One of the major problems in computational biology is the inability of existing classification models to incorporate expanding and new domain knowledge. This problem of static classification models is addressed in this paper by the introduction of incremental learning for problems in bioinformatics. Many machine learning tools have been applied to this problem using static machine learning structures such as neural networks or support vector machines that are unable to accommodate new information into their existing models. We utilize the fuzzy ARTMAP as an alternate machine learning system that has the ability of incrementally learning new data as it becomes available. The fuzzy ARTMAP is found to be comparable to many of the widespread machine learning systems. The use of an evolutionary strategy in the selection and combination of individual classifiers into an ensemble system, coupled with the incremental learning ability of the fuzzy ARTMAP is proven to be suitable as a pattern classifier. The algorithm presented is tested using data from the G-Coupled Protein Receptors Database and shows good accuracy of 83%. The system presented is also generally applicable, and can be used in problems in genomics and proteomics.

Ordinal regression is an important type of learning, which has properties of both classification and regression. Here we describe a simple and effective approach to adapt a traditional neural network to learn ordinal categories. Our approach is a generalization of the perceptron method for ordinal regression. On several benchmark datasets, our method (NNRank) outperforms a neural network classification method. Compared with the ordinal regression methods using Gaussian processes and support vector machines, NNRank achieves comparable performance. Moreover, NNRank has the advantages of traditional neural networks: learning in both online and batch modes, handling very large training datasets, and making rapid predictions. These features make NNRank a useful and complementary tool for large-scale data processing tasks such as information retrieval, web page ranking, collaborative filtering, and protein ranking in Bioinformatics.

In this paper we propose a new receiver for digital communications. We focus on the application of Gaussian Processes (GPs) to the multiuser detection (MUD) in code division multiple access (CDMA) systems to solve the near-far problem. Hence, we aim to reduce the interference from other users sharing the same frequency band. While usual approaches minimize the mean square error (MMSE) to linearly retrieve the user of interest, we exploit the same criteria but in the design of a nonlinear MUD. Since the optimal solution is known to be nonlinear, the performance of this novel method clearly improves that of the MMSE detectors. Furthermore, the GP based MUD achieves excellent interference suppression even for short training sequences. We also include some experiments to illustrate that other nonlinear detectors such as those based on Support Vector Machines (SVMs) exhibit a worse performance.

We determine the asymptotic limit of the function computed by support vector machines (SVM) and related algorithms that minimize a regularized empirical convex loss function in the reproducing kernel Hilbert space of the Gaussian RBF kernel, in the situation where the number of examples tends to infinity, the bandwidth of the Gaussian kernel tends to 0, and the regularization parameter is held fixed.

While classical kernel-based learning algorithms are based on a single kernel, in practice it is often desirable to use multiple kernels. Lankriet et al. (2004) considered conic combinations of kernel matrices for classification, leading to a convex quadratically constraint quadratic program. We show that it can be rewritten as a semi-infinite linear program that can be efficiently solved by recycling the standard SVM implementations. Moreover, we generalize the formulation and our method to a larger class of problems, including regression and one-class classification. Experimental results show that the proposed algorithm helps for automatic model selection, improving the interpretability of the learning result and works for hundred thousands of examples or hundreds of kernels to be combined.

In this paper we derive an algorithm that computes the entire solution path of the support vector regression, with essentially the same computational cost as fitting one SVR model. We also propose an unbiased estimate for the degrees of freedom of the SVR model, which allows convenient selection of the regularization parameter.

Kernel methods make it relatively easy to define complex highdimensional feature spaces. This raises the question of how we can identify the relevant subspaces for a particular learning task. When two views of the same phenomenon are available kernel Canonical Correlation Analysis (KCCA) has been shown to be an effective preprocessing step that can improve the performance of classification algorithms such as the Support Vector Machine (SVM). This paper takes this observation to its logical conclusion and proposes a method that combines this two stage learning (KCCA followed by SVM) into a single optimisation termed SVM-2K. We present both experimental and theoretical analysis of the approach showing encouraging results and insights.

In this paper we derive an algorithm that computes the entire solution path of the support vector regression, with essentially the same computational cost as fitting one SVR model. We also propose an unbiased estimate for the degrees of freedom of the SVR model, which allows convenient selection of the regularization parameter.

We determine the asymptotic limit of the function computed by support vector machines (SVM) and related algorithms that minimize a regularized empirical convex loss function in the reproducing kernel Hilbert space of the Gaussian RBF kernel, in the situation where the number of examples tends to infinity, the bandwidth of the Gaussian kernel tends to 0, and the regularization parameter is held fixed.

While classical kernel-based learning algorithms are based on a single kernel, in practice it is often desirable to use multiple kernels. Lankriet et al. (2004) considered conic combinations of kernel matrices for classification, leading to a convex quadratically constraint quadratic program. We show that it can be rewritten as a semi-infinite linear program that can be efficiently solved by recycling the standard SVM implementations. Moreover, we generalize the formulation and our method to a larger class of problems, including regression and one-class classification. Experimental results show that the proposed algorithm helps for automatic model selection, improving the interpretability of the learning result and works for hundred thousands of examples or hundreds of kernels to be combined.