User hints for optimisation processes

Innovative improvements in the area of Human-Computer Interaction and User Interfaces have en-abled intuitive and effective applications for a variety of problems. On the other hand, there has also been the realization that several real-world optimization problems still cannot be totally auto-mated. Very often, user interaction is necessary for refining the optimization problem, managing the computational resources available, or validating or adjusting a computer-generated solution. This thesis investigates how humans can help optimization methods to solve such difficult prob-lems. It presents an interactive framework where users play a dynamic and important role by pro-viding hints. Hints are actions that help to insert domain knowledge, to escape from local minima, to reduce the space of solutions to be explored, or to avoid ambiguity when there is more than one optimal solution. Examples of user hints are adjustments of constraints and of an objective function, focusing automatic methods on a subproblem of higher importance, and manual changes of an ex-isting solution. User hints are given in an intuitive way through a graphical interface. Visualization tools are also included in order to inform about the state of the optimization process. We apply the User Hints framework to three combinatorial optimization problems: Graph Clus-tering, Graph Drawing and Map Labeling. Prototype systems are presented and evaluated for each problem. The results of the study indicate that optimization processes can benefit from human interaction. The main goal of this thesis is to list cases where human interaction is helpful, and provide an ar-chitecture for supporting interactive optimization. Our contributions include the general User Hints framework and particular implementations of it for each optimization problem. We also present a general process, with guidelines, for applying our framework to other optimization problems

An approach to display layout of dynamic windows

The development of windows based user interface has introduced a new dimension to the field of human computer interaction. Now a user is able to perform multiple tasks at a time, often switching from one task to another. However windows environment also imposes the burden of manual windows management on the user. Several studies have suggested that manual window management is an unproductive chore often resulting in clutter and confusion on the display screen. Therefore we need a automatic windows layout generator to free the user to perform other useful tasks. This thesis introduces SPORDAC {Shadow Propagation for Overlap Removal and Display Area Compaction) algorithm. This algorithm aims to remove overlap from the display layout and encapsulate the layout in the finite display area. The SPORDAC prototype integrates the SPORDAC algorithm with simulated annealing to optimise the display area usage. The usefulness and applicability of the SPORDAC approach are illustrated with the implementation of a prototype, samples of generated layouts and analysis of the collected dat

Research in constraint-based layout, visualization, CAD, and related topics : a bibliographical survey

The present work compiles numerous papers in the area of computer-aided design, graphics, layout configuration, and user interfaces in general. There is nearly no conference on graphics, multimedia, and user interfaces that does not include a section on constraint-based graphics; on the other hand most conferences on constraint processing favour applications in graphics. This work of bibliographical pointers may serve as a basis for a detailed and comprehensive survey of this important and challenging field in the intersection of constraint processing and graphics. In order to reach this ambitious aim, and also to keep this study up-to-date, the authors appreciate any comment and update information

Structural and functional analysis of cellular networks with CellNetAnalyzer

BACKGROUND: Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. An important class of methods in Systems Biology deals with structural or topological (parameter-free) analysis of cellular networks. So far, software tools providing such methods for both mass-flow (metabolic) as well as signal-flow (signalling and regulatory) networks are lacking. RESULTS: Herein we introduce CellNetAnalyzer, a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks. The particular strengths of CellNetAnalyzer are methods for functional network analysis, i.e. for characterising functional states, for detecting functional dependencies, for identifying intervention strategies, or for giving qualitative predictions on the effects of perturbations. CellNetAnalyzer extends its predecessor FluxAnalyzer (originally developed for metabolic network and pathway analysis) by a new modelling framework for examining signal-flow networks. Two of the novel methods implemented in CellNetAnalyzer are discussed in more detail regarding algorithmic issues and applications: the computation and analysis (i) of shortest positive and shortest negative paths and circuits in interaction graphs and (ii) of minimal intervention sets in logical networks. CONCLUSION: CellNetAnalyzer provides a single suite to perform structural and qualitative analysis of both mass-flow- and signal-flow-based cellular networks in a user-friendly environment. It provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis.CellNetAnalyzer is freely available for academic use

NETEMBED: A Network Resource Mapping Service for Distributed Applications

Emerging configurable infrastructures such as large-scale overlays and grids, distributed testbeds, and sensor networks comprise diverse sets of available computing resources (e.g., CPU and OS capabilities and memory constraints) and network conditions (e.g., link delay, bandwidth, loss rate, and jitter) whose characteristics are both complex and time-varying. At the same time, distributed applications to be deployed on these infrastructures exhibit increasingly complex constraints and requirements on resources they wish to utilize. Examples include selecting nodes and links to schedule an overlay multicast file transfer across the Grid, or embedding a network experiment with specific resource constraints in a distributed testbed such as PlanetLab. Thus, a common problem facing the efficient deployment of distributed applications on these infrastructures is that of "mapping" application-level requirements onto the network in such a manner that the requirements of the application are realized, assuming that the underlying characteristics of the network are known. We refer to this problem as the network embedding problem. In this paper, we propose a new approach to tackle this combinatorially-hard problem. Thanks to a number of heuristics, our approach greatly improves performance and scalability over previously existing techniques. It does so by pruning large portions of the search space without overlooking any valid embedding. We present a construction that allows a compact representation of candidate embeddings, which is maintained by carefully controlling the order via which candidate mappings are inserted and invalid mappings are removed. We present an implementation of our proposed technique, which we call NETEMBED – a service that identify feasible mappings of a virtual network configuration (the query network) to an existing real infrastructure or testbed (the hosting network). We present results of extensive performance evaluation experiments of NETEMBED using several combinations of real and synthetic network topologies. Our results show that our NETEMBED service is quite effective in identifying one (or all) possible embeddings for quite sizable queries and hosting networks – much larger than what any of the existing techniques or services are able to handle.National Science Foundation (CNS Cybertrust 0524477, NSF CNS NeTS 0520166, NSF CNS ITR 0205294, EIA RI 0202067

A Causal Interpretation of Selection Theory

The following dissertation is an inferentialist account of classical population genetics. I present the theory as a definite body of interconnected inferential rules for generating mathematical models of population dynamics. To state those rules, I use the notion of causation as a primitive. First, I put forward a rule stating the circumstances of application of the theory, one that uses causal language to pick out the types of entities over which the theory may be deployed. Next, I offer a rule for grouping such entities into populations based on their competitive causal relationships. Then I offer a general algorithm for generating classical population genetics models for such populations on the basis of what causal influences operate within them.Dynamical models in population genetics are designed to demystify natural phenomena, chiefly to show how adaptation, altruism, and genetic polymorphism can be explained in terms of natural rather than supernatural processes. In order for the theory to serve this purpose, it must be possible to understand, in a principled fashion, when and how to deploy the theory. By presenting the theory as a system of ordered inferential rules that takes causal information as its critical input and yields dynamical models as its outputs, I show explicitly how classical population genetics functions as a non-circular theoretical apparatus for generating explanations. The generalization of the theory achieved by presenting it using causal vocabulary shows how the scope of the theory of natural selection extends beyond its traditional domain of systems distinguished by genetic variations