A Theory of Networks for Appxoimation and Learning

Learning an input-output mapping from a set of examples, of the type that many neural networks have been constructed to perform, can be regarded as synthesizing an approximation of a multi-dimensional function, that is solving the problem of hypersurface reconstruction. From this point of view, this form of learning is closely related to classical approximation techniques, such as generalized splines and regularization theory. This paper considers the problems of an exact representation and, in more detail, of the approximation of linear and nolinear mappings in terms of simpler functions of fewer variables. Kolmogorov's theorem concerning the representation of functions of several variables in terms of functions of one variable turns out to be almost irrelevant in the context of networks for learning. We develop a theoretical framework for approximation based on regularization techniques that leads to a class of three-layer networks that we call Generalized Radial Basis Functions (GRBF), since they are mathematically related to the well-known Radial Basis Functions, mainly used for strict interpolation tasks. GRBF networks are not only equivalent to generalized splines, but are also closely related to pattern recognition methods such as Parzen windows and potential functions and to several neural network algorithms, such as Kanerva's associative memory, backpropagation and Kohonen's topology preserving map. They also have an interesting interpretation in terms of prototypes that are synthesized and optimally combined during the learning stage. The paper introduces several extensions and applications of the technique and discusses intriguing analogies with neurobiological data.

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.