Kernel Methods for Document Filtering

This paper describes the algorithms implemented by the KerMIT consortium for its participation in the Trec 2002 Filtering track. The consortium submitted runs for the routing task using a linear SVM, for the batch task using the same SVM in combination with an innovation threshold-selection mechanism, and for the adaptive task using both a second-order perceptron and a combination of SVM and perceptron with uneven margin. Results seem to indicate that these algorithm performed relatively well on the extensive TREC benchmark

Infinite factorization of multiple non-parametric views

Combined analysis of multiple data sources has increasing application interest, in particular for distinguishing shared and source-specific aspects. We extend this rationale of classical canonical correlation analysis into a flexible, generative and non-parametric clustering setting, by introducing a novel non-parametric hierarchical mixture model. The lower level of the model describes each source with a flexible non-parametric mixture, and the top level combines these to describe commonalities of the sources. The lower-level clusters arise from hierarchical Dirichlet Processes, inducing an infinite-dimensional contingency table between the views. The commonalities between the sources are modeled by an infinite block model of the contingency table, interpretable as non-negative factorization of infinite matrices, or as a prior for infinite contingency tables. With Gaussian mixture components plugged in for continuous measurements, the model is applied to two views of genes, mRNA expression and abundance of the produced proteins, to expose groups of genes that are co-regulated in either or both of the views. Cluster analysis of co-expression is a standard simple way of screening for co-regulation, and the two-view analysis extends the approach to distinguishing between pre- and post-translational regulation

A probabilistic framework for mismatch and profile string kernels

There has recently been numerous applications of kernel methods in the field of bioinformatics. In particular, the problem of protein homology has served as a benchmark for the performance of many new kernels which operate directly on strings (such as amino-acid sequences). Several new kernels have been developed and successfully applied to this type of data, including spectrum, string, mismatch, and profile kernels. In this paper we introduce a general probabilistic framework for string kernels which uses the fisher-kernel approach and includes spectrum, mismatch and profile kernels, among others, as special cases. The use of a probabilistic model however provides additional flexibility both in definition and for the re-weighting of features through feature selection methods, prior knowledge or semi-supervised approaches which use data repositories such as BLAST. We give details of the framework and also give preliminary experimental results which show the applicability of the technique

String Kernels, Fisher Kernels and Finite State Automata

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 kernel 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 reflects the statistics of the training corpus. Furthermore, the probabilistic modelling approach suggests extending the Markov process 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

A Probabilistic Framework for the Hierachic Organisation & Classification of Document Collections

This paper presents a probabilistic mixture modeling framework for the hierarchic organisation of document collections. It is demonstrated that the probabilistic corpus model which emerges from the automatic or unsupervised hierarchical organisation of a document collection can be further exploited to create a kernel which boosts the performance of state-of-the-art support vector machine document classifiers. It is shown that the performance of such a classifier is further enhanced when employing the kernel derived from an appropriate hierarchic mixture model used for partitioning a document corpus rather than the kernel associated with a flat non-hierarchic mixture model. This has important implications for document classification when a hierarchic ordering of topics exists. This can be considered as the effective combination of documents with no topic or class labels (unlabeled data), labeled documents, and prior domain knowledge (in the form of the known hierarchic structure), in providing enhanced document classification performance

A probabilistic hierarchical clustering method for organising collections of text documents

In this paper a generic probabilistic framework for the unsupervised hierarchical clustering of large-scale sparse high-dimensional data collections is proposed. The framework is based on a hierarchical probabilistic mixture methodology. Two classes of models emerge from the analysis and these have been termed as symmetric and asymmetric models. For text data specifically both asymmetric and symmetric models based on the multinomial and binomial distributions are most appropriate. An Expectation Maximisation parameter estimation method is provided for all of these models. An experimental comparison of the models is obtained for two extensive online document collections. © 2000 IEEE

The organisation and visualisation of document corpora: A probabilistic approach

In this paper a generic probabilistic framework for the unsupervised organisation and visualisation of document collections is presented. The probabilistic hierarchical clustering of large-scale sparse and high-dimensional data collections is achieved by the development of a family of latent class models which are parameterized using the expectation maximisation algorithm. The framework is based on a hierarchical probabilistic mixture methodology. Two classes of models emerge from the analysis and these have been termed as symmetric and asymmetric models. For text data specifically, both asymmetric and symmetric models based on the multinomial and binomial distributions are most appropriate. The subsequent visualisation of document collections is achieved by exploiting the topographic relations between similar documents. A latent trait model is developed which provides the means of viewing vector space document representations on a 2D grid and thereby visualising the inherent structure of the document collection. A number of experiments are provided to demonstrate the technique and a concluding discussion on the proposed models is given. © 2000 IEEE