Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Kernel methods in machine learning

We review machine learning methods employing positive definite kernels. These methods formulate learning and estimation problems in a reproducing kernel Hilbert space (RKHS) of functions defined on the data domain, expanded in terms of a kernel. Working in linear spaces of function has the benefit of facilitating the construction and analysis of learning algorithms while at the same time allowing large classes of functions. The latter include nonlinear functions as well as functions defined on nonvectorial data. We cover a wide range of methods, ranging from binary classifiers to sophisticated methods for estimation with structured data.Comment: Published in at http://dx.doi.org/10.1214/009053607000000677 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Fuzzy Least Squares Twin Support Vector Machines

Least Squares Twin Support Vector Machine (LST-SVM) has been shown to be an efficient and fast algorithm for binary classification. It combines the operating principles of Least Squares SVM (LS-SVM) and Twin SVM (T-SVM); it constructs two non-parallel hyperplanes (as in T-SVM) by solving two systems of linear equations (as in LS-SVM). Despite its efficiency, LST-SVM is still unable to cope with two features of real-world problems. First, in many real-world applications, labels of samples are not deterministic; they come naturally with their associated membership degrees. Second, samples in real-world applications may not be equally important and their importance degrees affect the classification. In this paper, we propose Fuzzy LST-SVM (FLST-SVM) to deal with these two characteristics of real-world data. Two models are introduced for FLST-SVM: the first model builds up crisp hyperplanes using training samples and their corresponding membership degrees. The second model, on the other hand, constructs fuzzy hyperplanes using training samples and their membership degrees. Numerical evaluation of the proposed method with synthetic and real datasets demonstrate significant improvement in the classification accuracy of FLST-SVM when compared to well-known existing versions of SVM