Search

In this paper, we deal with the problem of implementing an abstract machine for a stochastic version of the Brane Calculus. Instead of defining an ad hoc abstract machine, we consider the generic stochastic abstract machine introduced by Lakin, Paulev\'e and Phillips. The nested structure of membranes is flattened into a set of species where the hierarchical structure is represented by means of names. In order to reduce the overhead introduced by this encoding, we modify the machine by adding a copy-on-write optimization strategy. We prove that this implementation is adequate with respect to the stochastic structural operational semantics recently given for the Brane Calculus. These techniques can be ported also to other stochastic calculi dealing with nested structures., Comment: In Proceedings MeCBIC 2012, arXiv:1211.3476

We give an analog of the Myhill-Nerode methods from formal language theory for hypergraphs and use it to derive the following results for two NP-hard hypergraph problems: * We provide an algorithm for testing whether a hypergraph has cutwidth at most k that runs in linear time for constant k. In terms of parameterized complexity theory, the problem is fixed-parameter linear parameterized by k. * We show that it is not expressible in monadic second-order logic whether a hypergraph has bounded (fractional, generalized) hypertree width. The proof leads us to conjecture that, in terms of parameterized complexity theory, these problems are W[1]-hard parameterized by the incidence treewidth (the treewidth of the incidence graph). Thus, in the form of the Myhill-Nerode theorem for hypergraphs, we obtain a method to derive linear-time algorithms and to obtain indicators for intractability for hypergraph problems parameterized by incidence treewidth. In an appendix, we point out an error and a fix to the proof of the Myhill-Nerode theorem for graphs in Downey and Fellow's book on parameterized complexity., Comment: A preliminary version of this article appeared in the proceedings of ISAAC 2013. This extended and revised version contains the full proof details, more figures, and corollaries to make the application of the Myhill-Nerode theorem for hypergraphs easier in an algorithmic setting. Moreover, it provides a fix to the proof of the Myhill-Nerode theorem for graphs in the books of Downey and Fellows

This paper presents a formalization of decreasing diagrams in the theorem prover Isabelle. It discusses mechanical proofs showing that any locally decreasing abstract rewrite system is confluent. The valley and the conversion version of decreasing diagrams are considered., Comment: 17 pages; valley and conversion version; RTA 2013

This paper is concerned with the automated complexity analysis of term rewrite systems (TRSs for short) and the ramification of these in implicit computational complexity theory (ICC for short). We introduce a novel path order with multiset status, the polynomial path order POP*. Essentially relying on the principle of predicative recursion as proposed by Bellantoni and Cook, its distinct feature is the tight control of resources on compatible TRSs: The (innermost) runtime complexity of compatible TRSs is polynomially bounded. We have implemented the technique, as underpinned by our experimental evidence our approach to the automated runtime complexity analysis is not only feasible, but compared to existing methods incredibly fast. As an application in the context of ICC we provide an order-theoretic characterisation of the polytime computable functions. To be precise, the polytime computable functions are exactly the functions computable by an orthogonal constructor TRS compatible with POP*.

We consider symbolic tree automata (sta) and symbolic tree transducers (stt). We characterize s-recognizable tree languages (which are the tree languages recognizable by sta) in terms of (classical) recognizable tree languages and relabelings. We prove that sta and the recently introduced variable tree automata are incomparable with respect to their recognition power. We define symbolic regular tree grammars and characterize s-regular tree languages in terms of regular tree languages and relabelings. As a consequence, we obtain that s-recognizable tree languages are the same as s-regular tree languages. We show that the syntactic composition of two stt computes the composition of the tree transformations computed by each stt, provided that (1) the first one is deterministic or the second one is linear and (2) the first one is total or the second is nondeleting. We consider forward application and backward application of stt and prove that the backward application of an stt to any s-recognizable tree language yields an s-recognizable tree language. We give a linear stt of which the range is not an s-recognizable tree language. We show that the forward application of simple and linear stt preserves s-recognizability. As a corollary, we obtain that the type checking problem of simple and linear stt and the inverse type checking problem of arbitrary stt is decidable.

In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the compartment on which they are defined. Local rules are dynamic: they can be added, moved and erased. We enrich the new calculus with a parallel semantics where a reduction step is lead by any number of global and local rules that could be performed in parallel. A type system is developed to enforce the property that a compartment must contain only local rules with specific features. As a running example we model some interactions happening in a cell starting from its nucleus and moving towards its mitochondria., Comment: In Proceedings DCM 2011, arXiv:1207.6821

This report is meant to be used as auxiliary material for the guided grammar convergence technique proposed earlier as problem-specific improvement in the topic of convergence of grammars. It contains a narrated MegaL megamodel, as well as full results of the guided grammar convergence experiment on the Factorial Language, with details about each grammar source packaged in a readable form. All formulae used within this document, are generated automatically by the convergence infrastructure in order to avoid any mistakes. The generator source code and the source of the introduction text can be found publicly available in the Software Language Processing Suite repository.

Burkart, Caucal, Steffen (1995) showed a procedure deciding bisimulation equivalence of processes in Basic Process Algebra (BPA), i.e. of sequential processes generated by context-free grammars. They improved the previous decidability result of Christensen, H\"uttel, Stirling (1992), since their procedure has obviously an elementary time complexity and the authors claim that a close analysis would reveal a double exponential upper bound. Here a self-contained direct proof of the membership in 2-ExpTime is given. This is done via a Prover-Refuter game which shows that there is an alternating Turing machine deciding the problem in exponential space. The proof uses similar ingredients (size-measures, decompositions, bases) as the previous proofs, but one new simplifying factor is an explicit addition of infinite regular strings to the state space. An auxiliary claim also shows an explicit exponential upper bound on the equivalence level of nonbisimilar normed BPA processes. The importance of clarifying the 2-ExpTime upper bound for BPA bisimilarity has recently increased due to the shift of the known lower bound from PSpace (Srba, 2002) to ExpTime (Kiefer, 2012)., Comment: Final version accepted to LMCS

Unravelings are transformations from a conditional term rewriting system (CTRS, for short) over an original signature into an unconditional term rewriting systems (TRS, for short) over an extended signature. They are not sound w.r.t. reduction for every CTRS, while they are complete w.r.t. reduction. Here, soundness w.r.t. reduction means that every reduction sequence of the corresponding unraveled TRS, of which the initial and end terms are over the original signature, can be simulated by the reduction of the original CTRS. In this paper, we show that an optimized variant of Ohlebusch's unraveling for a deterministic CTRS is sound w.r.t. reduction if the corresponding unraveled TRS is left-linear or both right-linear and non-erasing. We also show that soundness of the variant implies that of Ohlebusch's unraveling. Finally, we show that soundness of Ohlebusch's unraveling is the weakest in soundness of the other unravelings and a transformation, proposed by Serbanuta and Rosu, for (normal) deterministic CTRSs, i.e., soundness of them respectively implies that of Ohlebusch's unraveling., Comment: 49 pages, 1 table, publication in Special Issue: Selected papers of the "22nd International Conference on Rewriting Techniques and Applications (RTA'11)"

A theory is developed which uses "networks" (directed acyclic graphs with some extra structure) as a formalism for expressions in multilinear algebra. It is shown that this formalism is valid for arbitrary PROPs (short for 'PROducts and Permutations category'), and conversely that the PROP axioms are implicit in the concept of evaluating a network. Ordinary terms and operads constitute the special case that the graph underlying the network is a rooted tree. Furthermore a rewriting theory for networks is developed. Included in this is a subexpression concept for which is given both algebraic and effective graph-theoretical characterisations, a construction of reduction maps from rewriting systems, and an analysis of the obstructions to confluence that can occur. Several Diamond Lemmas for this rewriting theory are given. In addition there is much supporting material on various related subjects. In particular there is a "toolbox" for the construction of custom orders on the free PROP, so that an order can be tailored to suit a specific rewriting system. Other subjects treated are the abstract index notation in a general PROP context and the use of feedbacks (sometimes called traces) in PROPs., Comment: 188 pages, numerous inlined figures

We revisit known transformations from Jinja bytecode to rewrite systems from the viewpoint of runtime complexity. Suitably generalising the constructions proposed in the literature, we define an alternative representation of Jinja bytecode (JBC) executions as "computation graphs" from which we obtain a novel representation of JBC executions as "constrained rewrite systems". We prove non-termination and complexity preservation of the transformation. We restrict to well-formed JBC programs that only make use of non-recursive methods and expect tree-shaped objects as input. Our approach allows for simplified correctness proofs and provides a framework for the combination of the computation graph method with standard techniques from static program analysis like for example "reachability analysis"., Comment: 36 pages

This paper proves a long standing conjecture in formal language theory. It shows that all regular languages are Church-Rosser congruential. The class of Church-Rosser congruential languages was introduced by McNaughton, Narendran, and Otto in 1988. A language L is Church-Rosser congruential, if there exists a finite confluent, and length-reducing semi-Thue system S such that L is a finite union of congruence classes modulo S. It was known that there are deterministic linear context-free languages which are not Church-Rosser congruential, but on the other hand it was strongly believed that all regular language are of this form. Actually, this paper proves a more general result.

We extend the theory of Cellular Automata to arbitrary, time-varying graphs. In other words we formalize, and prove theorems about, the intuitive idea of a labelled graph which evolves in time - but under the natural constraint that information can only ever be transmitted at a bounded speed, with respect to the distance given by the graph. The notion of translation-invariance is also generalized. The definition we provide for these "causal graph dynamics" is simple and axiomatic. The theorems we provide also show that it is robust. For instance, causal graph dynamics are stable under composition and under restriction to radius one. In the finite case some fundamental facts of Cellular Automata theory carry through: causal graph dynamics admit a characterization as continuous functions, and they are stable under inversion. The provided examples suggest a wide range of applications of this mathematical object, from complex systems science to theoretical physics. KEYWORDS: Dynamical networks, Boolean networks, Generative networks automata, Cayley cellular automata, Graph Automata, Graph rewriting automata, Parallel graph transformations, Amalgamated graph transformations, Time-varying graphs, Regge calculus, Local, No-signalling., Comment: 25 pages, 9 figures, LaTeX, v2: Minor presentation improvements, v3: Typos corrected, figure added

We propose a new order, the small polynomial path order (sPOP* for short). The order sPOP* provides a characterisation of the class of polynomial time computable function via term rewrite systems. Any polynomial time computable function gives rise to a rewrite system that is compatible with sPOP*. On the other hand any function defined by a rewrite system compatible with sPOP* is polynomial time computable. Technically sPOP* is a tamed recursive path order with product status. Its distinctive feature is the precise control provided. For any rewrite system that is compatible with sPOP* that makes use of recursion up to depth d, the (innermost) runtime complexity is bounded from above by a polynomial of degree d., Comment: Technical Report

The authors' "metatools" are a collection of tools for generic programming. This includes generating Java sources from mathematically well-founded specifications, as well as the creation of strictly typed document object models for XML encoded texts. In this context, almost every computer-internal structure is treated as a "model", and every computation is a kind of model transformation. This concept differs significantly from "classical model transformation" executed by specialized tools and languages. Therefore it seemed promising to the organizers of the TTC 2011, as well as to the authors, to apply metatools to one of the challenges, namely to the "compiler optimization task". This is a report on the resulting experiences., Comment: In Proceedings TTC 2011, arXiv:1111.4407

In this paper, a compressed membership problem for finite automata, both deterministic and non-deterministic, with compressed transition labels is studied. The compression is represented by straight-line programs (SLPs), i.e. context-free grammars generating exactly one string. A novel technique of dealing with SLPs is introduced: the SLPs are recompressed, so that substrings of the input text are encoded in SLPs labelling the transitions of the NFA (DFA) in the same way, as in the SLP representing the input text. To this end, the SLPs are locally decompressed and then recompressed in a uniform way. Furthermore, such recompression induces only small changes in the automaton, in particular, the size of the automaton remains polynomial. Using this technique it is shown that the compressed membership for NFA with compressed labels is in NP, thus confirming the conjecture of Plandowski and Rytter and extending the partial result of Lohrey and Mathissen; as it is already known, that this problem is NP-hard, we settle its exact computational complexity. Moreover, the same technique applied to the compressed membership for DFA with compressed labels yields that this problem is in P; for this problem, only trivial upper-bound PSPACE was known.

Parikh's theorem states that every Context Free Language (CFL) has the same Parikh image as that of a regular language. A finite state automaton accepting such a regular language is called a Parikh-equivalent automaton. In the worst case, the number of states in any non-deterministic Parikh-equivalent automaton is exponentially large in the size of the Context Free Grammar (CFG). We associate a regularity width d with a CFG that measures the closeness of the CFL with regular languages. The degree m of a CFG is one less than the maximum number of variable occurrences in the right hand side of any production. Given a CFG with n variables, we construct a Parikh-equivalent non-deterministic automaton whose number of states is upper bounded by a polynomial in $n (d^{2d(m+1)}), the degree of the polynomial being a small fixed constant. Our procedure is constructive and runs in time polynomial in the size of the automaton. In the terminology of parameterized complexity, we prove that constructing a Parikh-equivalent automaton for a given CFG is Fixed Parameter Tractable (FPT) when the degree m and regularity width d are parameters. We also give an example from program verification domain where the degree and regularity are small compared to the size of the grammar.

Arbuscular mycorrhiza (AM) is the most wide-spread plant-fungus symbiosis on earth. Investigating this kind of symbiosis is considered one of the most promising ways to develop methods to nurture plants in more natural manners, avoiding the complex chemical productions used nowadays to produce artificial fertilizers. In previous work we used the Calculus of Wrapped Compartments (CWC) to investigate different phases of the AM symbiosis. In this paper, we continue this line of research by modelling the colonisation of the plant root cells by the fungal hyphae spreading in the soil. This study requires the description of some spatial interaction. Although CWC has no explicit feature modelling a spatial geometry, the compartment labelling feature can be effectively exploited to define a discrete surface topology outlining the relevant sectors which determine the spatial properties of the system under consideration. Different situations and interesting spatial properties can be modelled and analysed in such a lightweight framework (which has not an explicit notion of geometry with coordinates and spatial metrics), thus exploiting the existing CWC simulation tool., Comment: In Proceedings CompMod 2011, arXiv:1109.1044

Mathematical knowledge is a central component in science, engineering, and technology (documentation). Most of it is represented informally, and -- in contrast to published research mathematics -- subject to continual change. Unfortunately, machine support for change management has either been very coarse grained and thus barely useful, or restricted to formal languages, where automation is possible. In this paper, we report on an effort to extend change management to collections of semi-formal documents which flexibly intermix mathematical formulas and natural language and to integrate it into a semantic publishing system for mathematical knowledge. We validate the long-standing assumption that the semantic annotations in these flexiformal documents that drive the machine-supported interaction with documents can support semantic impact analyses at the same time. But in contrast to the fully formal setting, where adaptations of impacted documents can be automated to some degree, the flexiformal setting requires much more user interaction and thus a much tighter integration into document management workflows., Comment: 16 pages, Conference on Intelligent Computer Mathematics 2011, July, Bertinoro, Italy

Existing grammar frameworks do not work out particularly well for controlled natural languages (CNL), especially if they are to be used in predictive editors. I introduce in this paper a new grammar notation, called Codeco, which is designed specifically for CNLs and predictive editors. Two different parsers have been implemented and a large subset of Attempto Controlled English (ACE) has been represented in Codeco. The results show that Codeco is practical, adequate and efficient.

We develop a new analysis for the length of controlled bad sequences in well-quasi-orderings based on Higman's Lemma. This leads to tight multiply-recursive upper bounds that readily apply to several verification algorithms for well-structured systems.

The relationship between Term Graph Rewriting and Term Rewriting is well understood: a single term graph reduction may correspond to several term reductions, due to sharing. It is also known that if term graphs are allowed to contain cycles, then one term graph reduction may correspond to infinitely many term reductions. We stress that this fact can be interpreted in two ways. According to the "sequential interpretation", a term graph reduction corresponds to an infinite sequence of term reductions, as formalized by Kennaway et.al. using strongly converging derivations over the complete metric space of infinite terms. Instead according to the "parallel interpretation" a term graph reduction corresponds to the parallel reduction of an infinite set of redexes in a rational term. We formalize the latter notion by exploiting the complete partial order of infinite and possibly partial terms, and we stress that this interpretation allows to explain the result of reducing circular redexes in several approaches to term graph rewriting., Comment: In Proceedings TERMGRAPH 2011, arXiv:1102.2268

We construct an example of proof within the main formal system from arXiv:1010.4760v3, which is intended to capture the bisimulation equivalence for non-deterministic first-order grammars, and show that its conclusion is semantically false. We then locate and analyze the flawed argument in the soundness (meta)-proof of the above reference., Comment: 12 pages, 9 figures

The LR(1) Parser Generation System generates full LR(1) parsers that are comparable in speed and size to those generated by LALR(1) parser generators, such as yacc [5]. LR contains a number of novel feature. This paper discusses three of them in detail: an LR(1) grammar specified automatic error recovery algorithm, oracles, and generic tokens., Comment: 6 pages

The 12th annual workshop, Descriptional Complexity of Formal Systems 2010, is taking place in Saskatoon, Canada, on August 8-10, 2010. It is jointly organized by the IFIP Working Group 1.2 on Descriptional Complexity and by the Department of Computer Science at the University of Saskatchewan. This volume contains the papers of the invited lectures and the accepted contributions., Comment: These proceedings are dedicated to Chandra M. R. Kintala, who passed away on November 05, 2009, at the age of 61. We, the DCFS community, remember him as Chair of the IFIP Working Group 1.2 on Descriptional Complexity, as a co-initiator of the area of descriptional complexity with limited resources and as a co-founder of the workshops DCAGRS and DCFS. He was on the program committee for this DCFS2010 and did unfortunately not live to see the results of the submission and reviewing process

Properties of Term Rewriting Systems are called modular iff they are preserved under (and reflected by) disjoint union, i.e. when combining two Term Rewriting Systems with disjoint signatures. Convergence is the property of Infinitary Term Rewriting Systems that all reduction sequences converge to a limit. Strong Convergence requires in addition that redex positions in a reduction sequence move arbitrarily deep. In this paper it is shown that both Convergence and Strong Convergence are modular properties of non-collapsing Infinitary Term Rewriting Systems, provided (for convergence) that the term metrics are granular. This generalises known modularity results beyond metric \infty.

We present decidability results for termination of classes of term rewriting systems modulo permutative theories. Termination and innermost termination modulo permutative theories are shown to be decidable for term rewrite systems (TRS) whose right-hand side terms are restricted to be shallow (variables occur at depth at most one) and linear (each variable occurs at most once). Innermost termination modulo permutative theories is also shown to be decidable for shallow TRS. We first show that a shallow TRS can be transformed into a flat (only variables and constants occur at depth one) TRS while preserving termination and innermost termination. The decidability results are then proved by showing that (a) for right-flat right-linear (flat) TRS, non-termination (respectively, innermost non-termination) implies non-termination starting from flat terms, and (b) for right-flat TRS, the existence of non-terminating derivations starting from a given term is decidable. On the negative side, we show PSPACE-hardness of termination and innermost termination for shallow right-linear TRS, and undecidability of termination for flat TRS., Comment: 20 pages

Term unification plays an important role in many areas of computer science, especially in those related to logic. The universal mechanism of grammar-based compression for terms, in particular the so-called Singleton Tree Grammars (STG), have recently drawn considerable attention. Using STGs, terms of exponential size and height can be represented in linear space. Furthermore, the term representation by directed acyclic graphs (dags) can be efficiently simulated. The present paper is the result of an investigation on term unification and matching when the terms given as input are represented using different compression mechanisms for terms such as dags and Singleton Tree Grammars. We describe a polynomial time algorithm for context matching with dags, when the number of different context variables is fixed for the problem. For the same problem, NP-completeness is obtained when the terms are represented using the more general formalism of Singleton Tree Grammars. For first-order unification and matching polynomial time algorithms are presented, each of them improving previous results for those problems., Comment: This paper is posted at the Computing Research Repository (CoRR) as part of the process of submission to the journal ACM Transactions on Computational Logic (TOCL).

Recently, many techniques have been introduced that allow the (automated) classification of the runtime complexity of term rewrite systems (TRSs for short). In earlier work, the authors have shown that for confluent TRSs, innermost polynomial runtime complexity induces polytime computability of the functions defined. In this paper, we generalise the above result to full rewriting. Following our previous work, we exploit graph rewriting. We give a new proof of the adequacy of graph rewriting for full rewriting that allows for a precise control of the resources copied. In sum we completely describe an implementation of rewriting on a Turing machine (TM for short). We show that the runtime complexity of the TRS and the runtime complexity of the TM is polynomially related. Our result strengthens the evidence that the complexity of a rewrite system is truthfully represented through the length of derivations. Moreover our result allows the classification of non-deterministic polytime-computation based on runtime complexity analysis of rewrite systems., Comment: Submitted to RTA 2010

We study normalising reduction strategies for infinitary Combinatory Reduction Systems (iCRSs). We prove that all fair, outermost-fair, and needed-fair strategies are normalising for orthogonal, fully-extended iCRSs. These facts properly generalise a number of results on normalising strategies in first-order infinitary rewriting and provide the first examples of normalising strategies for infinitary lambda calculus.

Membrane system computations proceed in a synchronous fashion: at each step all the applicable rules are actually applied. Hence each step depends on the previous one. This coarse view can be refined by looking at the dependencies among rule occurrences, by recording, for an object, which was the a rule that produced it and subsequently (in a later step), which was the a rule that consumed it. In this paper we propose a way to look also at the other main ingredient in membrane system computations, namely the simultaneity in the rule applications. This is achieved using zero-safe nets that allows to synchronize transitions, i.e., rule occurrences. Zero-safe nets can be unfolded into occurrence nets in a classical way, and to this unfolding an event structure can be associated. The capability of capturing simultaneity of zero-safe nets is transferred on the level of event structure by adding a way to express which events occur simultaneously.

We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences.

We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-de\"ined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes.

We tackle the problem of graph transformation with a particular focus on node cloning. We propose a new approach to graph rewriting where nodes can be cloned zero, one or more times. A node can be cloned together with all its incident edges, with only its outgoing edges, with only its incoming edges or with none of its incident edges. We thus subsume previous works such as the sesqui-pushout, the heterogeneous pushout and the adaptive star grammars approaches. A rewrite rule is defined as a span where the right-hand and left-hand sides are graphs while the interface is a polarized graph. A polarized graph is a graph endowed with some annotations on nodes. The way a node is cloned is indicated by its polarization annotation. We use these annotations for designing graph transformation with polarized cloning. We show how a clone of a node can be built according to the different possible polarizations and define a rewrite step as a final pullback complement followed by a pushout. This is called the polarized sesqui-pushout approach. We also provide an algorithmic presentation of the proposed graph transformation with polarized cloning.

We study confluence in the setting of higher-order infinitary rewriting, in particular for infinitary Combinatory Reduction Systems (iCRSs). We prove that fully-extended, orthogonal iCRSs are confluent modulo identification of hypercollapsing subterms. As a corollary, we obtain that fully-extended, orthogonal iCRSs have the normal form property and the unique normal form property (with respect to reduction). We also show that, unlike the case in first-order infinitary rewriting, almost non-collapsing iCRSs are not necessarily confluent.

We study the interplay between principal pivot transform (pivot) and loop complementation for graphs. This is done by generalizing loop complementation (in addition to pivot) to set systems. We show that the operations together, when restricted to single vertices, form the permutation group S_3. This leads, e.g., to a normal form for sequences of pivots and loop complementation on graphs. The results have consequences for the operations of local complementation and edge complementation on simple graphs: an alternative proof of a classic result involving local and edge complementation is obtained, and the effect of sequences of local complementations on simple graphs is characterized., Comment: 21 pages, 7 figures, significant additions w.r.t. v3 are Thm 7 and Remark 25

Finite-turn pushdown automata (PDA) are investigated concerning their descriptional complexity. It is known that they accept exactly the class of ultralinear context-free languages. Furthermore, the increase in size when converting arbitrary PDAs accepting ultralinear languages to finite-turn PDAs cannot be bounded by any recursive function. The latter phenomenon is known as non-recursive trade-off. In this paper, finite-turn PDAs accepting bounded languages are considered. First, letter-bounded languages are studied. We prove that in this case the non-recursive trade-off is reduced to a recursive trade-off, more precisely, to an exponential trade-off. A conversion algorithm is presented and the optimality of the construction is shown by proving tight lower bounds. Furthermore, the question of reducing the number of turns of a given finite-turn PDA is studied. Again, a conversion algorithm is provided which shows that in this case the trade-off is at most polynomial. Finally, the more general case of word-bounded languages is investigated. We show how the results obtained for letter-bounded languages can be extended to word-bounded languages., Comment: 31 pages, 1 figure. A preliminary version was presented at DLT 2007. The full version is submitted to a journal

We propose a procedure for automated implicit inductive theorem proving for equational specifications made of rewrite rules with conditions and constraints. The constraints are interpreted over constructor terms (representing data values), and may express syntactic equality, disequality, ordering and also membership in a fixed tree language. Constrained equational axioms between constructor terms are supported and can be used in order to specify complex data structures like sets, sorted lists, trees, powerlists... Our procedure is based on tree grammars with constraints, a formalism which can describe exactly the initial model of the given specification (when it is sufficiently complete and terminating). They are used in the inductive proofs first as an induction scheme for the generation of subgoals at induction steps, second for checking validity and redundancy criteria by reduction to an emptiness problem, and third for defining and solving membership constraints. We show that the procedure is sound and refutationally complete. It generalizes former test set induction techniques and yields natural proofs for several non-trivial examples presented in the paper, these examples are difficult to specify and carry on automatically with related induction procedures., Comment: This is the long version of a paper which appeared in IJCAR 2008. 38 pages

We address the problem of cyclic termgraph rewriting. We propose a new framework where rewrite rules are tuples of the form $(L,R,\tau,\sigma)$ such that $L$ and $R$ are termgraphs representing the left-hand and the right-hand sides of the rule, $\tau$ is a mapping from the nodes of $L$ to those of $R$ and $\sigma$ is a partial function from nodes of $R$ to nodes of $L$. $\tau$ describes how incident edges of the nodes in $L$ are connected in $R$. $\tau$ is not required to be a graph morphism as in classical algebraic approaches of graph transformation. The role of $\sigma$ is to indicate the parts of $L$ to be cloned (copied). Furthermore, we introduce a new notion of \emph{cloning pushout} and define rewrite steps as cloning pushouts in a given category. Among the features of the proposed rewrite systems, we quote the ability to perform local and global redirection of pointers, addition and deletion of nodes as well as cloning and collapsing substructures.

Adding rewriting to a proof assistant based on the Curry-Howard isomorphism, such as Coq, may greatly improve usability of the tool. Unfortunately adding an arbitrary set of rewrite rules may render the underlying formal system undecidable and inconsistent. While ways to ensure termination and confluence, and hence decidability of type-checking, have already been studied to some extent, logical consistency has got little attention so far. In this paper we show that consistency is a consequence of canonicity, which in turn follows from the assumption that all functions defined by rewrite rules are complete. We provide a sound and terminating, but necessarily incomplete algorithm to verify this property. The algorithm accepts all definitions that follow dependent pattern matching schemes presented by Coquand and studied by McBride in his PhD thesis. It also accepts many definitions by rewriting, containing rules which depart from standard pattern matching., Comment: 20 pages

The derivation trees of a tree adjoining grammar provide a first insight into the sentence semantics, and are thus prime targets for generation systems. We define a formalism, feature-based regular tree grammars, and a translation from feature based tree adjoining grammars into this new formalism. The translation preserves the derivation structures of the original grammar, and accounts for feature unification., Comment: 12 pages, 4 figures In TAG+9, Ninth International Workshop on Tree Adjoining Grammars and Related Formalisms, 2008

The new approach to representation of syntax of formal languages-- a formalism of syntax diagrams is offered. Syntax diagrams look a convenient language for the description of syntactic relations in the languages having nonlinear representation of texts, for example, for representation of syntax lows of the language of structural chemical formulas. The formalism of neighbourhood grammar is used to describe the set of correct syntax constructs. The neighbourhood the grammar consists of a set of families of "neighbourhoods"-- the diagrams defined for each symbol of the language's alphabet. The syntax diagram is correct if each symbol is included into this diagram together with some neighbourhood. In other words, correct diagrams are needed to be covered by elements of the neighbourhood grammar. Thus, the grammar of formal language can be represented as system of the covers defined for each correct syntax diagram., Comment: 10 pages

Because of the wide variety of contemporary practices used in the automatic syntactic parsing of natural languages, it has become necessary to analyze and evaluate the strengths and weaknesses of different approaches. This research is all the more necessary because there are currently no genre- and domain-independent parsers that are able to analyze unrestricted text with 100% preciseness (I use this term to refer to the correctness of analyses assigned by a parser). All these factors create a need for methods and resources that can be used to evaluate and compare parsing systems. This research describes: (1) A theoretical analysis of current achievements in parsing and parser evaluation. (2) A framework (called FEPa) that can be used to carry out practical parser evaluations and comparisons. (3) A set of new evaluation resources: FiEval is a Finnish treebank under construction, and MGTS and RobSet are parser evaluation resources in English. (4) The results of experiments in which the developed evaluation framework and the two resources for English were used for evaluating a set of selected parsers., Comment: PhD dissertation. 264 pages

In 2002 Jurdzinski and Lorys settled a long-standing conjecture that palindromes are not a Church-Rosser language. Their proof required a sophisticated theory about computation graphs of 2-stack automata. We present their proof in terms of 1-tape Turing machines.We also provide an alternative proof of Buntrock and Otto's result that the set of non-square bitstrings, which is context-free, is not Church-Rosser., Comment: 15 pages

This work is motivated by the necessity to automate the discovery of structure in vast and evergrowing collection of relational data commonly represented as graphs, for example genomic networks. A novel algorithm, dubbed Graphitour, for structure induction by lossless graph compression is presented and illustrated by a clear and broadly known case of nested structure in a DNA molecule. This work extends to graphs some well established approaches to grammatical inference previously applied only to strings. The bottom-up graph compression problem is related to the maximum cardinality (non-bipartite) maximum cardinality matching problem. The algorithm accepts a variety of graph types including directed graphs and graphs with labeled nodes and arcs. The resulting structure could be used for representation and classification of graphs., Comment: 10 pages, 7 figures, 2 tables published in Proceedings of the Data Compression Conference, 2007

We provide a computational definition of the notions of vector space and bilinear functions. We use this result to introduce a minimal language combining higher-order computation and linear algebra. This language extends the Lambda-calculus with the possibility to make arbitrary linear combinations of terms alpha.t + beta.u. We describe how to "execute" this language in terms of a few rewrite rules, and justify them through the two fundamental requirements that the language be a language of linear operators, and that it be higher-order. We mention the perspectives of this work in the field of quantum computation, whose circuits we show can be easily encoded in the calculus. Finally, we prove the confluence of the entire calculus., Comment: The complementary note "On the critical pairs of a rewrite system for vector spaces" is provided in the source files. Short version : "Linear-algebraic Lambda-calculus : higher-order and confluence", Proceedings of RTA 08, Hagenberg, July 2008. LNCS 5117, 17, (2008). Long version : LMCS

We consider, as a means of making programming languages more flexible and powerful, a parsing algorithm in which the parser may freely modify the grammar while parsing. We are particularly interested in a modification of the canonical LR(1) parsing algorithm in which, after the reduction of certain productions, we examine the source sentence seen so far to determine the grammar to use to continue parsing. A naive modification of the canonical LR(1) parsing algorithm along these lines cannot be guaranteed to halt; as a result, we develop a test which examines the grammar as it changes, stopping the parse if the grammar changes in a way that would invalidate earlier assumptions made by the parser. With this test in hand, we can develop our parsing algorithm and prove that it is correct. That being done, we turn to earlier, related work; the idea of programming languages which can be extended to include new syntactic constructs has existed almost as long as the idea of high-level programming languages. Early efforts to construct such a programming language were hampered by an immature theory of formal languages. More recent efforts to construct transformative languages relied either on an inefficient chain of source-to-source translators; or they have a defect, present in our naive parsing algorithm, in that they cannot be known to halt. The present algorithm does not have these undesirable properties, and as such, it should prove a useful foundation for a new kind of programming language., Comment: 68 pages, 4 figures. Numerous stylistic and grammatical fixes; new material in Sections 2.2 and 4.2

The word problem for discrete groups is well-known to be undecidable by a Turing Machine; more precisely, it is reducible both to and from and thus equivalent to the discrete Halting Problem. The present work introduces and studies a real extension of the word problem for a certain class of groups which are presented as quotient groups of a free group and a normal subgroup. Most important, the free group will be generated by an uncountable set of generators with index running over certain sets of real numbers. This allows to include many mathematically important groups which are not captured in the framework of the classical word problem. Our contribution extends computational group theory from the discrete to the Blum-Shub-Smale (BSS) model of real number computation. We believe this to be an interesting step towards applying BSS theory, in addition to semi-algebraic geometry, also to further areas of mathematics. The main result establishes the word problem for such groups to be not only semi-decidable (and thus reducible FROM) but also reducible TO the Halting Problem for such machines. It thus provides the first non-trivial example of a problem COMPLETE, that is, computationally universal for this model., Comment: corrected Section 4.5

Packrat parsing is a novel technique for implementing parsers in a lazy functional programming language. A packrat parser provides the power and flexibility of top-down parsing with backtracking and unlimited lookahead, but nevertheless guarantees linear parse time. Any language defined by an LL(k) or LR(k) grammar can be recognized by a packrat parser, in addition to many languages that conventional linear-time algorithms do not support. This additional power simplifies the handling of common syntactic idioms such as the widespread but troublesome longest-match rule, enables the use of sophisticated disambiguation strategies such as syntactic and semantic predicates, provides better grammar composition properties, and allows lexical analysis to be integrated seamlessly into parsing. Yet despite its power, packrat parsing shares the same simplicity and elegance as recursive descent parsing; in fact converting a backtracking recursive descent parser into a linear-time packrat parser often involves only a fairly straightforward structural change. This paper describes packrat parsing informally with emphasis on its use in practical applications, and explores its advantages and disadvantages with respect to the more conventional alternatives., Comment: 12 pages, 5 figures

We propose a generic termination proof method for rewriting under strategies, based on an explicit induction on the termination property. Rewriting trees on ground terms are modeled by proof trees, generated by alternatively applying narrowing and abstracting steps. The induction principle is applied through the abstraction mechanism, where terms are replaced by variables representing any of their normal forms. The induction ordering is not given a priori, but defined with ordering constraints, incrementally set during the proof. Abstraction constraints can be used to control the narrowing mechanism, well known to easily diverge. The generic method is then instantiated for the innermost, outermost and local strategies., Comment: 49 pages