Model Checking Spatial Logics for Closure Spaces

Spatial aspects of computation are becoming increasingly relevant in Computer Science, especially in the field of collective adaptive systems and when dealing with systems distributed in physical space. Traditional formal verification techniques are well suited to analyse the temporal evolution of programs; however, properties of space are typically not taken into account explicitly. We present a topology-based approach to formal verification of spatial properties depending upon physical space. We define an appropriate logic, stemming from the tradition of topological interpretations of modal logics, dating back to earlier logicians such as Tarski, where modalities describe neighbourhood. We lift the topological definitions to the more general setting of closure spaces, also encompassing discrete, graph-based structures. We extend the framework with a spatial surrounded operator, a propagation operator and with some collective operators. The latter are interpreted over arbitrary sets of points instead of individual points in space. We define efficient model checking procedures, both for the individual and the collective spatial fragments of the logic and provide a proof-of-concept tool

Specifying and Verifying Properties of Space - Extended Version

The interplay between process behaviour and spatial aspects of computation has become more and more relevant in Computer Science, especially in the field of collective adaptive systems, but also, more generally, when dealing with systems distributed in physical space. Traditional verification techniques are well suited to analyse the temporal evolution of programs; properties of space are typically not explicitly taken into account. We propose a methodology to verify properties depending upon physical space. We define an appropriate logic, stemming from the tradition of topological interpretations of modal logics, dating back to earlier logicians such as Tarski, where modalities describe neighbourhood. We lift the topological definitions to a more general setting, also encompassing discrete, graph-based structures. We further extend the framework with a spatial until operator, and define an efficient model checking procedure, implemented in a proof-of-concept tool.Comment: Presented at "Theoretical Computer Science" 2014, Rom

A system of relational syllogistic incorporating full Boolean reasoning

We present a system of relational syllogistic, based on classical propositional logic, having primitives of the following form: Some A are R-related to some B; Some A are R-related to all B; All A are R-related to some B; All A are R-related to all B. Such primitives formalize sentences from natural language like `All students read some textbooks'. Here A and B denote arbitrary sets (of objects), and R denotes an arbitrary binary relation between objects. The language of the logic contains only variables denoting sets, determining the class of set terms, and variables denoting binary relations between objects, determining the class of relational terms. Both classes of terms are closed under the standard Boolean operations. The set of relational terms is also closed under taking the converse of a relation. The results of the paper are the completeness theorem with respect to the intended semantics and the computational complexity of the satisfiability problem.Comment: Available at http://link.springer.com/article/10.1007/s10849-012-9165-

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

Verifying Real-Time Systems using Explicit-time Description Methods

Timed model checking has been extensively researched in recent years. Many new formalisms with time extensions and tools based on them have been presented. On the other hand, Explicit-Time Description Methods aim to verify real-time systems with general untimed model checkers. Lamport presented an explicit-time description method using a clock-ticking process (Tick) to simulate the passage of time together with a group of global variables for time requirements. This paper proposes a new explicit-time description method with no reliance on global variables. Instead, it uses rendezvous synchronization steps between the Tick process and each system process to simulate time. This new method achieves better modularity and facilitates usage of more complex timing constraints. The two explicit-time description methods are implemented in DIVINE, a well-known distributed-memory model checker. Preliminary experiment results show that our new method, with better modularity, is comparable to Lamport's method with respect to time and memory efficiency