Approximations for Stochastic Graph Rewriting

In this note we present a method to compute approximate descriptions of a class of stochastic systems. For the method to apply, the system must be presented as a Markov chain on a state space consisting in graphs or graph-like objects, and jumps must be described by transformations which follow a finite set of local rules

Rate Equations for Graphs

In this paper, we combine ideas from two different scientific traditions: 1) graph transformation systems (GTSs) stemming from the theory of formal languages and concurrency, and 2) mean field approximations (MFAs), a collection of approximation techniques ubiquitous in the study of complex dynamics. Using existing tools from algebraic graph rewriting, as well as new ones, we build a framework which generates rate equations for stochastic GTSs and from which one can derive MFAs of any order (no longer limited to the humanly computable). The procedure for deriving rate equations and their approximations can be automated. An implementation and example models are available online at https://rhz.github.io/fragger. We apply our techniques and tools to derive an expression for the mean velocity of a two-legged walker protein on DNA.Comment: to be presented at the 18th International Conference on Computational Methods in Systems Biology (CMSB 2020

Stochastic mechanics of graph rewriting

International audienceWe propose an algebraic approach to stochastic graph-rewriting which extends the classical construction of the Heisenberg-Weyl algebra and its canonical representation on the Fock space. Rules are seen as particular elements of an algebra of 'diagrams' (the diagram algebra D). Diagrams can be thought of as formal computational traces represented in partial time. They span a vector space which carries a natural filtered Hopf algebra structure. Diagrams can be evaluated to normal diagrams (each corresponding to a rule) and generate an associative unital (non-commutative) ˚-algebra of rules (the rule algebra R). Evaluation becomes a morphism of uni-tal associative algebras which maps general diagrams in D to normal ones in R. In this algebraic reformulation, usual distinctions between graph observables (real-valued maps on the set of graphs defined by counting subgraphs), and rules disappear. Instead, natural algebraic substructures of R arise: formal observables are seen as rules with equal left and right hand sides and form a commutative subalgebra, the ones counting subgraphs forming a sub-subalgebra of identity rules. Actual graph-rewriting (of the DPO type) is recovered as a canonical representation of the rule algebra as linear operators over the vector field generated by (isomorphism classes of) finite graphs. The construction of the representation is in close analogy and subsumes the classical (multi-type bosonic) Fock space representation of the Heisenberg-Weyl algebra. This subtle shift of point of view (away from its canonical representation to the rule algebra itself) has far-reaching and unexpected consequences. We find that natural variants of the evaluation mor-phism map give rise to concepts of graph transformations hitherto not considered (these will be described in a separate paper, as in this extended abstract we limit ourselves to the simplest concept namely that of DPO-rewriting). We prove very simply a DPO version of the jump-closure theorem, namely that the sub-space of representations of formal graph observables closed under the action of any rule set. From this new jump-closure result follows that for any set of rules R, one can derive a formal and self-consistent Kolmogorov backward equation for (representations) of formal observables

Rate Equations for Graphs

International audienceIn this paper, we combine ideas from two different scientifictraditions: 1) graph transformation systems (GTSs) stemming from thetheory of formal languages and concurrency, and 2) mean field approx-imations (MFAs), a collection of approximation techniques ubiquitousin the study of complex dynamics. Using existing tools from algebraicgraph rewriting, as well as new ones, we build a framework which gener-ates rate equations for stochastic GTSs and from which one can deriveMFAs of any order (no longer limited to the humanly computable). Theprocedure for deriving rate equations and their approximations can beautomated. An implementation and example models are available onlineat https://rhz.github.io/fragger. We apply our techniques and tools toderive an expression for the mean velocity of a two-legged walker proteinon DNA

Higher-Order Subtyping with Type Intervals

Modern, statically typed programming languages provide various abstraction facilities at both the term- and type-level. Common abstraction mechanisms for types include parametric polymorphism -- a hallmark of functional languages -- and subtyping -- which is pervasive in object-oriented languages. Additionally, both kinds of languages may allow parametrized (or generic) datatype definitions in modules or classes. When several of these features are present in the same language, new and more expressive combinations arise, such as (1) bounded quantification, (2) bounded operator abstractions and (3) translucent type definitions. An example of such a language is Scala, which features all three of the aforementioned type-level constructs. This increases the expressivity of the language, but also the complexity of its type system. From a theoretical point of view, the various abstraction mechanisms have been studied through different extensions of Girard's higher-order polymorphic lambda-calculus F-omega. Higher-order subtyping and bounded polymorphism (1 and 2) have been formalized in F-omega-sub and its many variants; type definitions of various degrees of opacity (3) have been formalized through extensions of F-omega with singleton types. In this dissertation, I propose type intervals as a unifying concept for expressing (1--3) and other related constructs. In particular, I develop an extension of F-omega with interval kinds as a formal theory of higher-order subtyping with type intervals, and show how the familiar concepts of higher-order bounded quantification, bounded operator abstraction and singleton kinds can all be encoded in a semantics-preserving way using interval kinds. Going beyond the status quo, the theory is expressive enough to also cover less familiar constructs, such as lower-bounded operator abstractions and first-class, higher-order inequality constraints. I establish basic metatheoretic properties of the theory: I prove that subject reduction holds for well-kinded types w.r.t. full beta-reduction, that types and kinds are weakly normalizing, and that the theory is type safe w.r.t. its call-by-value operational reduction semantics. Key to this metatheoretic development is the use of hereditary substitution and the definition of an equivalent, canonical presentation of subtyping, which involves only normal types and kinds. The resulting metatheory is entirely syntactic, i.e. does not involve any model constructions, and has been fully mechanized in Agda. The extension of F-omega with interval kinds constitutes a stepping stone to the development of a higher-order version of the calculus of Dependent Object Types (DOT) -- the theoretical foundation of Scala's type system. In the last part of this dissertation, I briefly sketch a possible extension of the theory toward this goal and discuss some of the challenges involved in adapting the existing metatheory to that extension