A software architecture for reconstructability analysis

Abstract

Software packages for Reconstructability Analysis (RA), as well as for related Log Linear modeling, generally provide a fixed set of functions. Such packages are suitable for end-users applying RA in various domains, but do not provide a platform for research into the RA methods themselves.A new software system, Occam3, is being developed which is intended to address three goals which often conflict with one another: to provide (1) a general and flexible infrastructure for experimentation with RA methods and algorithms; (2) an easily-configured system allowing methods to be combined in novel ways, without requiring deep software expertise; and (3) a system which can be easily utilized by domain researchers who are not computer specialists.Meeting these goals has led to an architecture which strictly separates functions into three layers: the Core, which provides representation of datasets, relations, and models; the Management Layer, which provides extensible objects for development of new algorithms; and the Script Layer, which allows the other facilities to be combined in novel ways to address a particular domain analysis problem.

Reconstructability Analysis of Epistasis

“…Calculations for the examples below were done by the IRA program, OCCAM (Willett & Zwick, 2004;Fusion et al, 2010;Zwick, 2010), and by separate SRA and state-based IRA (Johnson, 2005) programs also developed at Portland State University. (2002); B and G there are here renamed A and B.…”

Reconstructability analysis of genetic loci associated with Alzheimer disease

“…The earliest program was developed by Zwick and Hosseini [33]; reviews of RA methodology [19], [20], a list of recent RA papers, an OCCAM manual [34] and a description of OCCAM architecture [35] are available.…”

Using Reconstructability Analysis for Input Variable Reduction: A Business Example

“…The earliest of these programs was developed by Zwick and Hosseini [13]; a list of recent RA papers of the PSU group is given in [14] and [15].…”