Equivalence and Reduction of Hidden Markov Models

This report studies when and why two Hidden Markov Models (HMMs) may represent the same stochastic process. HMMs are characterized in terms of equivalence classes whose elements represent identical stochastic processes. This characterization yields polynomial time algorithms to detect equivalent HMMs. We also find fast algorithms to reduce HMMs to essentially unique and minimal canonical representations. The reduction to a canonical form leads to the definition of 'Generalized Markov Models' which are essentially HMMs without the positivity constraint on their parameters. We discuss how this generalization can yield more parsimonious representations of stochastic processes at the cost of the probabilistic interpretation of the model parameters.

Basis Reduction Algorithms and Subset Sum Problems

This thesis investigates a new approach to lattice basis reduction suggested by M. Seysen. Seysen's algorithm attempts to globally reduce a lattice basis, whereas the Lenstra, Lenstra, Lovasz (LLL) family of reduction algorithms concentrates on local reductions. We show that Seysen's algorithm is well suited for reducing certain classes of lattice bases, and often requires much less time in practice than the LLL algorithm. We also demonstrate how Seysen's algorithm for basis reduction may be applied to subset sum problems. Seysen's technique, used in combination with the LLL algorithm, and other heuristics, enables us to solve a much larger class of subset sum problems than was previously possible.

Residual Vibration Reduction in Computer Controlled Machines

Control of machines that exhibit flexibility becomes important when designers attempt to push the state of the art with faster, lighter machines. Three steps are necessary for the control of a flexible planet. First, a good model of the plant must exist. Second, a good controller must be designed. Third, inputs to the controller must be constructed using knowledge of the system dynamic response. There is a great deal of literature pertaining to modeling and control but little dealing with the shaping of system inputs. Chapter 2 examines two input shaping techniques based on frequency domain analysis. The first involves the use of the first deriviate of a gaussian exponential as a driving function template. The second, acasual filtering, involves removal of energy from the driving functions at the resonant frequencies of the system. Chapter 3 presents a linear programming technique for generating vibration-reducing driving functions for systems. Chapter 4 extends the results of the previous chapter by developing a direct solution to the new class of driving functions. A detailed analysis of the new technique is presented from five different perspectives and several extensions are presented. Chapter 5 verifies the theories of the previous two chapters with hardware experiments. Because the new technique resembles common signal filtering, chapter 6 compares the new approach to eleven standard filters. The new technique will be shown to result in less residual vibrations, have better robustness to system parameter uncertainty, and require less computation than other currently used shaping techniques.

Noise Reduction Using Low Weight and Constant Weight Coding Techniques

Signalling off-chip requires significant current. As a result, a chip's power-supply current changes drastically during certain output-bus transitions. These current fluctuations cause a voltage drop between the chip and circuit board due to the parasitic inductance of the power-supply package leads. Digital designers often go to great lengths to reduce this "transmitted" noise. Cray, for instance, carefully balances output signals using a technique called differential signalling to guarantee a chip has constant output current. Transmitted-noise reduction costs Cray a factor of two in output pins and wires. Coding achieves similar results at smaller costs.

Using Recurrent Networks for Dimensionality Reduction

This report explores how recurrent neural networks can be exploited for learning high-dimensional mappings. Since recurrent networks are as powerful as Turing machines, an interesting question is how recurrent networks can be used to simplify the problem of learning from examples. The main problem with learning high-dimensional functions is the curse of dimensionality which roughly states that the number of examples needed to learn a function increases exponentially with input dimension. This thesis proposes a way of avoiding this problem by using a recurrent network to decompose a high-dimensional function into many lower dimensional functions connected in a feedback loop.

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.

Model Order Reduction for Determining Bubble Parameters to Attain a Desired Fluid Surface Shape

In this paper, a new methodology for predicting fluid free surface shape using Model Order Reduction (MOR) is presented. Proper Orthogonal Decomposition combined with a linear interpolation procedure for its coefficient is applied to a problem involving bubble dynamics near to a free surface. A model is developed to accurately and efficiently capture the variation of the free surface shape with different bubble parameters. In addition, a systematic approach is developed within the MOR framework to find the best initial locations and pressures for a set of bubbles beneath the quiescent free surface such that the resultant free surface attained is close to a desired shape. Predictions of the free surface in two-dimensions and three-dimensions are presented.