A Perturbation Scheme for Spherical Arrangements with Application to Molecular Modeling

We describe a software package for computing and manipulating the subdivision of a sphere by a collection of (not necessarily great) circles and for computing the boundary surface of the union of spheres. We present problems that arise in the implementation of the software and the solutions that we have found for them. At the core of the paper is a novel perturbation scheme to overcome degeneracies and precision problems in computing spherical arrangements while using floating point arithmetic. The scheme is relatively simple, it balances between the efficiency of computation and the magnitude of the perturbation, and it performs well in practice. In one O(n) time pass through the data, it perturbs the inputs necessary to insure no potential degeneracies and then passes the perturbed inputs on to the geometric algorithm. We report and discuss experimental results. Our package is a major component in a larger package aimed to support geometric queries on molecular models; it is currently employed by chemists working in "rational drug design." The spherical subdivisions are used to construct a geometric model of a molecule where each sphere represents an atom. We also give an overview of the molecular modeling package and detail additional features and implementation issues.

ARLO: Another Representation Language Offer

This paper describes ARLO, a representation language loosely modelled after Greiner and Lenant's RLL-1. ARLO is a structure-based representation language for describing structure-based representation languages, including itself. A given representation language is specified in ARLO by a collection of structures describing how its descriptions are interpreted, defaulted, and verified. This high level description is compiles into lisp code and ARLO structures whose interpretation fulfills the specified semantics of the representation. In addition, ARLO itself- as a representation language for expressing and compiling partial and complete language specifications- is described and interpreted in the same manner as the language it describes and implements. This self-description can be extended of modified to expand or alter the expressive power of ARLO's initial configuration. Languages which describe themselves like ARLO- provide powerful mediums for systems which perform automatic self-modification, optimization, debugging, or documentation. AI systems implemented in such a self-descriptive language can reflect on their own capabilities and limitations, applying general learning and problem solving strategies to enlarge or alleviate them.

Learning from Ambiguity

There are many learning problems for which the examples given by the teacher are ambiguously labeled. In this thesis, we will examine one framework of learning from ambiguous examples known as Multiple-Instance learning. Each example is a bag, consisting of any number of instances. A bag is labeled negative if all instances in it are negative. A bag is labeled positive if at least one instance in it is positive. Because the instances themselves are not labeled, each positive bag is an ambiguous example. We would like to learn a concept which will correctly classify unseen bags. We have developed a measure called Diverse Density and algorithms for learning from multiple-instance examples. We have applied these techniques to problems in drug design, stock prediction, and image database retrieval. These serve as examples of how to translate the ambiguity in the application domain into bags, as well as successful examples of applying Diverse Density techniques.