98 research outputs found

    What is a Qualitative Calculus? A General Framework

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    What is a qualitative calculus? Many qualitative spatial and temporal calculi arise from a set of JEPD (jointly exhaustive and pairwise disjoint) relations: a stock example is Allen's calculus, which is based on thirteen basic relations between interval

    Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures

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    We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full characterization of the spectrum and eigenmodes of vibration at various temperatures by merely exploiting the knowledge of the protein native structure. It is shown that the rate at which perturbations decay at the folding transition correlates well with experimental folding rates. This validation is carried out on a list of about 30 two-state folders. Furthermore, the qualitative analysis of residues mean square displacements (shown to accurately reproduce crystallographic data) provides a reliable and statistically accurate method to identify crucial folding sites/contacts. This novel strategy is validated against clinical data for HIV-1 Protease. Finally, we compare the spectra and eigenmodes of vibration of natural proteins against randomly-generated compact structures and regular random graphs. The comparison reveals a distinctive enhanced flexibility of natural structures accompanied by slow relaxation times at the folding temperature. The fact that these properties are intimately connected to the presence and assembly of secondary motifs hints at the special criteria adopted by evolution in the selection of viable folds.Comment: Revtex 17 pages, 13 eps figure

    Inductive Pattern Formation

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    With the extended computational limits of algorithmic recursion, scientific investigation is transitioning away from computationally decidable problems and beginning to address computationally undecidable complexity. The analysis of deductive inference in structure-property models are yielding to the synthesis of inductive inference in process-structure simulations. Process-structure modeling has examined external order parameters of inductive pattern formation, but investigation of the internal order parameters of self-organization have been hampered by the lack of a mathematical formalism with the ability to quantitatively define a specific configuration of points. This investigation addressed this issue of quantitative synthesis. Local space was developed by the Poincare inflation of a set of points to construct neighborhood intersections, defining topological distance and introducing situated Boolean topology as a local replacement for point-set topology. Parallel development of the local semi-metric topological space, the local semi-metric probability space, and the local metric space of a set of points provides a triangulation of connectivity measures to define the quantitative architectural identity of a configuration and structure independent axes of a structural configuration space. The recursive sequence of intersections constructs a probabilistic discrete spacetime model of interacting fields to define the internal order parameters of self-organization, with order parameters external to the configuration modeled by adjusting the morphological parameters of individual neighborhoods and the interplay of excitatory and inhibitory point sets. The evolutionary trajectory of a configuration maps the development of specific hierarchical structure that is emergent from a specific set of initial conditions, with nested boundaries signaling the nonlinear properties of local causative configurations. This exploration of architectural configuration space concluded with initial process-structure-property models of deductive and inductive inference spaces. In the computationally undecidable problem of human niche construction, an adaptive-inductive pattern formation model with predictive control organized the bipartite recursion between an information structure and its physical expression as hierarchical ensembles of artificial neural network-like structures. The union of architectural identity and bipartite recursion generates a predictive structural model of an evolutionary design process, offering an alternative to the limitations of cognitive descriptive modeling. The low computational complexity of these models enable them to be embedded in physical constructions to create the artificial life forms of a real-time autonomously adaptive human habitat

    Design of Evolutionary Methods Applied to the Learning of Bayesian Network Structures

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    Bayesian Network, Ahmed Rebai (Ed.), ISBN: 978-953-307-124-4, pp. 13-38

    SCENELAB: Scene Labelling by a Society of Agents; A Distributed Constraint Propagation System

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    This paper describes SCENELAB, a computer system for labelling line drawings of scenes in simple polyhedral worlds. The key idea behind SCENELAB is to bring together the concept of contraint-based filtering algorithms and the paradigm of societies of cooperating agents. The problem of finding labellings for pictures drawn from blocks world scenes has been taken as a sample application. Clearly, this makes SCENELAB no vision system, but we claim that a system designed along these lines could be part of a real vision system. Following e.g. Alan Mackworth, we argue that constraint exploitation on resp. between various representational levels is a key technique of ‘seeing things'. Furthermore, constraints and constraint propagation neatly fit into the framework of societies of agents, realized by asynchronuously concurrent processing units and message passing mechanisms. SCENELAB, as it is actually running, can be used to specify and solve arbitrary Labelling problems that can be seen as instances of a particular class of simple constraint problems based on finite, pseudo-transitive binary constraints. However, it is felt that the overall approach generalizes to arbitrary constraint problems. Emphasis is given to a mathematical model of the problem and its solution, to be able to specify the reasoning techniques of SCENELAB, and to identify the class of problems it can handle. I tried to shed some Light onto the methodological background of SCENELAB, which seems necessary to judge the achievements and disachievements of the present work. After some introductory chapters on the key concepts involved in SCENELAB, (scene) labelling problems, constraint propagation, and societies of agents, an overview on both the structure and behavior of SCENELAB is given in part B of the paper. In part C, then, an algebraic model is introduced, which serves as a base for discussing several approaches to labelling problems, namely Waltz's original Landmark algorithm, a synchronized parallel solution suggested by Azriel Rosenfeld, and clearly, the present approach. A proof of the correctness of SCENELABs algorithms is included. This proof takes into account the specifities of systems of asynchronously communicating agents where no global state is observable

    Qualitative Process Analysis : Theoretical Requirements and Practical Implementation in Naval Domain

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    Understanding complex behaviours is an essential component of everyday life, integrated into daily routines as well as specialised research. To handle the increasing amount of data available from (logistic) dynamic scenarios, analysis of the behaviour of agents in a given environment is becoming more automated and thus requires reliable new analytical methods. This thesis seeks to improve analysis of observed data in dynamic scenarios by developing a new model for transforming sparse behavioural observations into realistic explanations of agent behaviours, with the goal of testing that model in a real-world maritime navigation scenario
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