Synthesizing Regularity Exposing Attributes in Large Protein Databases

This thesis describes a system that synthesizes regularity exposing attributes from large protein databases. After processing primary and secondary structure data, this system discovers an amino acid representation that captures what are thought to be the three most important amino acid characteristics (size, charge, and hydrophobicity) for tertiary structure prediction. A neural network trained using this 16 bit representation achieves a performance accuracy on the secondary structure prediction problem that is comparable to the one achieved by a neural network trained using the standard 24 bit amino acid representation. In addition, the thesis describes bounds on secondary structure prediction accuracy, derived using an optimal learning algorithm and the probably approximately correct (PAC) model.

Trajectory and Force Control of a Direct Drive Arm

Using the MIT Serial Link Direct Drive Arm as the main experimental device, various issues in trajectory and force control of manipulators were studied in this thesis. Since accurate modeling is important for any controller, issues of estimating the dynamic model of a manipulator and its load were addressed first. Practical and effective algorithms were developed fro the Newton-Euler equations to estimate the inertial parameters of manipulator rigid-body loads and links. Load estimation was implemented both on PUMA 600 robot and on the MIT Serial Link Direct Drive Arm. With the link estimation algorithm, the inertial parameters of the direct drive arm were obtained. For both load and link estimation results, the estimated parameters are good models of the actual system for control purposes since torques and forces can be predicted accurately from these estimated parameters. The estimated model of the direct drive arm was them used to evaluate trajectory following performance by feedforward and computed torque control algorithms. The experimental evaluations showed that the dynamic compensation can greatly improve trajectory following accuracy. Various stability issues of force control were studied next. It was determined that there are two types of instability in force control. Dynamic instability, present in all of the previous force control algorithms discussed in this thesis, is caused by the interaction of a manipulator with a stiff environment. Kinematics instability is present only in the hybrid control algorithm of Raibert and Craig, and is caused by the interaction of the inertia matrix with the Jacobian inverse coordinate transformation in the feedback path. Several methods were suggested and demonstrated experimentally to solve these stability problems. The result of the stability analyses were then incorporated in implementing a stable force/position controller on the direct drive arm by the modified resolved acceleration method using both joint torque and wrist force sensor feedbacks.

Comparing Support Vector Machines with Gaussian Kernels to Radial Basis Function Classifiers

The Support Vector (SV) machine is a novel type of learning machine, based on statistical learning theory, which contains polynomial classifiers, neural networks, and radial basis function (RBF) networks as special cases. In the RBF case, the SV algorithm automatically determines centers, weights and threshold such as to minimize an upper bound on the expected test error. The present study is devoted to an experimental comparison of these machines with a classical approach, where the centers are determined by $k$--means clustering and the weights are found using error backpropagation. We consider three machines, namely a classical RBF machine, an SV machine with Gaussian kernel, and a hybrid system with the centers determined by the SV method and the weights trained by error backpropagation. Our results show that on the US postal service database of handwritten digits, the SV machine achieves the highest test accuracy, followed by the hybrid approach. The SV approach is thus not only theoretically well--founded, but also superior in a practical application.

On Convergence Properties of the EM Algorithm for Gaussian Mixtures

"Expectation-Maximization'' (EM) algorithm and gradient-based approaches for maximum likelihood learning of finite Gaussian mixtures. We show that the EM step in parameter space is obtained from the gradient via a projection matrix $P$, and we provide an explicit expression for the matrix. We then analyze the convergence of EM in terms of special properties of $P$ and provide new results analyzing the effect that $P$ has on the likelihood surface. Based on these mathematical results, we present a comparative discussion of the advantages and disadvantages of EM and other algorithms for the learning of Gaussian mixture models.