A Planning System for Robot Construction Tasks

This paper describes BUILD, a computer program which generates plans for building specified structures out of simple objects such as toy blocks. A powerful heuristic control structure enables BUILD to use a number of sophisticated construction techniques in its plans. Among these are the incorporation of pre-existing structure into the final design, pre-assembly of movable sub-structures on the table, and use of the extra blocks as temporary supports and counterweights in the course of construction. BUILD does its planning in a modeled 3-space in which blocks of various shapes and sizes can be represented in any orientation and location. The modeling system can maintain several world models at once, and contains modules for displaying states, testing them for inter-object contact and collision, and for checking the stability of complex structures involving frictional forces. Various alternative approaches are discussed, and suggestions are included for the extension of BUILD-like systems to other domains. Also discussed are the merits of BUILD's implementation language, CONNIVER, for this type of problem solving.

Understanding Subsystems in Biology through Dimensionality Reduction, Graph Partitioning and Analytical Modeling

Biological systems exhibit rich and complex behavior through the orchestrated interplay of a large array of components. It is hypothesized that separable subsystems with some degree of functional autonomy exist; deciphering their independent behavior and functionality would greatly facilitate understanding the system as a whole. Discovering and analyzing such subsystems are hence pivotal problems in the quest to gain a quantitative understanding of complex biological systems. In this work, using approaches from machine learning, physics and graph theory, methods for the identification and analysis of such subsystems were developed. A novel methodology, based on a recent machine learning algorithm known as non-negative matrix factorization (NMF), was developed to discover such subsystems in a set of large-scale gene expression data. This set of subsystems was then used to predict functional relationships between genes, and this approach was shown to score significantly higher than conventional methods when benchmarking them against existing databases. Moreover, a mathematical treatment was developed to treat simple network subsystems based only on their topology (independent of particular parameter values). Application to a problem of experimental interest demonstrated the need for extentions to the conventional model to fully explain the experimental data. Finally, the notion of a subsystem was evaluated from a topological perspective. A number of different protein networks were examined to analyze their topological properties with respect to separability, seeking to find separable subsystems. These networks were shown to exhibit separability in a nonintuitive fashion, while the separable subsystems were of strong biological significance. It was demonstrated that the separability property found was not due to incomplete or biased data, but is likely to reflect biological structure.