An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

Apperceptive patterning: Artefaction, extensional beliefs and cognitive scaffolding

In “Psychopower and Ordinary Madness” my ambition, as it relates to Bernard Stiegler’s recent literature, was twofold: 1) critiquing Stiegler’s work on exosomatization and artefactual posthumanism—or, more specifically, nonhumanism—to problematize approaches to media archaeology that rely upon technical exteriorization; 2) challenging how Stiegler engages with Giuseppe Longo and Francis Bailly’s conception of negative entropy. These efforts were directed by a prevalent techno-cultural qualifier: the rise of Synthetic Intelligence (including neural nets, deep learning, predictive processing and Bayesian models of cognition). This paper continues this project but first directs a critical analytic lens at the Derridean practice of the ontologization of grammatization from which Stiegler emerges while also distinguishing how metalanguages operate in relation to object-oriented environmental interaction by way of inferentialism. Stalking continental (Kapp, Simondon, Leroi-Gourhan, etc.) and analytic traditions (e.g., Carnap, Chalmers, Clark, Sutton, Novaes, etc.), we move from artefacts to AI and Predictive Processing so as to link theories related to technicity with philosophy of mind. Simultaneously drawing forth Robert Brandom’s conceptualization of the roles that commitments play in retrospectively reconstructing the social experiences that lead to our endorsement(s) of norms, we compliment this account with Reza Negarestani’s deprivatized account of intelligence while analyzing the equipollent role between language and media (both digital and analog)

Concurrent Lexicalized Dependency Parsing: The ParseTalk Model

A grammar model for concurrent, object-oriented natural language parsing is introduced. Complete lexical distribution of grammatical knowledge is achieved building upon the head-oriented notions of valency and dependency, while inheritance mechanisms are used to capture lexical generalizations. The underlying concurrent computation model relies upon the actor paradigm. We consider message passing protocols for establishing dependency relations and ambiguity handling.Comment: 90kB, 7pages Postscrip

A Logical Verification Methodology for Service-Oriented Computing

We introduce a logical verification methodology for checking behavioural properties of service-oriented computing systems. Service properties are described by means of SocL, a branching-time temporal logic that we have specifically designed to express in an effective way distinctive aspects of services, such as, e.g., acceptance of a request, provision of a response, and correlation among service requests and responses. Our approach allows service properties to be expressed in such a way that they can be independent of service domains and specifications. We show an instantiation of our general methodology that uses the formal language COWS to conveniently specify services and the expressly developed software tool CMC to assist the user in the task of verifying SocL formulae over service specifications. We demonstrate feasibility and effectiveness of our methodology by means of the specification and the analysis of a case study in the automotive domain

Reasoning about Action: An Argumentation - Theoretic Approach

We present a uniform non-monotonic solution to the problems of reasoning about action on the basis of an argumentation-theoretic approach. Our theory is provably correct relative to a sensible minimisation policy introduced on top of a temporal propositional logic. Sophisticated problem domains can be formalised in our framework. As much attention of researchers in the field has been paid to the traditional and basic problems in reasoning about actions such as the frame, the qualification and the ramification problems, approaches to these problems within our formalisation lie at heart of the expositions presented in this paper