Fast equivalence-checking for normed context-free processes

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

Binary Reachability of Timed Pushdown Automata via Quantifier Elimination and Cyclic Order Atoms

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

New Pumping Technique for 2-Dimensional VASS

We propose a new pumping technique for 2-dimensional vector addition systems with states (2-VASS) building on natural geometric properties of runs. We illustrate its applicability by reproving an exponential bound on the length of the shortest accepting run, and by proving a new pumping lemma for languages of 2-VASS. The technique is expected to be useful for settling questions concerning languages of 2-VASS, e.g., for establishing decidability status of the regular separability problem

Homomorphism Problems for First-Order Definable Structures

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

Regular Separability of Parikh Automata

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

Efficient seeding techniques for protein similarity search

We apply the concept of subset seeds proposed in [1] 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 an analysis of seeds built over those alphabet and compare them with the standard Blastp seeding method [2,3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seed is less expressive (but less costly to implement) than the accumulative 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

Separability of Reachability Sets of Vector Addition Systems

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

Efficient seeding techniques for protein similarity search

We apply the concept of subset seeds proposed in [1] 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 an analysis of seeds built over those alphabet and compare them with the standard Blastp seeding method [2,3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seed is less expressive (but less costly to implement) than the accumulative 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