enjoys: deterministic nested word automata are as expressive as their nondeterministic counterparts; the class is closed under union, intersection, complementation, concatenation, Kleene*, prefixes, and language homomorphisms; membership, emptiness, language inclusion, and language equivalence are all decidable; and definability in monadic second order logic corresponds exactly to finitestate recognizability. We also consider regular languages of infinite nested words and show that the closure properties, MSOcharacterization, and decidability of decision problems carry over. The linear encodings of nested words give the class of visibly pushdown languages of words, and this class lies between balanced languages and deterministic contextfree languages. We argue that for algorithmic verification of structured programs, instead of viewing the program as a contextfree language over words, one should view it as a regular language of nested words (or equivalently, a visibly pushdown language), and this would allow model checking of many properties (such as stack inspection, prepost conditions) that are not expressible in existing specification logics. We also study the relationship between ordered trees and nested words, and the corresponding automata: while the analysis complexity of nested word automata is the same as that of classical tree automata, they combine both bottomup and topdown traversals, and enjoy expressiveness and succinctness benefits over tree automata. 1
Sequencing from compomers: Using mass spectrometry for DNA denovo sequencing of 200+ nt
 J. Comput. Biol
"... Abstract. One of the main endeavors in today’s Life Science remains the efficient sequencing of long DNA molecules. Today, most denovo sequencing of DNA is still performed using electrophoresisbased Sanger Sequencing, based on the Sanger concept of 1977. Methods using mass spectrometry to acquire ..."
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Cited by 20 (6 self)
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Abstract. One of the main endeavors in today’s Life Science remains the efficient sequencing of long DNA molecules. Today, most denovo sequencing of DNA is still performed using electrophoresisbased Sanger Sequencing, based on the Sanger concept of 1977. Methods using mass spectrometry to acquire the Sanger Sequencing data are limited by short sequencing lengths of 15–25 nt. We propose a new method for DNA sequencing using basespecific cleavage and mass spectrometry, that appears to be a promising alternative to classical DNA sequencing approaches. A single stranded DNA or RNA molecule is cleaved by a basespecific (bio)chemical reaction using, for example, RNAses. The cleavage reaction is modified such that not all, but only a certain percentage of those bases are cleaved. The resulting mixture of fragments is then analyzed using MALDITOF mass spectrometry, whereby we acquire the molecular masses of fragments. For every peak in the mass spectrum, we calculate those base compositions that will potentially create a peak of the observed mass and, repeating the cleavage reaction for all four bases, finally try to uniquely reconstruct the underlying sequence from these observed spectra. This leads us to the combinatorial problem of Sequencing From Compomers and, finally, to the graphtheoretical problem of finding a walk in a subgraph of the de Bruijn graph. Application of this method to simulated data indicates that it might be capable of sequencing DNA molecules with 200+ nt. 1
Dynamic compilation of weighted contextfree grammars
 in Proceedings of ACL ’98
, 1998
"... Weighted contextfree grammars are a convenient formalism for representing grammatical constructions and their likelihoods in a variety of languageprocessing applications. In particular, speech understanding applications require appropriate grammars both to constrain speech recognition and to hel ..."
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Cited by 17 (4 self)
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Weighted contextfree grammars are a convenient formalism for representing grammatical constructions and their likelihoods in a variety of languageprocessing applications. In particular, speech understanding applications require appropriate grammars both to constrain speech recognition and to help extract the meaning of utterances. In many of those applications, the actual languages described are regular, but contextfree representations are much more concise and easier to create. We describe an efficient algorithm for compiling into weighted finite automata an interesting class of weighted contextflee grammars that represent regular languages. The resulting automata can then be combined with other speech recognition components. Our method allows the recognizer to dynamically activate or deactivate grammar rules and substitute a new regular language for some terminal symbols, depending on previously recognized inputs, all without recompilation. We also report experimental results showing the practicality of the approach. 1.
On Monotonic Automata with a Restart Operation
, 1999
"... Automata with a restart operation de ne a special class of rewrite (reduction) systems which has a close relation to the dependency syntax of natural languages. We impose a natural condition of monotonocity and introduce a hierarchical structure of several versions of such automata. The language ..."
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Cited by 15 (7 self)
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Automata with a restart operation de ne a special class of rewrite (reduction) systems which has a close relation to the dependency syntax of natural languages. We impose a natural condition of monotonocity and introduce a hierarchical structure of several versions of such automata. The language classes recognized by these automata form a proper hierarchy, with the class of contextfree languages on the top, and with the class of deterministic contextfree languages on the bottom. In particular, the deterministic monotonic versions of all the introduced automata recognize the same class of languages { namely that of deterministic contextfree languages.
Transformation Rules for Locally Stratified Constraint Logic Programs
, 2004
"... We propose a set of transformation rules for constraint logic programs with negation. We assume that every program is locally strati ed and, thus, it has a unique perfect model. We give sucient conditions which ensure that the proposed set of transformation rules preserves the perfect model of ..."
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Cited by 14 (13 self)
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We propose a set of transformation rules for constraint logic programs with negation. We assume that every program is locally strati ed and, thus, it has a unique perfect model. We give sucient conditions which ensure that the proposed set of transformation rules preserves the perfect model of the programs. Our rules extend in some respects the rules for logic programs and constraint logic programs already considered in the literature and, in particular, they include a rule for unfolding a clause with respect to a negative literal.
The Descriptive Complexity Approach to LOGCFL
, 1998
"... Building upon the known generalizedquantifierbased firstorder characterization of LOGCFL, we lay the groundwork for a deeper investigation. Specifically, we examine subclasses of LOGCFL arising from varying the arity and nesting of groupoidal quantifiers. Our work extends the elaborate theory ..."
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Cited by 11 (5 self)
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Building upon the known generalizedquantifierbased firstorder characterization of LOGCFL, we lay the groundwork for a deeper investigation. Specifically, we examine subclasses of LOGCFL arising from varying the arity and nesting of groupoidal quantifiers. Our work extends the elaborate theory relating monoidal quantifiers to NC and its subclasses. In the absence of the BIT predicate, we resolve the main issues: we show in particular that no single outermost unary groupoidal quantifier with FO can capture all the contextfree languages, and we obtain the surprising result that a variant of Greibach's "hardest contextfree language" is LOGCFLcomplete under quantifierfree BITfree projections. We then prove that FO with unary groupoidal quantifiers is strictly more expressive with the BIT predicate than without. Considering a particular groupoidal quantifier, we prove that firstorder logic with majority of pairs is strictly more expressive than firstorder with major...