Kernel methods in genomics and computational biology

Support vector machines and kernel methods are increasingly popular in genomics and computational biology, due to their good performance in real-world applications and strong modularity that makes them suitable to a wide range of problems, from the classification of tumors to the automatic annotation of proteins. Their ability to work in high dimension, to process non-vectorial data, and the natural framework they provide to integrate heterogeneous data are particularly relevant to various problems arising in computational biology. In this chapter we survey some of the most prominent applications published so far, highlighting the particular developments in kernel methods triggered by problems in biology, and mention a few promising research directions likely to expand in the future

Spectral Norm of Random Kernel Matrices with Applications to Privacy

Kernel methods are an extremely popular set of techniques used for many important machine learning and data analysis applications. In addition to having good practical performances, these methods are supported by a well-developed theory. Kernel methods use an implicit mapping of the input data into a high dimensional feature space defined by a kernel function, i.e., a function returning the inner product between the images of two data points in the feature space. Central to any kernel method is the kernel matrix, which is built by evaluating the kernel function on a given sample dataset. In this paper, we initiate the study of non-asymptotic spectral theory of random kernel matrices. These are n x n random matrices whose (i,j)th entry is obtained by evaluating the kernel function on $x_i$ and $x_j$, where $x_1,...,x_n$ are a set of n independent random high-dimensional vectors. Our main contribution is to obtain tight upper bounds on the spectral norm (largest eigenvalue) of random kernel matrices constructed by commonly used kernel functions based on polynomials and Gaussian radial basis. As an application of these results, we provide lower bounds on the distortion needed for releasing the coefficients of kernel ridge regression under attribute privacy, a general privacy notion which captures a large class of privacy definitions. Kernel ridge regression is standard method for performing non-parametric regression that regularly outperforms traditional regression approaches in various domains. Our privacy distortion lower bounds are the first for any kernel technique, and our analysis assumes realistic scenarios for the input, unlike all previous lower bounds for other release problems which only hold under very restrictive input settings.Comment: 16 pages, 1 Figur

Asymptotic Normality of Support Vector Machine Variants and Other Regularized Kernel Methods

In nonparametric classification and regression problems, regularized kernel methods, in particular support vector machines, attract much attention in theoretical and in applied statistics. In an abstract sense, regularized kernel methods (simply called SVMs here) can be seen as regularized M-estimators for a parameter in a (typically infinite dimensional) reproducing kernel Hilbert space. For smooth loss functions, it is shown that the difference between the estimator, i.e.\ the empirical SVM, and the theoretical SVM is asymptotically normal with rate $\sqrt{n}$. That is, the standardized difference converges weakly to a Gaussian process in the reproducing kernel Hilbert space. As common in real applications, the choice of the regularization parameter may depend on the data. The proof is done by an application of the functional delta-method and by showing that the SVM-functional is suitably Hadamard-differentiable