Fisher kernels have been successfully applied to many problems in bioinformatics. However, their success depends on the quality of the generative model upon which they are built. For Fisher kernel techniques to be used on novel problems, a mechanism for creating accurate generative models is required. A novel framework is presented for automatically creating domain-specific generative models that can be used to produce Fisher kernels for support vector machines (SVMs) and other kernel methods. The framework enables the capture of prior knowledge and addresses the issue of domain-specific kernels, both of which are current areas that are lacking in many kernel-based methods. To obtain the generative model, genetic algorithms are used to evolve the structure of hidden Markov models (HMMs). A Fisher kernel is subsequently created from the HMM, and used in conjunction with an SVM, to improve the discriminative power. This paper investigates the effectiveness of the proposed method, named GA-SVM. We show that its performance is comparable if not better than other state of the art methods in classifying secretory protein sequences of malaria. More interestingly, it showed better results than the sequence-similarity-based approach, without the need for additional homologous sequence information in protein enzyme family classification. The experiments clearly demonstrate that the GA-SVM is a novel way to find features with good performance from biological sequences, that does not require extensive tuning of a complex model.

Abstract — In this paper, we present an effective computational approach for learning patterns of brain activity from the fMRI data. The procedure involved correcting motion artifacts, spatial smoothing, removing low frequency drifts and applying multivariate linear and non-linear kernel methods. Two novel techniques are applied: one utilizes the Cosine Transform to remove low-frequency drifts over time and the other involves using prior knowledge about the spatial contribution of different brain regions for the various tasks. Our experiment results on the PBAIC2007 competition data set show a great improvement for brain activity prediction, especially on some sensory experience such as hearing and vision. I.

We present a kernel-based algorithm for hierarchical text classification where the documents are allowed to belong to more than one category at a time. The classification model is a variant of the Maximum Margin Markov Network framework, where the classification hierarchy is represented as a Markov tree equipped with an exponential family defined on the edges. We present an efficient optimization algorithm based on incremental conditional gradient ascent in single-example subspaces spanned by the marginal dual variables. The optimization is facilitated with a dynamic programming based algorithm that computes best update directions in the feasible set. Experiments show that the algorithm can feasibly optimize training sets of thousands of examples and classification hierarchies consisting of hundreds of nodes. Training of the full hierarchical model is as efficient as training independent SVM-light classifiers for each node. The algorithm's predictive accuracy was found to be competitive with other recently introduced hierarchical multi-category or multilabel classification learning algorithms.

We present a kernel-based algorithm for hierarchical text classification where the documents are allowed to belong to more than one category at a time. The classification model is a variant of the Maximum Margin Markov Network framework, where the classification hierarchy is represented as a Markov tree equipped with an exponential family defined on the edges. We present an efficient optimization algorithm based on incremental conditional gradient ascent in single-example subspaces spanned by the marginal dual variables. Experiments show that the algorithm can feasibly optimize training sets of thousands of examples and classification hierarchies consisting of hundreds of nodes. The algorithm's predictive accuracy is competitive with other recently introduced hierarchical multi-category or multilabel classification learning algorithms.

In this paper we show how the generation of documents can be thought of as a k-stage Markov process, which leads to a Fisher ker(cid:173) nel from which the n-gram and string kernels can be re-constructed. The Fisher kernel view gives a more flexible insight into the string kernel and suggests how it can be parametrised in a way that re(cid:173) flects the statistics of the training corpus. Furthermore, the prob(cid:173) abilistic modelling approach suggests extending the Markov pro(cid:173) cess to consider sub-sequences of varying length, rather than the standard fixed-length approach used in the string kernel. We give a procedure for determining which sub-sequences are informative features and hence generate a Finite State Machine model, which can again be used to obtain a Fisher kernel. By adjusting the parametrisation we can also influence the weighting received by the features . In this way we are able to obtain a logarithmic weighting in a Fisher kernel. Finally, experiments are reported comparing the different kernels using the standard Bag of Words kernel as a baseline.