One-class classifiers based on entropic spanning graphs

One-class classifiers offer valuable tools to assess the presence of outliers in data. In this paper, we propose a design methodology for one-class classifiers based on entropic spanning graphs. Our approach takes into account the possibility to process also non-numeric data by means of an embedding procedure. The spanning graph is learned on the embedded input data and the outcoming partition of vertices defines the classifier. The final partition is derived by exploiting a criterion based on mutual information minimization. Here, we compute the mutual information by using a convenient formulation provided in terms of the $\alpha$-Jensen difference. Once training is completed, in order to associate a confidence level with the classifier decision, a graph-based fuzzy model is constructed. The fuzzification process is based only on topological information of the vertices of the entropic spanning graph. As such, the proposed one-class classifier is suitable also for data characterized by complex geometric structures. We provide experiments on well-known benchmarks containing both feature vectors and labeled graphs. In addition, we apply the method to the protein solubility recognition problem by considering several representations for the input samples. Experimental results demonstrate the effectiveness and versatility of the proposed method with respect to other state-of-the-art approaches.Comment: Extended and revised version of the paper "One-Class Classification Through Mutual Information Minimization" presented at the 2016 IEEE IJCNN, Vancouver, Canad

Learning from the machine: interpreting machine learning algorithms for point- and extended- source classification

We investigate star-galaxy classification for astronomical surveys in the context of four methods enabling the interpretation of black-box machine learning systems. The first is outputting and exploring the decision boundaries as given by decision tree based methods, which enables the visualization of the classification categories. Secondly, we investigate how the Mutual Information based Transductive Feature Selection (MINT) algorithm can be used to perform feature pre-selection. If one would like to provide only a small number of input features to a machine learning classification algorithm, feature pre-selection provides a method to determine which of the many possible input properties should be selected. Third is the use of the tree-interpreter package to enable popular decision tree based ensemble methods to be opened, visualized, and understood. This is done by additional analysis of the tree based model, determining not only which features are important to the model, but how important a feature is for a particular classification given its value. Lastly, we use decision boundaries from the model to revise an already existing method of classification, essentially asking the tree based method where decision boundaries are best placed and defining a new classification method. We showcase these techniques by applying them to the problem of star-galaxy separation using data from the Sloan Digital Sky Survey (hereafter SDSS). We use the output of MINT and the ensemble methods to demonstrate how more complex decision boundaries improve star-galaxy classification accuracy over the standard SDSS frames approach (reducing misclassifications by up to $\approx33\%$). We then show how tree-interpreter can be used to explore how relevant each photometric feature is when making a classification on an object by object basis.Comment: 12 pages, 8 figures, 8 table

Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks

We present a procedure for effective estimation of entropy and mutual information from small-sample data, and apply it to the problem of inferring high-dimensional gene association networks. Specifically, we develop a James-Stein-type shrinkage estimator, resulting in a procedure that is highly efficient statistically as well as computationally. Despite its simplicity, we show that it outperforms eight other entropy estimation procedures across a diverse range of sampling scenarios and data-generating models, even in cases of severe undersampling. We illustrate the approach by analyzing E. coli gene expression data and computing an entropy-based gene-association network from gene expression data. A computer program is available that implements the proposed shrinkage estimator.Comment: 18 pages, 3 figures, 1 tabl