We study a generalisation of Büchi-Landweber games to the timed setting. The winning condition is specified by a non-deterministic timed automaton, and one of the players can elapse time. We perform a systematic study of synthesis problems in all variants of timed games, depending on which player’s winning condition is specified, and which player’s strategy (or controller, a finite-memory strategy) is sought. As our main result we prove ubiquitous undecidability in all the variants, both for strategy and controller synthesis, already for winning conditions specified by one-clock automata. This strengthens and generalises previously known undecidability results. We also fully characterise those cases where finite memory is sufficient to win, namely existence of a strategy implies existence of a controller. All our results are stated in the timed setting, while analogous results hold in the data setting where one-clock automata are replaced by one-register ones.

The reachability problem in 3-dimensional vector addition systems with states (3-VASS) is known to be PSpace-hard, and to belong to Tower. We significantly narrow down the complexity gap by proving the problem to be solvable in doubly-exponential space. The result follows from a new upper bound on the length of the shortest path: if there is a path between two configurations of a 3-VASS then there is also one of at most triply-exponential length. We show it by introducing a novel technique of approximating the reachability sets of 2-VASS by small semi-linear sets.

Vector addition systems with states (VASS), also known as Petri nets, are a popular model of concurrent systems. Many problems from many areas reduce to the reachability problem for VASS, which consists of deciding whether a target configuration of a VASS is reachable from a given initial configuration. In this paper, we obtain an Ackermannian (primitive-recursive in fixed dimension) upper bound for the reachability problem in VASS with nested zero tests. Furthermore, we provide a uniform approach which also allows to decide most related problems, for example semilinearity and separability, in the same complexity. For some of these problems like semilinearity the complexity was unknown even for plain VASS.

We investigate the reachability problem in symmetric vector addition systems with states (vass), where transitions are invariant under a group of permutations of coordinates. One extremal case, the trivial groups, yields general vass. In another extremal case, the symmetric groups, we show that the reachability problem can be solved in PSpace, regardless of the dimension of input vass (to be contrasted with Ackermannian complexity in general vass). We also consider other groups, in particular alternating and cyclic ones. Furthermore, motivated by the open status of the reachability problem in data vass, we estimate the gain in complexity when the group arises as a combination of the trivial and symmetric groups.

An infinite set is orbit-finite if, up to permutations of atoms, it has only finitely many elements. We study a generalisation of linear programming where constraints are expressed by an orbit-finite system of linear inequalities. As our principal contribution we provide a decision procedure for checking if such a system has a real solution, and for computing the minimal/maximal value of a linear objective function over the solution set. We also show undecidability of these problems in case when only integer solutions are considered. Therefore orbit-finite linear programming is decidable, while orbit-finite integer linear programming is not.

This note is a product of digestion of the famous proof of decidability of the reachability problem for vector addition systems with states (VASS), as first established by Mayr in 1981 and then simplified by Kosaraju in 1982. The note is neither intended to be rigorously formal nor complete; it is rather intended to be an intuitive but precise enough description of main concepts exploited in the proof. Very roughly, the overall idea is to provide a decidable condition Theta on a VASS such that Theta implies reachability and its negation implies that the size of VASS can be reduced. With these two properties, the size of input can be incrementally reduced until the problem becomes trivial. We proceed in three steps: we first formulate the condition Theta for plain VASS, then adapt it to more general VASS with unconstrained coordinates, and finally to generalized VASS of Kosaraju.

We study existence and computability of finite bases for ideals of polynomials over infinitely many variables. In our setting, variables come from a countable logical structure A, and embeddings from A to A act on polynomials by renaming variables. First, we give a sufficient and necessary condition for A to guarantee the following generalisation of Hilbert's Basis Theorem: every polynomial ideal which is equivariant, i.e. invariant under renaming of variables, is finitely generated. Second, we develop an extension of classical Buchberger's algorithm to compute a Gröbner basis of a given equivariant ideal. This implies decidability of the membership problem for equivariant ideals. Finally, we sketch upon various applications of these results to register automata, Petri nets with data, orbitfinitely generated vector spaces, and orbit-finite systems of linear equations.

This special issue presents selected papers from the 44th International Conference on Application and Theory of Petri Nets and Concurrency (Petri Nets 2023), which was organised by the R&D Group on Reconfigurable and Embedded Systems at NOVA School of Science and Technology, NOVA University Lisbon, in June 2023.The Program Committee selected 17 regular papers and 4 tool papers out of 47 papers submitted to Petri Nets 2023.Each paper was single-blind reviewed by at least four reviewers.After the conference, four papers were distinguished by the Program Committee members, whose authors were invited to revise and substantially enhance their conference papers for this special issue.The extended submissions have been reviewed in a separate reviewing process to meet the standards of Fundamenta Informaticae.The four selected papers in this special issue cover a variety of new results in theory as well as in applications.

International audience

An infinite set is orbit-finite if, up to permutations of the underlying structure of atoms, it has only finitely many elements. We study a generalisation of linear programming where constraints are expressed by an orbit-finite system of linear inequalities. As our principal contribution we provide a decision procedure for checking if such a system has a real solution, and for computing the minimal/maximal value of a linear objective function over the solution set. We also show undecidability of these problems in case when only integer solutions are considered. Therefore orbit-finite linear programming is decidable, while orbit-finite integer linear programming is not.

We study orbit-finite systems of linear equations, in the setting of sets with atoms. Our principal contribution is a decision procedure for solvability of such systems. The procedure works for every field (and even commutative ring) under mild effectiveness assumptions, and reduces a given orbit-finite system to a number of finite ones: exponentially many in general, but polynomially many when the atom dimension of input systems is fixed. Towards obtaining the procedure we push further the theory of vector spaces generated by orbit-finite sets, and show that each such vector space admits an orbit-finite basis. This fundamental property is a key tool in our development, but should be also of wider interest.

Petri nets, equivalently presentable as vector addition systems with states, are an established model of concurrency with widespread applications. The reachability problem, where we ask whether from a given initial configuration there exists a sequence of valid execution steps reaching a given final configuration, is the central algorithmic problem for this model. The complexity of the problem has remained, until recently, one of the hardest open questions in verification of concurrent systems. A first upper bound has been provided only in 2015 by Leroux and Schmitz, then refined by the same authors to non-primitive recursive Ackermannian upper bound in 2019. The exponential space lower bound, shown by Lipton already in 1976, remained the only known for over 40 years until a breakthrough non-elementary lower bound by Czerwi{ń}ski, Lasota, Lazic, Leroux and Mazowiecki in 2019. Finally, a matching Ackermannian lower bound announced this year by Czerwi{ń}ski and Orlikowski, and independently by Leroux, established the complexity of the problem. Our primary contribution is an improvement of the former construction, making it conceptually simpler and more direct. On the way we improve the lower bound for vector addition systems with states in fixed dimension (or, equivalently, Petri nets with fixed number of places): while Czerwi{ń}ski and Orlikowski prove $F_k$-hardness (hardness for $k$th level in Grzegorczyk Hierarchy) in dimension $6k$, our simplified construction yields $F_k$-hardness already in dimension $3k+2$.

The deterministic membership problem for timed automata asks whether the timed language given by a nondeterministic timed automaton can be recognised by a deterministic timed automaton. An analogous problem can be stated in the setting of register automata. We draw the complete decidability/complexity landscape of the deterministic membership problem, in the setting of both register and timed automata. For register automata, we prove that the deterministic membership problem is decidable when the input automaton is a nondeterministic one-register automaton (possibly with epsilon transitions) and the number of registers of the output deterministic register automaton is fixed. This is optimal: We show that in all the other cases the problem is undecidable, i.e., when either (1) the input nondeterministic automaton has two registers or more (even without epsilon transitions), or (2) it uses guessing, or (3) the number of registers of the output deterministic automaton is not fixed. The landscape for timed automata follows a similar pattern. We show that the problem is decidable when the input automaton is a one-clock nondeterministic timed automaton without epsilon transitions and the number of clocks of the output deterministic timed automaton is fixed. Again, this is optimal: We show that the problem in all the other cases is undecidable, i.e., when either (1) the input nondeterministic timed automaton has two clocks or more, or (2) it uses epsilon transitions, or (3) the number of clocks of the output deterministic automaton is not fixed.

Abstract We prove that if a data language and its complement are both recognized by nondeterministic register automata (without guessing), then they are also recognized by deterministic ones.

As it has been recently shown, Parikh images of languages of nondeterministic one-register automata are rational (but not semilinear in general), but it is still open if the property extends to all register automata. We identify a subclass of nondeterministic register automata, called hierarchical register automata (HRA), with the following two properties: every rational language is recognised by a HRA; and Parikh image of the language of every HRA is rational. In consequence, these two properties make HRA an automata-theoretic characterisation of languages of nondeterministic register automata with rational Parikh images.

We investigate computational complexity of the reachability problem for vector addition systems (or, equivalently, Petri nets), the central algorithmic problem in verification of concurrent systems. Concerning its complexity, after 40 years of stagnation, a non-elementary lower bound has been shown recently: the problem needs a tower of exponentials of time or space, where the height of tower is linear in the input size. We improve on this lower bound, by increasing the height of tower from linear to exponential. As a side-effect, we obtain better lower bounds for vector addition systems of fixed dimension.

We investigate commutative images of languages recognised by register automata and grammars. Semi-linear and rational sets can be naturally extended to this setting by allowing for orbit-finite unions instead of only finite ones. We prove that commutative images of languages of one-register automata are not always semi-linear, but they are always rational. We also lift the latter result to grammars: commutative images of one- register context-free languages are rational, and in consequence commutatively equivalent to register automata. We conjecture analogous results for automata and grammars with arbitrarily many registers.

The Program Committee selected 23 out of 41 papers submitted to Petri Nets 2020 by authors from 19 different countries.Each paper was reviewed by three reviewers.After the conference, five papers were distinguished by the Program Committee members.The authors were invited to revise and extend their conference papers for this special issue, and the extended submissions have been reviewed in a separate reviewing process, to meet the standards of Fundamenta Informaticae.Three of these works address the synthesis problem, albeit from rather different points of views (complexity, compositionality and synthesis in a timed context).New results on the complexity and expressiveness of Recursive Petri nets and an in-depth investigation of the intricate connection between sequential and concurrent semantics in Petri nets reversibility, complete this special issue.

This special issue presents selected papers from the 41st International Conference on Application and Theory of Petri Nets and Concurrency (Petri Nets 2020), which was organized by the LoVe (Logics and Verification) team of the computer science laboratory LIPN (Laboratoire dInformatique de Paris Nord), University Sorbonne Paris Nord, and CNRS, jointly with the members of the Paris region MeFoSy-LoMa group (Méthodes Formelles pour les Systemes Logiciels et Matériels) in June 2020.The conference took place online due to the covid pandemics.The Program Committee selected 23 out of 56 papers submitted to Petri Nets 2020 by authors from 21 different countries.Each paper was reviewed by three reviewers.After the conference, five papers were distinguished by the Program Committee members, whose authors were invited to revise and extend their conference papers for this special issue.The extended submissions have been reviewed in a separate reviewing process to meet the standards of Fundamenta Informaticae.

The deterministic membership problem for timed automata asks whether the timed language recognised by a nondeterministic timed automaton can be recognised by a deterministic timed automaton. We show that the problem is decidable when the input automaton is a one-clock nondeterministic timed automaton without epsilon transitions and the number of clocks of the deterministic timed automaton is fixed. We show that the problem in all the other cases is undecidable, i.e., when either 1) the input nondeterministic timed automaton has two clocks or more, or 2) it uses epsilon transitions, or 3) the number of clocks of the output deterministic automaton is not fixed.

The reachability problem is a central decision problem in verification of vector addition systems with states (VASS). In spite of recent progress, the complexity of the reachability problem remains unsettled, and it is closely related to the lengths of shortest VASS runs that witness reachability. We obtain three main results for VASS of fixed dimension. For the first two, we assume that the integers in the input are given in unary, and that the control graph of the given VASS is flat (i.e., without nested cycles). We obtain a family of VASS in dimension 3 whose shortest runs are exponential, and we show that the reachability problem is NP-hard in dimension 7. These results resolve negatively questions that had been posed by the works of Blondin et al. in LICS 2015 and Englert et al. in LICS 2016, and contribute a first construction that distinguishes 3-dimensional flat VASS from 2-dimensional ones. Our third result, by means of a novel family of products of integer fractions, shows that 4-dimensional VASS can have doubly exponentially long shortest runs. The smallest dimension for which this was previously known is 14.

We study a generalisation of Büchi-Landweber games to the timed setting. The winning condition is specified by a non-deterministic timed automaton with epsilon transitions and only Player I can elapse time. We show that for fixed number of clocks and maximal numerical constant available to Player II, it is decidable whether she has a winning timed controller using these resources. More interestingly, we also show that the problem remains decidable even when the maximal numerical constant is not specified in advance, which is an important technical novelty not present in previous literature on timed games. We complement these two decidability result by showing undecidability when the number of clocks available to Player II is not fixed. As an application of timed games, and our main motivation to study them, we show that they can be used to solve the deterministic separability problem for nondeterministic timed automata with epsilon transitions. This is a novel decision problem about timed automata which has not been studied before. We show that separability is decidable when the number of clocks of the separating automaton is fixed and the maximal constant is not. The problem whether separability is decidable without bounding the number of clocks of the separator remains an interesting open problem.

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Petri nets, also known as vector addition systems, are a long established model of concurrency with extensive applications in modelling and analysis of hardware, software and database systems, as well as chemical, biological and business processes. The central algorithmic problem for Petri nets is reachability: whether from the given initial configuration there exists a sequence of valid execution steps that reaches the given final configuration. The complexity of the problem has remained unsettled since the 1960s, and it is one of the most prominent open questions in the theory of verification. Decidability was proved by Mayr in his seminal STOC 1981 work, and the currently best published upper bound is non-primitive recursive Ackermannian of Leroux and Schmitz from LICS 2019. We establish a non-elementary lower bound, i.e. that the reachability problem needs a tower of exponentials of time and space. Until this work, the best lower bound has been exponential space, due to Lipton in 1976. The new lower bound is a major breakthrough for several reasons. Firstly, it shows that the reachability problem is much harder than the coverability (i.e., state reachability) problem, which is also ubiquitous but has been known to be complete for exponential space since the late 1970s. Secondly, it implies that a plethora of problems from formal languages, logic, concurrent systems, process calculi and other areas, that are known to admit reductions from the Petri nets reachability problem, are also not elementary. Thirdly, it makes obsolete the currently best lower bounds for the reachability problems for two key extensions of Petri nets: with branching and with a pushdown stack.

We investigate the isomorphism problem in the setting of definable sets (equivalent to sets with atoms): given two definable relational structures, are they related by a definable isomorphism? Under mild assumptions on the underlying structure of atoms, we prove decidability of the problem. The core result is parameter-elimination: existence of an isomorphism definable with parameters implies existence of an isomorphism definable without parameters.

Timed-register pushdown automata constitute a very expressive class of automata, whose transitions may involve state, input, and top-of-stack timed registers with unbounded differences. They strictly subsume pushdown timed automata of Bouajjani et al., dense-timed pushdown automata of Abdulla et al., and orbit-finite timed-register pushdown automata of Clemente and Lasota. We give an effective logical characterisation of the reachability relation of timed-register pushdown automata. As a corollary, we obtain a doubly exponential time procedure for the non-emptiness problem. We show that the complexity reduces to singly exponential under the assumption of monotonic time. The proofs involve a novel model of one-dimensional integer branching vector addition systems with states. As a result interesting on its own, we show that reachability sets of the latter model are semilinear and computable in exponential time.

We investigate the languages recognized by well-structured transition systems (WSTS) with upward and downward compatibility. Our first result shows that, under very mild assumptions, every two disjoint WSTS languages are regular separable: There is a regular language containing one of them and being disjoint from the other. As a consequence, if a language as well as its complement are both recognized by WSTS, then they are necessarily regular. In particular, no subclass of WSTS languages beyond the regular languages is closed under complement. Our second result shows that for Petri nets, the complexity of the backwards coverability algorithm yields a bound on the size of the regular separator. We complement it by a lower bound construction.

Following a recently considered generalization of linear equations to unordered data vectors, we perform a further generalization to ordered data vectors. These generalized equations naturally appear in the analysis of vector addition systems (or Petri nets) extended with ordered data. We show that nonnegative-integer solvability of linear equations is computationally equivalent (up to an exponential blowup) with the reachability problem for (plain) vector addition systems. This high complexity is surprising, and contrasts with NP-completeness for unordered data vectors. Also surprisingly, we achieve polynomial time complexity of the solvability problem when the nonnegative-integer restriction on solutions is dropped.

We investigate data-enriched models, like Petri nets with data, where executability of a transition is conditioned by a relation between data values involved. Decidability status of various decision problems in such models may depend on the structure of data domain. According to the WQO Dichotomy Conjecture, if a data domain is homogeneous then it either exhibits a well quasi-order (in which case decidability follows by standard arguments), or essentially all the decision problems are undecidable for Petri nets over that data domain. We confirm the conjecture for data domains being 3-graphs (graphs with 2-colored edges). On the technical level, this results is a significant step beyond known classification results for homogeneous structures.

We study an expressive model of timed pushdown automata extended with modular and fractional clock constraints. We show that the binary reachability relation is effectively expressible in hybrid linear arithmetic with a rational and an integer sort. This subsumes analogous expressibility results previously known for finite and pushdown timed automata with untimed stack. As key technical tools, we use quantifier elimination for a fragment of hybrid linear arithmetic and for cyclic order atoms, and a reduction to register pushdown automata over cyclic order atoms.

We investigate a subclass of languages recognized by vector addition systems, namely languages of nondeterministic Parikh automata. While the regularity problem (is the language of a given automaton regular?) is undecidable for this model, we surprisingly show decidability of the regular separability problem: given two Parikh automata, is there a regular language that contains one of them and is disjoint from the other? We supplement this result by proving undecidability of the same problem already for languages of visibly one counter automata.

We prove that non-emptiness of timed register pushdown automata is decidable in doubly exponential time. This is a very expressive class of automata, whose transitions may involve state and top-of-stack clocks with unbounded differences. It strictly subsumes pushdown timed automata of Bouajjani et al., dense-timed pushdown automata of Abdulla et al., and orbit-finite timed register pushdown automata of Clemente and Lasota. Along the way, we prove two further decidability results of independent interest: for non-emptiness of least solutions to systems of equations over sets of integers with addition, union and intersections with ℕ and -ℕ, and for reachability in one-dimensional branching vector addition systems with states and subtraction, both in exponential time.

The regular separability problem asks, for two given languages, if there exists a regular language including one of them but disjoint from the other. Our main result is decidability, and PSPACE-completeness, of the regular separability problem for languages of one counter automata without zero tests (also known as one counter nets). This contrasts with undecidability of the regularity problem for one counter nets, and with undecidability of the regular separability problem for one counter automata, which is our second result.

Given two families of sets F and G, the F-separability problem for G asks whether for two given sets U, V in G there exists a set S in F, such that U is included in S and V is disjoint with S. We consider two families of sets F: modular sets S which are subsets of N^d, defined as unions of equivalence classes modulo some natural number n in N, and unary sets, which extend modular sets by requiring equality below a threshold n, and equivalence modulo n above n. Our main result is decidability of modular- and unary-separability for the class G of reachability sets of Vector Addition Systems, Petri Nets, Vector Addition Systems with States, and for sections thereof.

In Petri nets with data, every token carries a data value, and executability of a transition is conditioned by a relation between data values involved. Decidability status of various decision problems for Petri nets with data may depend on the structure of data domain. For instance, if data values are only tested for equality, decidability status of the reachability problem is unknown (but decidability is conjectured). On the other hand, the reachability problem is undecidable if data values are additionally equipped with a total ordering. We investigate the frontiers of decidability for Petri nets with various data, and formulate the WQO Dichotomy Conjecture : under a mild assumption, either a data domain exhibits a well quasi-order (in which case one can apply the general setting of well-structured transition systems to solve problems like coverability or boundedness), or essentially all the decision problems are undecidable for Petri nets over that data domain.

We investigate several variants of the homomorphism problem: given two relational structures, is there a homomorphism from one to the other? The input structures are possibly infinite, but definable by first-order interpretations in a fixed structure. Their signatures can be either finite or infinite but definable. The homomorphisms can be either arbitrary, or definable with parameters, or definable without parameters. For each of these variants, we determine its decidability status.

Timed and register automata are well-known models of computation over timed and data words, respectively. The former has clocks that allow to test the lapse of time between two events, whilst the latter includes registers that can store data values for later comparison. Although these two models behave differently in appearance, several decision problems have the same (un)decidability and complexity results for both models. As a prominent example, emptiness is decidable for alternating automata with one clock or register, both with non-primitive recursive complexity. This is not by chance. This work confirms that there is indeed a tight relationship between the two models. We show that a run of a timed automaton can be simulated by a register automaton over ordered data domain, and conversely that a run of a register automaton can be simulated by a timed automaton. These are exponential time reductions hold both in the finite and infinite words settings. Our results allow to transfer decidability results back and forth between these two kinds of models, as well complexity results modulo an exponential time reduction. We justify the usefulness of these reductions by obtaining new results on register automata.

We study pushdown systems where control states, stack alphabet, and transition relation, instead of being finite, are first-order definable in a fixed countably-infinite structure. We show that the reachability analysis can be addressed with the well-known saturation technique for the wide class of oligomorphic structures. Moreover, for the more restrictive homogeneous structures, we are able to give concrete complexity upper bounds. We show ample applicability of our technique by presenting several concrete examples of homogeneous structures, subsuming, with optimal complexity, known results from the literature. We show that infinitely many such examples of homogeneous structures can be obtained with the classical wreath product construction.

This paper contains two results on timed extensions of pushdown automata (PDA). As our first result we prove that the model of dense-timed PDA of Abdulla et al. Collapses: it is expressively equivalent to dense-timed PDA with timeless stack. Motivated by this result, we advocate the framework of first-order definable PDA, a specialization of PDA in sets with atoms, as the right setting to define and investigate timed extensions of PDA. The general model obtained in this way is Turing complete. As our second result we prove NEXPTIME upper complexity bound for the non-emptiness problem for an expressive subclass. As a byproduct, we obtain a tight EXPTIME complexity bound for a more restrictive subclass of PDA with timeless stack, thus subsuming the complexity bound known for dense-timed PDA.

In this paper we focus on the task of rating solutions to a programming exercise. State-of-the-art rating methods generally examine each solution against an exhaustive set of test cases, typically designed manually. Hence an issue of completeness arises. We propose the application of bounded model checking to the automatic generation of test cases. The experimental evaluation we have performed reveals a substantial increase in accuracy of ratings at a cost of a moderate increase in computation resources needed. Most importantly, application of model checking leads to the finding of errors in solutions that would previously have been classified as correct.

We investigate normed commutative context-free processes (Basic Parallel Processes). We show that branching bisimilarity admits the bounded response property : in the Bisimulation Game, Duplicator always has a response leading to a process of size linearly bounded with respect to the Spoiler’s process. The linear bound is effective, which leads to decidability of branching bisimilarity. For weak bisimilarity, we are able merely to show existence of some linear bound, which is not sufficient for decidability. We conjecture however that the same effective bound holds for weak bisimilarity as well. We suppose that further elaboration of novel techniques developed in this paper may be sufficient to demonstrate decidability.

One-counter nets (OCN) are Petri nets with exactly one unbounded place. They are equivalent to a subclass of one-counter automata with just a weak test for zero. Unlike many other semantic equivalences, strong and weak simulation preorder are decidable for OCN, but the computational complexity was an open problem. We show that both strong and weak simulation preorder on OCN are Pspace-complete.

We study Turing machines over sets with atoms, also known as nominal sets. Our main result is that deterministic machines are weaker than nondeterministic ones; in particular, P≠NP in sets with atoms. Our main construction is closely related to the Cai-Furer-Immerman graphs used in descriptive complexity theory.

Nominal sets are a different kind of set theory, with a more relaxed notion of finiteness. They offer an elegant formalism for describing lambda-terms modulo alpha-conversion, or automata on data words. This paper is an attempt at defining computation in nominal sets. We present a rudimentary programming language, called Nlambda. The key idea is that it includes a native type for finite sets in the nominal sense. To illustrate the power of our language, we write short programs that process automata on data words.

Our motivating question is a My hill-Nerode theorem for infinite alphabets. We consider several kinds of those: alphabets whose letters can be compared only for equality, but also ones with more structure, such as a total order or a partial order. We develop a framework for studying such alphabets, where the key role is played by the automorphism group of the alphabet. This framework builds on the idea of nominal sets of Gabbay and Pitts, nominal sets are the special case of our framework where letters can be only compared for equality. We use the framework to uniformly generalize to infinite alphabets parts of automata theory, including decidability results. In the case of letters compared for equality, we obtain automata equivalent in expressive power to finite memory automata, as defined by Francez and Kaminski.

Bisimulation equivalence is decidable in polynomial time over normed graphs generated by a context-free grammar. We present a new algorithm, working in time $O(n^5)$, thus improving the previously known complexity $O(n^8 * polylog(n))$. It also improves the previously known complexity $O(n^6 * polylog(n))$ of the equality problem for simple grammars.

We define a new kind of automata recognizing properties of data words or data trees and prove that the automata capture all queries definable in Regular XPath. We show that the automata-theoretic approach may be applied to answer decidability and expressibility questions for XPath. Finally, we use the newly introduced automata as a common framework to classify existing automata on data words and trees, including data automata, register automata and alternating register automata.

We apply the concept of subset seeds to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets. We then perform a comparative analysis of seeds built over those alphabets and compare them with the standard Blastp seeding method, as well as with the family of vector seeds. While the formalism of subset seeds is less expressive (but less costly to implement) than the cumulative principle used in Blastp and vector seeds, our seeds show a similar or even better performance than Blastp on Bernoulli models of proteins compatible with the common BLOSUM62 matrix. Finally, we perform a large-scale benchmarking of our seeds against several main databases of protein alignments. Here again, the results show a comparable or better performance of our seeds versus Blastp.

Logical relations and their generalisations are a fundamental tool in proving properties of lambda calculi, for example, for yielding sound principles for observational equivalence. We propose a natural notion of logical relations that is able to deal with the monadic types of Moggi's computational lambda calculus. The treatment is categorical, and is based on notions of subsconing, mono factorisation systems and monad morphisms. Our approach has a number of interesting applications, including cases for lambda calculi with non-determinism (where being in a logical relation means being bisimilar), dynamic name creation and probabilistic systems.

A notion of alternating timed automata is proposed. It is shown that such automata with only one clock have decidable emptiness problem over finite words. This gives a new class of timed languages that is closed under boolean operations and which has an effective presentation. We prove that the complexity of the emptiness problem for alternating timed automata with one clock is nonprimitive recursive. The proof gives also the same lower bound for the universality problem for nondeterministic timed automata with one clock. We investigate extension of the model with epsilon-transitions and prove that emptiness is undecidable. Over infinite words, we show undecidability of the universality problem.