Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.sourceforge.net.

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Scikit-learn: Machine Learning in Python

SUMMARY We propose a new method for estimation in linear models. The 'lasso' minimizes the residual sum of squares subject to the sum of the absolute value of the coefficients being less than a constant. Because of the nature of this constraint it tends to produce some coefficients that are exactly 0 and hence gives interpretable models. Our simulation studies suggest that the lasso enjoys some of the favourable properties of both subset selection and ridge regression. It produces interpretable models like subset selection and exhibits the stability of ridge regression. There is also an interesting relationship with recent work in adaptive function estimation by Donoho and Johnstone. The lasso idea is quite general and can be applied in a variety of statistical models: extensions to generalized regression models and tree-based models are briefly described.

/pdf/regression-shrinkage-and-selection-via-the-lasso-6mx35txfr5.pdf

Regression Shrinkage and Selection via the Lasso

Introduction to a Transient World. Fourier Kingdom. Discrete Revolution. Time Meets Frequency. Frames. Wavelet Zoom. Wavelet Bases. Wavelet Packet and Local Cosine Bases. An Approximation Tour. Estimations are Approximations. Transform Coding. Appendix A: Mathematical Complements. Appendix B: Software Toolboxes.

http://ahvazdownload.persiangig.com/document/article/39.pdf

A wavelet tour of signal processing

Summary. We propose the elastic net, a new regularization and variable selection method. Real world data and a simulation study show that the elastic net often outperforms the lasso, while enjoying a similar sparsity of representation. In addition, the elastic net encourages a grouping effect, where strongly correlated predictors tend to be in or out of the model together.The elastic net is particularly useful when the number of predictors (p) is much bigger than the number of observations (n). By contrast, the lasso is not a very satisfactory variable selection method in the

/pdf/regularization-and-variable-selection-via-the-elastic-net-4z8q6j5o0i.pdf

Regularization and variable selection via the elastic net

MOTIVATION: Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. RESULTS: We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. AVAILABILITY AND IMPLEMENTATION: featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.

featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features

A striking feature of curve estimation is that the smoothing parameter h 0 , which minimizes the squared error of a kernel or smoothing spline estimator, is very difficult to estimate. This is manifest both in slow rates of convergence and in high variability of standard methods such as cross-validation. We quantify this difficulty by describing nonparametric information bounds and exhibit asymptotically efficient estimators of h 0 that attain the bounds. The efficient estimators are substantially less variable than cross-validation (and other current procedures) and simulations suggest that they may offer improvements at moderate sample sizes, at least in terms of minimizing the squared error

https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2517-6161.1992.tb01892.x

Empirical functionals and efficient smoothing parameter selection

In Gaussian sequence models with Gaussian priors, we develop some simple examples to illustrate three perspectives on matching of posterior and frequentist probabilities when the dimension p increases with sample size n: (i) convergence of joint posterior distributions, (ii) behavior of a non-linear functional: squared error loss, and (iii) estimation of linear functionals. The three settings are progressively less demanding in terms of conditions needed for validity of the Bernstein-von Mises theorem.

/pdf/high-dimensional-bernstein-von-mises-simple-examples-3ba8t4co4o.pdf

Iain M. Johnstone

Papers

Empirical functionals and efficient smoothing parameter selection

High dimensional Bernstein-von Mises: simple examples.

Serum prostate-specific antigen and the biologic progression of prostate cancer.

Discretization effects in statistical inverse problems

On Inadmissibility of Some Unbiased Estimates of Loss