A framework for protein and membrane interactions

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

A coalgebraic semantics for causality in Petri nets

In this paper we revisit some pioneering efforts to equip Petri nets with compact operational models for expressing causality. The models we propose have a bisimilarity relation and a minimal representative for each equivalence class, and they can be fully explained as coalgebras on a presheaf category on an index category of partial orders. First, we provide a set-theoretic model in the form of a a causal case graph, that is a labeled transition system where states and transitions represent markings and firings of the net, respectively, and are equipped with causal information. Most importantly, each state has a poset representing causal dependencies among past events. Our first result shows the correspondence with behavior structure semantics as proposed by Trakhtenbrot and Rabinovich. Causal case graphs may be infinitely-branching and have infinitely many states, but we show how they can be refined to get an equivalent finitely-branching model. In it, states are equipped with symmetries, which are essential for the existence of a minimal, often finite-state, model. The next step is constructing a coalgebraic model. We exploit the fact that events can be represented as names, and event generation as name generation. Thus we can apply the Fiore-Turi framework: we model causal relations as a suitable category of posets with action labels, and generation of new events with causal dependencies as an endofunctor on this category. Then we define a well-behaved category of coalgebras. Our coalgebraic model is still infinite-state, but we exploit the equivalence between coalgebras over a class of presheaves and History Dependent automata to derive a compact representation, which is equivalent to our set-theoretical compact model. Remarkably, state reduction is automatically performed along the equivalence.Comment: Accepted by Journal of Logical and Algebraic Methods in Programmin

Causality and the semantics of provenance

Provenance, or information about the sources, derivation, custody or history of data, has been studied recently in a number of contexts, including databases, scientific workflows and the Semantic Web. Many provenance mechanisms have been developed, motivated by informal notions such as influence, dependence, explanation and causality. However, there has been little study of whether these mechanisms formally satisfy appropriate policies or even how to formalize relevant motivating concepts such as causality. We contend that mathematical models of these concepts are needed to justify and compare provenance techniques. In this paper we review a theory of causality based on structural models that has been developed in artificial intelligence, and describe work in progress on a causal semantics for provenance graphs.Comment: Workshop submissio

On an Intuitionistic Logic for Pragmatics

We reconsider the pragmatic interpretation of intuitionistic logic [21] regarded as a logic of assertions and their justications and its relations with classical logic. We recall an extension of this approach to a logic dealing with assertions and obligations, related by a notion of causal implication [14, 45]. We focus on the extension to co-intuitionistic logic, seen as a logic of hypotheses [8, 9, 13] and on polarized bi-intuitionistic logic as a logic of assertions and conjectures: looking at the S4 modal translation, we give a denition of a system AHL of bi-intuitionistic logic that correctly represents the duality between intuitionistic and co-intuitionistic logic, correcting a mistake in previous work [7, 10]. A computational interpretation of cointuitionism as a distributed calculus of coroutines is then used to give an operational interpretation of subtraction.Work on linear co-intuitionism is then recalled, a linear calculus of co-intuitionistic coroutines is dened and a probabilistic interpretation of linear co-intuitionism is given as in [9]. Also we remark that by extending the language of intuitionistic logic we can express the notion of expectation, an assertion that in all situations the truth of p is possible and that in a logic of expectations the law of double negation holds. Similarly, extending co-intuitionistic logic, we can express the notion of conjecture that p, dened as a hypothesis that in some situation the truth of p is epistemically necessary