A Classification Framework for Imbalanced Data

As information technology advances, the demands for developing a reliable and highly accurate predictive model from many domains are increasing. Traditional classification algorithms can be limited in their performance on highly imbalanced data sets. In this dissertation, we study two common problems when training data is imbalanced, and propose effective algorithms to solve them. Firstly, we investigate the problem in building a multi-class classification model from imbalanced class distribution. We develop an effective technique to improve the performance of the model by formulating the problem as a multi-class SVM with an objective to maximize G-mean value. A ramp loss function is used to simplify and solve the problem. Experimental results on multiple real-world datasets confirm that our new method can effectively solve the multi-class classification problem when the datasets are highly imbalanced. Secondly, we explore the problem in learning a global classification model from distributed data sources with privacy constraints. In this problem, not only data sources have different class distributions but combining data into one central data is also prohibited. We propose a privacy-preserving framework for building a global SVM from distributed data sources. Our new framework avoid constructing a global kernel matrix by mapping non-linear inputs to a linear feature space and then solve a distributed linear SVM from these virtual points. Our method can solve both imbalance and privacy problems while achieving the same level of accuracy as regular SVM. Finally, we extend our framework to handle high-dimensional data by utilizing Generalized Multiple Kernel Learning to select a sparse combination of features and kernels. This new model produces a smaller set of features, but yields much higher accuracy

Enhanced protein fold recognition through a novel data integration approach

<p>Abstract</p> <p>Background</p> <p>Protein fold recognition is a key step in protein three-dimensional (3D) structure discovery. There are multiple fold discriminatory data sources which use physicochemical and structural properties as well as further data sources derived from local sequence alignments. This raises the issue of finding the most efficient method for combining these different informative data sources and exploring their relative significance for protein fold classification. Kernel methods have been extensively used for biological data analysis. They can incorporate separate fold discriminatory features into kernel matrices which encode the similarity between samples in their respective data sources.</p> <p>Results</p> <p>In this paper we consider the problem of integrating multiple data sources using a kernel-based approach. We propose a novel information-theoretic approach based on a Kullback-Leibler (KL) divergence between the output kernel matrix and the input kernel matrix so as to integrate heterogeneous data sources. One of the most appealing properties of this approach is that it can easily cope with multi-class classification and multi-task learning by an appropriate choice of the output kernel matrix. Based on the position of the output and input kernel matrices in the KL-divergence objective, there are two formulations which we respectively refer to as <it>MKLdiv-dc </it>and <it>MKLdiv-conv</it>. We propose to efficiently solve MKLdiv-dc by a difference of convex (DC) programming method and MKLdiv-conv by a projected gradient descent algorithm. The effectiveness of the proposed approaches is evaluated on a benchmark dataset for protein fold recognition and a yeast protein function prediction problem.</p> <p>Conclusion</p> <p>Our proposed methods MKLdiv-dc and MKLdiv-conv are able to achieve state-of-the-art performance on the SCOP PDB-40D benchmark dataset for protein fold prediction and provide useful insights into the relative significance of informative data sources. In particular, MKLdiv-dc further improves the fold discrimination accuracy to 75.19% which is a more than 5% improvement over competitive Bayesian probabilistic and SVM margin-based kernel learning methods. Furthermore, we report a competitive performance on the yeast protein function prediction problem.</p

Out-of-sample generalizations for supervised manifold learning for classification

Supervised manifold learning methods for data classification map data samples residing in a high-dimensional ambient space to a lower-dimensional domain in a structure-preserving way, while enhancing the separation between different classes in the learned embedding. Most nonlinear supervised manifold learning methods compute the embedding of the manifolds only at the initially available training points, while the generalization of the embedding to novel points, known as the out-of-sample extension problem in manifold learning, becomes especially important in classification applications. In this work, we propose a semi-supervised method for building an interpolation function that provides an out-of-sample extension for general supervised manifold learning algorithms studied in the context of classification. The proposed algorithm computes a radial basis function (RBF) interpolator that minimizes an objective function consisting of the total embedding error of unlabeled test samples, defined as their distance to the embeddings of the manifolds of their own class, as well as a regularization term that controls the smoothness of the interpolation function in a direction-dependent way. The class labels of test data and the interpolation function parameters are estimated jointly with a progressive procedure. Experimental results on face and object images demonstrate the potential of the proposed out-of-sample extension algorithm for the classification of manifold-modeled data sets

Learning Discriminative Stein Kernel for SPD Matrices and Its Applications

Stein kernel has recently shown promising performance on classifying images represented by symmetric positive definite (SPD) matrices. It evaluates the similarity between two SPD matrices through their eigenvalues. In this paper, we argue that directly using the original eigenvalues may be problematic because: i) Eigenvalue estimation becomes biased when the number of samples is inadequate, which may lead to unreliable kernel evaluation; ii) More importantly, eigenvalues only reflect the property of an individual SPD matrix. They are not necessarily optimal for computing Stein kernel when the goal is to discriminate different sets of SPD matrices. To address the two issues in one shot, we propose a discriminative Stein kernel, in which an extra parameter vector is defined to adjust the eigenvalues of the input SPD matrices. The optimal parameter values are sought by optimizing a proxy of classification performance. To show the generality of the proposed method, three different kernel learning criteria that are commonly used in the literature are employed respectively as a proxy. A comprehensive experimental study is conducted on a variety of image classification tasks to compare our proposed discriminative Stein kernel with the original Stein kernel and other commonly used methods for evaluating the similarity between SPD matrices. The experimental results demonstrate that, the discriminative Stein kernel can attain greater discrimination and better align with classification tasks by altering the eigenvalues. This makes it produce higher classification performance than the original Stein kernel and other commonly used methods.Comment: 13 page