Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

Simplex basis function based sparse least squares support vector regression

In this paper, a novel sparse least squares support vector regression algorithm, referred to as LSSVR-SBF, is introduced which uses a new low rank kernel based on simplex basis function, which has a set of nonlinear parameters. It is shown that the proposed model can be represented as a sparse linear regression model based on simplex basis functions. We propose a fast algorithm for least squares support vector regression solution at the cost of O(N) by avoiding direct kernel matrix inversion. An iterative estimation algorithm has been proposed to optimize the nonlinear parameters associated with the simplex basis functions with the aim of minimizing model mean square errors using the gradient descent algorithm. The proposed fast least square solution and the gradient descent algorithm are alternatively applied. Finally it is shown that the model has a dual representation as a piecewise linear model with respect to the system input. Numerical experiments are carried out to demonstrate the effectiveness of the proposed approaches

Software reliability through fault-avoidance and fault-tolerance

The use of back-to-back, or comparison, testing for regression test or porting is examined. The efficiency and the cost of the strategy is compared with manual and table-driven single version testing. Some of the key parameters that influence the efficiency and the cost of the approach are the failure identification effort during single version program testing, the extent of implemented changes, the nature of the regression test data (e.g., random), and the nature of the inter-version failure correlation and fault-masking. The advantages and disadvantages of the technique are discussed, together with some suggestions concerning its practical use

Proceedings of the ECCS 2005 satellite workshop: embracing complexity in design - Paris 17 November 2005

Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr). Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr)

A Novel Machine Learning Classifier Based on a Qualia Modeling Agent (QMA)

This dissertation addresses a problem found in supervised machine learning (ML) classification, that the target variable, i.e., the variable a classifier predicts, has to be identified before training begins and cannot change during training and testing. This research develops a computational agent, which overcomes this problem. The Qualia Modeling Agent (QMA) is modeled after two cognitive theories: Stanovich\u27s tripartite framework, which proposes learning results from interactions between conscious and unconscious processes; and, the Integrated Information Theory (IIT) of Consciousness, which proposes that the fundamental structural elements of consciousness are qualia. By modeling the informational relationships of qualia, the QMA allows for retaining and reasoning-over data sets in a non-ontological, non-hierarchical qualia space (QS). This novel computational approach supports concept drift, by allowing the target variable to change ad infinitum without re-training while achieving classification accuracy comparable to or greater than benchmark classifiers. Additionally, the research produced a functioning model of Stanovich\u27s framework, and a computationally tractable working solution for a representation of qualia, which when exposed to new examples, is able to match the causal structure and generate new inferences