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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.

$\omega$-clones are multi-sorted structures that naturally emerge as algebras for infinite trees, just as $\omega$-semigroups are convenient algebras for infinite words. In the algebraic theory of languages, one hopes that a language is regular if and only if it is recognized by an algebra that is finite in some simple sense. We show that, for infinite trees, the situation is not so simple: there exists an $\omega$-clone that is finite on every sort and finitely generated, but recognizes a non-regular language.

We study an extension of modal $\mu$-calculus to sets with atoms and we study its basic properties. Model checking is decidable on orbit-finite structures, and a correspondence to parity games holds. On the other hand, satisfiability becomes undecidable. We also show expressive limitations of atom-enriched $\mu$-calculi, and explain how their expressive power depends on the structure of atoms used, and on the choice between basic or vectorial syntax.

We develop a simple functional programming language aimed at manipulating infinite, but first-order definable structures, such as the countably infinite clique graph or the set of all intervals with rational endpoints. Internally, such sets are represented by logical formulas that define them, and an external satisfiability modulo theories (SMT) solver is regularly run by the interpreter to check their basic properties. The language is implemented as a Haskell module.

We use modal logic as a framework for coalgebraic trace semantics, and show the flexibility of the approach with concrete examples such as the language semantics of weighted, alternating and tree automata, and the trace semantics of generative probabilistic systems. We provide a sufficient condition under which a logical semantics coincides with the trace semantics obtained via a given determinization construction. Finally, we consider a condition that guarantees the existence of a canonical determinization procedure that is correct with respect to a given logical semantics. That procedure is closely related to Brzozowski's minimization algorithm.

Some formats of well-behaved operational specifications, correspond to natural transformations of certain types (for example, GSOS and coGSOS laws). These transformations have a common generalization: distributive laws of monads over comonads. We prove that this elegant theoretical generalization has limited practical benefits: it does not translate to any concrete rule format that would be complete for specifications that contain both GSOS and coGSOS rules. This is shown for the case of labeled transition systems and deterministic stream systems.

We study languages over infinite alphabets equipped with some structure that can be tested by recognizing automata. We develop a framework for studying such alphabets and the ensuing automata theory, where the key role is played by an automorphism group of the alphabet. In the process, we generalize nominal sets due to Gabbay and Pitts.