Browsing Isolated Population Data

BACKGROUND: In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships. To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies. RESULTS: The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype), or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects. AVAILABILITY: PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our sit

Solving equations in the universe of hypersets

Ankara : Department of Computer Engineering and Information Science and Institute of Engineering and Science, Bilkent Univ., 1993.Thesis (Master's) -- Bilkent University, 1993.Includes bibliographical references leaves 46-50Hyperset Theory (a.k.a. ZFC~/AFA) of Peter Aczel is an enrichment of the classical ZFC set theory and uses a graphical representation for sets. By allowing non-well-founded sets, the theory provides an appropriate framework for modeling various phenomena involving circularity. Z F C /A F A has an important consequence that guarantees a solution to a set of equations in the universe of hypersets, viz. the Solution Lemma. This lemma asserts that a system of equations defined in the universe of hypersets has a unique solution, and has applications in areas like artificial intelligence, database theory, and situation theory. In this thesis, a program called HYPERSOLVER, which can solve systems of equations to which the Solution Lemma is applicable and which has built-in procedures to display the graphs depicting the solutions, is presented.Pakkan, MüjdatM.S

A new formulation for symbolic regression to identify physico-chemical laws from experimental data

A modification to the mixed-integer nonlinear programming (MINLP) formulation for symbolic regression was proposed with the aim of identification of physical models from noisy experimental data. In the proposed formulation, a binary tree in which equations are represented as directed, acyclic graphs, is fully constructed for a pre-defined number of layers. The introduced modification results in the reduction in the number of required binary variables and removal of redundancy due to possible symmetry of the tree formulation. The formulation was tested using numerical models and was found to be more efficient than the previous literature example with respect to the numbers of predictor variables and training data points. The globally optimal search was extended to identify physical models and to cope with noise in the experimental data predictor variable. The methodology was proven to be successful in identifying the correct physical models describing the relationship between shear stress and shear rate for both Newtonian and non-Newtonian fluids, and simple kinetic laws of chemical reactions. Future work will focus on addressing the limitations of the present formulation and solver to enable extension of target problems to larger, more complex physical models.EPSRC EP/R009902/

HYPERSOLVER: A graphical tool for commonsense set theory

This paper investigates an alternative set theory (due to Aczel) called the Hyperset Theory. Aczel uses a graphical representation for sets and thereby allows the representation of non-well-founded sets. A program, called hypersolver, which can solve systems of equations defined in terms of sets in the universe of this new theory is presented. This may be a useful tool for commonsense reasoning. © 1995

Exploring multiple trees through DAG representations

We present a Directed Acyclic Graph visualisation designed to allow interaction with a set of multiple classification trees, specifically to find overlaps and differences between groups of trees and individual trees. The work is motivated by the need to find a representation for multiple trees that has the space-saving property of a general graph representation and the intuitive parent-child direction cues present in individual representation of trees. Using example taxonomic data sets, we describe augmentations to the common barycenter DAG layout method that reveal shared sets of child nodes between common parents in a clearer manner. Other interactions such as displaying the multiple ancestor paths of a node when it occurs in several trees, and revealing intersecting sibling sets within the context of a single DAG representation are also discussed

An interaction paradigm for impact analysis

The Aerospace industry is concerned with huge software projects. Software development is an evolving process resulting in larger and larger software systems. As systems grow in size, they become more complex and hence harder to maintain. Thus it appears that the maintenance of software systems is the most expensive part of the software life-cycle, often consuming 50-90% of a project total budget. Yet while there has been much research carried out on the problems of program and system development very little work has been done on the problem of maintaining developed programs. Thus it will be essential to improve the software maintenance process and the environment for maintenance. Historically, the term Software Maintenance has been applied to the process of modifying a software program after it has been delivered and during its life time. The high cost of software during its life cycle can be attributed largely to software maintenance activities, and a major part of these activities is to deal with the modifications of the software. These modifications may involve changes at any level of abstraction of a software system (i.e design, specification, code,...). Software Maintenance has to deal with modifications which can have severe Ripple Effects at other points in the software system. Impact Analysis addresses the problem and attempts to localize these Ripple Effects. In this thesis the Software Maintenance process and more specifically the Impact Analysis process is examined. The different parts of the implementation for the Impact Analysis System are explained. The main results of the thesis are the dependencies generation and the graph tool used to visualize these dependencies as well as the impacts on general dependency graph for impact analysis purpose

PlanView & HViews : graphical user interfaces for viewing plan data

Visualizing and navigating through a plan is difficult without graphics. Two X applications, PlanView and HViews, are graphical user interfaces to an AI planner, OPIE, developed at the University of Oregon. In addition to a plan generator, OPIE includes a facility to generate operator abstractions which in turn are used in the development and refinement of a plan. Therefore, PlanView orchestrates a collection of windows that allows its user to graphically visualize and navigate through the plan, while HViews allow the user to visualize where plan components (e.g., operators and domain objects) reside in the hierarchy of component abstractions. This paper describes how three types of user interfaces are used and implemented: Graph View to visualize a directed graph, Graph Browser to view details specific to a node selected in the Graph View, and Domain Object List to view details about instances of domain objects. In addition, three different layout algorithms that were implemented and used by the Graph View interface are described