449 research outputs found

    Multi-Label Learning under Feature Extraction Budgets

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    We consider the problem of learning sparse linear models for multi-label prediction tasks under a hard constraint on the number of features. Such budget constraints are important in domains where the acquisition of the feature values is costly. We propose a greedy multi-label regularized least-squares algorithm that solves this problem by combining greedy forward selection search with a cross-validation based selection criterion in order to choose, which features to include in the model. We present a highly efficient algorithm for implementing this procedure with linear time and space complexities. This is achieved through the use of matrix update formulas for speeding up feature addition and cross-validation computations. Experimentally, we demonstrate that the approach allows finding sparse accurate predictors on a wide range of benchmark problems, typically outperforming the multi-task lasso baseline method when the budget is small.</p

    Linear Time Feature Selection for Regularized Least-Squares

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    We propose a novel algorithm for greedy forward feature selection for regularized least-squares (RLS) regression and classification, also known as the least-squares support vector machine or ridge regression. The algorithm, which we call greedy RLS, starts from the empty feature set, and on each iteration adds the feature whose addition provides the best leave-one-out cross-validation performance. Our method is considerably faster than the previously proposed ones, since its time complexity is linear in the number of training examples, the number of features in the original data set, and the desired size of the set of selected features. Therefore, as a side effect we obtain a new training algorithm for learning sparse linear RLS predictors which can be used for large scale learning. This speed is possible due to matrix calculus based short-cuts for leave-one-out and feature addition. We experimentally demonstrate the scalability of our algorithm and its ability to find good quality feature sets.Comment: 17 pages, 15 figure

    Learning Dynamic Feature Selection for Fast Sequential Prediction

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    We present paired learning and inference algorithms for significantly reducing computation and increasing speed of the vector dot products in the classifiers that are at the heart of many NLP components. This is accomplished by partitioning the features into a sequence of templates which are ordered such that high confidence can often be reached using only a small fraction of all features. Parameter estimation is arranged to maximize accuracy and early confidence in this sequence. Our approach is simpler and better suited to NLP than other related cascade methods. We present experiments in left-to-right part-of-speech tagging, named entity recognition, and transition-based dependency parsing. On the typical benchmarking datasets we can preserve POS tagging accuracy above 97% and parsing LAS above 88.5% both with over a five-fold reduction in run-time, and NER F1 above 88 with more than 2x increase in speed.Comment: Appears in The 53rd Annual Meeting of the Association for Computational Linguistics, Beijing, China, July 201

    Sparse Predictive Modeling : A Cost-Effective Perspective

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    Many real life problems encountered in industry, economics or engineering are complex and difficult to model by conventional mathematical methods. Machine learning provides a wide variety of methods and tools for solving such problems by learning mathematical models from data. Methods from the field have found their way to applications such as medical diagnosis, financial forecasting, and web-search engines. The predictions made by a learned model are based on a vector of feature values describing the input to the model. However, predictions do not come for free in real world applications, since the feature values of the input have to be bought, measured or produced before the model can be used. Feature selection is a process of eliminating irrelevant and redundant features from the model. Traditionally, it has been applied for achieving interpretable and more accurate models, while the possibility of lowering prediction costs has received much less attention in the literature. In this thesis we consider novel feature selection techniques for reducing prediction costs. The contributions of this thesis are as follows. First, we propose several cost types characterizing the cost of performing prediction with a trained model. Particularly, we consider costs emerging from multitarget prediction problems as well as a number of cost types arising when the feature extraction process is structured. Second, we develop greedy regularized least-squares methods to maximize the predictive performance of the models under given budget constraints. Empirical evaluations are performed on numerous benchmark data sets as well as on a novel water quality analysis application. The results demonstrate that in settings where the considered cost types apply, the proposed methods lead to substantial cost savings compared to conventional methods

    Scalable Feature Selection Applications for Genome-Wide Association Studies of Complex Diseases

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    Personalized medicine will revolutionize our capabilities to combat disease. Working toward this goal, a fundamental task is the deciphering of geneticvariants that are predictive of complex diseases. Modern studies, in the formof genome-wide association studies (GWAS) have afforded researchers with the opportunity to reveal new genotype-phenotype relationships through the extensive scanning of genetic variants. These studies typically contain over half a million genetic features for thousands of individuals. Examining this with methods other than univariate statistics is a challenging task requiring advanced algorithms that are scalable to the genome-wide level. In the future, next-generation sequencing studies (NGS) will contain an even larger number of common and rare variants. Machine learning-based feature selection algorithms have been shown to have the ability to effectively create predictive models for various genotype-phenotype relationships. This work explores the problem of selecting genetic variant subsets that are the most predictive of complex disease phenotypes through various feature selection methodologies, including filter, wrapper and embedded algorithms. The examined machine learning algorithms were demonstrated to not only be effective at predicting the disease phenotypes, but also doing so efficiently through the use of computational shortcuts. While much of the work was able to be run on high-end desktops, some work was further extended so that it could be implemented on parallel computers helping to assure that they will also scale to the NGS data sets. Further, these studies analyzed the relationships between various feature selection methods and demonstrated the need for careful testing when selecting an algorithm. It was shown that there is no universally optimal algorithm for variant selection in GWAS, but rather methodologies need to be selected based on the desired outcome, such as the number of features to be included in the prediction model. It was also demonstrated that without proper model validation, for example using nested cross-validation, the models can result in overly-optimistic prediction accuracies and decreased generalization ability. It is through the implementation and application of machine learning methods that one can extract predictive genotype–phenotype relationships and biological insights from genetic data sets.Siirretty Doriast

    Sparse multinomial kernel discriminant analysis (sMKDA)

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    Dimensionality reduction via canonical variate analysis (CVA) is important for pattern recognition and has been extended variously to permit more flexibility, e.g. by "kernelizing" the formulation. This can lead to over-fitting, usually ameliorated by regularization. Here, a method for sparse, multinomial kernel discriminant analysis (sMKDA) is proposed, using a sparse basis to control complexity. It is based on the connection between CVA and least-squares, and uses forward selection via orthogonal least-squares to approximate a basis, generalizing a similar approach for binomial problems. Classification can be performed directly via minimum Mahalanobis distance in the canonical variates. sMKDA achieves state-of-the-art performance in terms of accuracy and sparseness on 11 benchmark datasets

    A Reduction of the Elastic Net to Support Vector Machines with an Application to GPU Computing

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    The past years have witnessed many dedicated open-source projects that built and maintain implementations of Support Vector Machines (SVM), parallelized for GPU, multi-core CPUs and distributed systems. Up to this point, no comparable effort has been made to parallelize the Elastic Net, despite its popularity in many high impact applications, including genetics, neuroscience and systems biology. The first contribution in this paper is of theoretical nature. We establish a tight link between two seemingly different algorithms and prove that Elastic Net regression can be reduced to SVM with squared hinge loss classification. Our second contribution is to derive a practical algorithm based on this reduction. The reduction enables us to utilize prior efforts in speeding up and parallelizing SVMs to obtain a highly optimized and parallel solver for the Elastic Net and Lasso. With a simple wrapper, consisting of only 11 lines of MATLAB code, we obtain an Elastic Net implementation that naturally utilizes GPU and multi-core CPUs. We demonstrate on twelve real world data sets, that our algorithm yields identical results as the popular (and highly optimized) glmnet implementation but is one or several orders of magnitude faster.Comment: 10 page
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