The accuracy and complexity of machine learning algorithms based on kernel optimization are determined by the set of kernels over which they are able to optimize. An ideal set of kernels should: admit a linear parameterization (for tractability); be dense in the set of all kernels (for robustness); be universal (for accuracy). Recently, a framework was proposed for using positive matrices to parameterize a class of positive semi-separable kernels. Although this class can be shown to meet all three criteria, previous algorithms for optimization of such kernels were limited to classification and furthermore relied on computationally complex Semidefinite Programming (SDP) algorithms. In this paper, we pose the problem of learning semiseparable kernels as a minimax optimization problem and propose a SVD-QCQP primal-dual algorithm which dramatically reduces the computational complexity as compared with previous SDP-based approaches. Furthermore, we provide an efficient implementation of this algorithm for both classification and regression -- an implementation which enables us to solve problems with 100 features and up to 30,000 datums. Finally, when applied to benchmark data, the algorithm demonstrates the potential for significant improvement in accuracy over typical (but non-convex) approaches such as Neural Nets and Random Forest with similar or better computation time.

The immune response is a dynamic process by which the body determines whether an antigen is self or nonself. The state of this dynamic process is defined by the relative balance and population of inflammatory and regulatory actors which comprise this decision making process. The goal of immunotherapy as applied to, e.g. Rheumatoid Arthritis (RA), then, is to bias the immune state in favor of the regulatory actors - thereby shutting down autoimmune pathways in the response. While there are several known approaches to immunotherapy, the effectiveness of the therapy will depend on how this intervention alters the evolution of this state. Unfortunately, this process is determined not only by the dynamics of the process, but the state of the system at the time of intervention - a state which is difficult if not impossible to determine prior to application of the therapy. To identify such states we consider a mouse model of RA (Collagen-Induced Arthritis (CIA)) immunotherapy; collect high dimensional data on T cell markers and populations of mice after treatment with a recently developed immunotherapy for CIA; and use feature selection algorithms in order to select a lower dimensional subset of this data which can be used to predict both the full set of T cell markers and populations, along with the efficacy of immunotherapy treatment.

The accuracy and complexity of kernel learning algorithms is determined by the set of kernels over which it is able to optimize. An ideal set of kernels should: admit a linear parameterization (tractability); be dense in the set of all kernels (accuracy); and every member should be universal so that the hypothesis space is infinite-dimensional (scalability). Currently, there is no class of kernel that meets all three criteria - e.g. Gaussians are not tractable or accurate; polynomials are not scalable. We propose a new class that meet all three criteria - the Tessellated Kernel (TK) class. Specifically, the TK class: admits a linear parameterization using positive matrices; is dense in all kernels; and every element in the class is universal. This implies that the use of TK kernels for learning the kernel can obviate the need for selecting candidate kernels in algorithms such as SimpleMKL and parameters such as the bandwidth. Numerical testing on soft margin Support Vector Machine (SVM) problems show that algorithms using TK kernels outperform other kernel learning algorithms and neural networks. Furthermore, our results show that when the ratio of the number of training data to features is high, the improvement of TK over MKL increases significantly.