Multiple kernel learning

About: Multiple kernel learning is a research topic. Over the lifetime, 1630 publications have been published within this topic receiving 56082 citations.

Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery.

Abstract: Motivation: Despite ongoing cancer research, available therapies are still limited in quantity and effectiveness, and making treatment decisions for individual patients remains a hard problem. Established subtypes, which help guide these decisions, are mainly based on individual data types. However, the analysis of multidimensional patient data involving the measurements of various molecular features could reveal intrinsic characteristics of the tumor. Large-scale projects accumulate this kind of data for various cancer types, but we still lack the computational methods to reliably integrate this information in a meaningful manner. Therefore, we apply and extend current multiple kernel learning for dimensionality reduction approaches. On the one hand, we add a regularization term to avoid overfitting during the optimization procedure, and on the other hand, we show that one can even use several kernels per data type and thereby alleviate the user from having to choose the best kernel functions and kernel parameters for each data type beforehand. Results: We have identified biologically meaningful subgroups for five different cancer types. Survival analysis has revealed significant differences between the survival times of the identified subtypes, with P values comparable or even better than state-of-the-art methods. Moreover, our resulting subtypes reflect combined patterns from the different data sources, and we demonstrate that input kernel matrices with only little information have less impact on the integrated kernel matrix. Our subtypes show different responses to specific therapies, which could eventually assist in treatment decision making. Availability and implementation: An executable is available upon request. Contact: ed.gpm.fni-ipm@aron or ed.gpm.fni-ipm@refiefpn

Sparsity in multiple kernel learning

Abstract: The problem of multiple kernel learning based on penalized empirical risk minimization is discussed. The complexity penalty is determined jointly by the empirical $L_2$ norms and the reproducing kernel Hilbert space (RKHS) norms induced by the kernels with a data-driven choice of regularization parameters. The main focus is on the case when the total number of kernels is large, but only a relatively small number of them is needed to represent the target function, so that the problem is sparse. The goal is to establish oracle inequalities for the excess risk of the resulting prediction rule showing that the method is adaptive both to the unknown design distribution and to the sparsity of the problem.

Low-rank Kernel Learning for Graph-based Clustering

Abstract: Constructing the adjacency graph is fundamental to graph-based clustering. Graph learning in kernel space has shown impressive performance on a number of benchmark data sets. However, its performance is largely determined by the chosen kernel matrix. To address this issue, previous multiple kernel learning algorithm has been applied to learn an optimal kernel from a group of predefined kernels. This approach might be sensitive to noise and limits the representation ability of the consensus kernel. In contrast to existing methods, we propose to learn a low-rank kernel matrix which exploits the similarity nature of the kernel matrix and seeks an optimal kernel from the neighborhood of candidate kernels. By formulating graph construction and kernel learning in a unified framework, the graph and consensus kernel can be iteratively enhanced by each other. Extensive experimental results validate the efficacy of the proposed method.