Graph models for reachability analysis of concurrent programs

Reachability analysis is an attractive technique for analysis of concurrent programs because it is simple and relatively straightforward to automate, and can be used in conjunction with model-checking procedures to check for application-specific as well as general properties. Several techniques have been proposed differing mainly on the model used; some of these propose the use of flowgraph based models, some others of Petri nets.This paper addresses the question: What essential difference does it make, if any, what sort of finite-state model we extract from program texts for purposes of reachability analysis? How do they differ in expressive power, decision power, or accuracy? Since each is intended to model synchronization structure while abstracting away other features, one would expect them to be roughly equivalent.We confirm that there is no essential semantic difference between the most well known models proposed in the literature by providing algorithms for translation among these models. This implies that the choice of model rests on other factors, including convenience and efficiency.Since combinatorial explosion is the primary impediment to application of reachability analysis, a particular concern in choosing a model is facilitating divide-and-conquer analysis of large programs. Recently, much interest in finite-state verification systems has centered on algebraic theories of concurrency. Yeh and Young have exploited algebraic structure to decompose reachability analysis based on a flowgraph model. The semantic equivalence of graph and Petri net based models suggests that one ought to be able to apply a similar strategy for decomposing Petri nets. We show this is indeed possible through application of category theory

Lambek vs. Lambek: Functorial Vector Space Semantics and String Diagrams for Lambek Calculus

The Distributional Compositional Categorical (DisCoCat) model is a mathematical framework that provides compositional semantics for meanings of natural language sentences. It consists of a computational procedure for constructing meanings of sentences, given their grammatical structure in terms of compositional type-logic, and given the empirically derived meanings of their words. For the particular case that the meaning of words is modelled within a distributional vector space model, its experimental predictions, derived from real large scale data, have outperformed other empirically validated methods that could build vectors for a full sentence. This success can be attributed to a conceptually motivated mathematical underpinning, by integrating qualitative compositional type-logic and quantitative modelling of meaning within a category-theoretic mathematical framework. The type-logic used in the DisCoCat model is Lambek's pregroup grammar. Pregroup types form a posetal compact closed category, which can be passed, in a functorial manner, on to the compact closed structure of vector spaces, linear maps and tensor product. The diagrammatic versions of the equational reasoning in compact closed categories can be interpreted as the flow of word meanings within sentences. Pregroups simplify Lambek's previous type-logic, the Lambek calculus, which has been extensively used to formalise and reason about various linguistic phenomena. The apparent reliance of the DisCoCat on pregroups has been seen as a shortcoming. This paper addresses this concern, by pointing out that one may as well realise a functorial passage from the original type-logic of Lambek, a monoidal bi-closed category, to vector spaces, or to any other model of meaning organised within a monoidal bi-closed category. The corresponding string diagram calculus, due to Baez and Stay, now depicts the flow of word meanings.Comment: 29 pages, pending publication in Annals of Pure and Applied Logi

A Compositional Semantics for Stochastic Reo Connectors

In this paper we present a compositional semantics for the channel-based coordination language Reo which enables the analysis of quality of service (QoS) properties of service compositions. For this purpose, we annotate Reo channels with stochastic delay rates and explicitly model data-arrival rates at the boundary of a connector, to capture its interaction with the services that comprise its environment. We propose Stochastic Reo automata as an extension of Reo automata, in order to compositionally derive a QoS-aware semantics for Reo. We further present a translation of Stochastic Reo automata to Continuous-Time Markov Chains (CTMCs). This translation enables us to use third-party CTMC verification tools to do an end-to-end performance analysis of service compositions.Comment: In Proceedings FOCLASA 2010, arXiv:1007.499

State-of-the-art on evolution and reactivity

This report starts by, in Chapter 1, outlining aspects of querying and updating resources on the Web and on the Semantic Web, including the development of query and update languages to be carried out within the Rewerse project. From this outline, it becomes clear that several existing research areas and topics are of interest for this work in Rewerse. In the remainder of this report we further present state of the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs; in Chapter 4 event-condition-action rules, both in the context of active database systems and in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Programmable models of growth and mutation of cancer-cell populations

In this paper we propose a systematic approach to construct mathematical models describing populations of cancer-cells at different stages of disease development. The methodology we propose is based on stochastic Concurrent Constraint Programming, a flexible stochastic modelling language. The methodology is tested on (and partially motivated by) the study of prostate cancer. In particular, we prove how our method is suitable to systematically reconstruct different mathematical models of prostate cancer growth - together with interactions with different kinds of hormone therapy - at different levels of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104

A Survey of Languages for Specifying Dynamics: A Knowledge Engineering Perspective

A number of formal specification languages for knowledge-based systems has been developed. Characteristics for knowledge-based systems are a complex knowledge base and an inference engine which uses this knowledge to solve a given problem. Specification languages for knowledge-based systems have to cover both aspects. They have to provide the means to specify a complex and large amount of knowledge and they have to provide the means to specify the dynamic reasoning behavior of a knowledge-based system. We focus on the second aspect. For this purpose, we survey existing approaches for specifying dynamic behavior in related areas of research. In fact, we have taken approaches for the specification of information systems (Language for Conceptual Modeling and TROLL), approaches for the specification of database updates and logic programming (Transaction Logic and Dynamic Database Logic) and the generic specification framework of abstract state machine