Our winning submission to the 2014 Kaggle competition for Large Scale Hierarchical Text Classification (LSHTC) consists mostly of an ensemble of sparse generative models extending Multinomial Naive Bayes. The base-classifiers consist of hierarchically smoothed models combining document, label, and hierarchy level Multinomials, with feature pre-processing using variants of TF-IDF and BM25. Additional diversification is introduced by different types of folds and random search optimization for different measures. The ensemble algorithm optimizes macroFscore by predicting the documents for each label, instead of the usual prediction of labels per document. Scores for documents are predicted by weighted voting of base-classifier outputs with a variant of Feature-Weighted Linear Stacking. The number of documents per label is chosen using label priors and thresholding of vote scores. This document describes the models and software used to build our solution. Reproducing the results for our solution can be done by running the scripts included in the Kaggle package. A package omitting precomputed result files is also distributed. All code is open source, released under GNU GPL 2.0, and GPL 3.0 for Weka and Meka dependencies.

We propose a novel non-parametric adaptive anomaly detection algorithm for high dimensional data based on rank-SVM. Data points are first ranked based on scores derived from nearest neighbor graphs on n-point nominal data. We then train a rank-SVM using this ranked data. A test-point is declared as an anomaly at alpha-false alarm level if the predicted score is in the alpha-percentile. The resulting anomaly detector is shown to be asymptotically optimal and adaptive in that for any false alarm rate alpha, its decision region converges to the alpha-percentile level set of the unknown underlying density. In addition we illustrate through a number of synthetic and real-data experiments both the statistical performance and computational efficiency of our anomaly detector.

In recent years, the task of automatically linking pieces of text (anchors) mentioned in a document to Wikipedia articles that represent the meaning of these anchors has received extensive research attention. Typically, link-to-Wikipedia systems try to find a set of Wikipedia articles that are candidates to represent the meaning of the anchor and, later, rank these candidates to select the most appropriate one. In this ranking process the systems rely on context information obtained from the document where the anchor is mentioned and/or from Wikipedia. In this paper we center our attention in the use of Wikipedia links as context information. In particular, we offer a review of several candidate ranking approaches in the state-of-the-art that rely on Wikipedia link information. In addition, we provide a comparative empirical evaluation of the different approaches on five different corpora: the TAC 2010 corpus and four corpora built from actual Wikipedia articles and news items.

Graphical models are commonly used tools for modeling multivariate random variables. While there exist many convenient multivariate distributions such as Gaussian distribution for continuous data, mixed data with the presence of discrete variables or a combination of both continuous and discrete variables poses new challenges in statistical modeling. In this paper, we propose a semiparametric model named latent Gaussian copula model for binary and mixed data. The observed binary data are assumed to be obtained by dichotomizing a latent variable satisfying the Gaussian copula distribution or the nonparanormal distribution. The latent Gaussian model with the assumption that the latent variables are multivariate Gaussian is a special case of the proposed model. A novel rank-based approach is proposed for both latent graph estimation and latent principal component analysis. Theoretically, the proposed methods achieve the same rates of convergence for both precision matrix estimation and eigenvector estimation, as if the latent variables were observed. Under similar conditions, the consistency of graph structure recovery and feature selection for leading eigenvectors is established. The performance of the proposed methods is numerically assessed through simulation studies, and the usage of our methods is illustrated by a genetic dataset.

We establish optimal convergence rates for a decomposition-based scalable approach to kernel ridge regression. The method is simple to describe: it randomly partitions a dataset of size N into m subsets of equal size, computes an independent kernel ridge regression estimator for each subset, then averages the local solutions into a global predictor. This partitioning leads to a substantial reduction in computation time versus the standard approach of performing kernel ridge regression on all N samples. Our two main theorems establish that despite the computational speed-up, statistical optimality is retained: as long as m is not too large, the partition-based estimator achieves the statistical minimax rate over all estimators using the set of N samples. As concrete examples, our theory guarantees that the number of processors m may grow nearly linearly for finite-rank kernels and Gaussian kernels and polynomially in N for Sobolev spaces, which in turn allows for substantial reductions in computational cost. We conclude with experiments on both simulated data and a music-prediction task that complement our theoretical results, exhibiting the computational and statistical benefits of our approach.

Annotation errors can significantly hurt classifier performance, yet datasets are only growing noisier with the increased use of Amazon Mechanical Turk and techniques like distant supervision that automatically generate labels. In this paper, we present a robust extension of logistic regression that incorporates the possibility of mislabelling directly into the objective. Our model can be trained through nearly the same means as logistic regression, and retains its efficiency on high-dimensional datasets. Through named entity recognition experiments, we demonstrate that our approach can provide a significant improvement over the standard model when annotation errors are present.

Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measurements. Two main supervised frameworks have been proposed: the local approach, which trains a separate model for each network node, and the global approach, which trains a single model over pairs of nodes. Here, we systematically investigate, theoretically and empirically, the exploitation of tree-based ensemble methods in the context of these two approaches for biological network inference. We first formalize the problem of network inference as classification of pairs, unifying in the process homogeneous and bipartite graphs and discussing two main sampling schemes. We then present the global and the local approaches, extending the later for the prediction of interactions between two unseen network nodes, and discuss their specializations to tree-based ensemble methods, highlighting their interpretability and drawing links with clustering techniques. Extensive computational experiments are carried out with these methods on various biological networks that clearly highlight that these methods are competitive with existing methods.

This paper presents a study in task-oriented approach to stroke rehabilitation by controlling a haptic device via near-infrared spectroscopy-based brain-computer interface (BCI). The task is to command the haptic device to move in opposing directions of leftward and rightward movement. Our study consists of data acquisition, signal preprocessing, and classification. In data acquisition, we conduct experiments based on two different mental tasks: one on pure motor imagery, and another on combined motor imagery and action observation. The experiments were conducted in both offline and online modes. In the signal preprocessing, we use localization method to eliminate channels that are irrelevant to the mental task, as well as perform feature extraction for subsequent classification. We propose multiple support vector machine classifiers with a majority-voting scheme for improved classification results. And lastly, we present test results to demonstrate the efficacy of our proposed approach to possible stroke rehabilitation practice.

Scoring systems are classification models that only require users to add, subtract and multiply a few meaningful numbers to make a prediction. These models are often used because they are practical and interpretable. In this paper, we introduce an off-the-shelf tool to create scoring systems that both accurate and interpretable, known as a Supersparse Linear Integer Model (SLIM). SLIM is a discrete optimization problem that minimizes the 0-1 loss to encourage a high level of accuracy, regularizes the L0-norm to encourage a high level of sparsity, and constrains coefficients to a set of interpretable values. We illustrate the practical and interpretable nature of SLIM scoring systems through applications in medicine and criminology, and show that they are are accurate and sparse in comparison to state-of-the-art classification models using numerical experiments.

Conformal prediction is a method of producing prediction sets that can be applied on top of a wide range of prediction algorithms. The method has a guaranteed coverage probability under the standard IID assumption regardless of whether the assumptions (often considerably more restrictive) of the underlying algorithm are satisfied. However, for the method to be really useful it is desirable that in the case where the assumptions of the underlying algorithm are satisfied, the conformal predictor loses little in efficiency as compared with the underlying algorithm (whereas being a conformal predictor, it has the stronger guarantee of validity). In this paper we explore the degree to which this additional requirement of efficiency is satisfied in the case of Bayesian ridge regression; we find that asymptotically conformal prediction sets differ little from ridge regression prediction intervals when the standard Bayesian assumptions are satisfied.