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

In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

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.

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Regression Shrinkage and Selection via the Lasso

We propose a deep convolutional neural network architecture codenamed Inception that achieves the new state of the art for classification and detection in the ImageNet Large-Scale Visual Recognition Challenge 2014 (ILSVRC14). The main hallmark of this architecture is the improved utilization of the computing resources inside the network. By a carefully crafted design, we increased the depth and width of the network while keeping the computational budget constant. To optimize quality, the architectural decisions were based on the Hebbian principle and the intuition of multi-scale processing. One particular incarnation used in our submission for ILSVRC14 is called GoogLeNet, a 22 layers deep network, the quality of which is assessed in the context of classification and detection.

/pdf/going-deeper-with-convolutions-1yobw2o2ds.pdf

Going deeper with convolutions

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 this http URL.

In this study, we consider several regularization path algorithms with grouped variable selection for modeling gene-interactions. When tting with categorical factors, including the genotype measurements, we often dene a set of dummy variables that represent a single factor/interaction of factors. Yuan & Lin (2006) proposed the groupLars and the group-Lasso methods through which these groups of indicators can be selected simultaneously. Here we introduce another version of group-Lars. In addition, we propose a path-following algorithm for the group-Lasso method applied to generalized linear models. We then use all these path algorithms, which select the grouped variables in a smooth way, to identify gene-interactions aecting disease status in an example. We further compare their performances to that of L2 penalized logistic regression with forward stepwise variable selection discussed in Park & Hastie (2006b).

Regularization Path Algorithms for Detecting Gene Interactions

Ridge or more formally l2 regularization shows up in many areas of statistics and machine learning It is one of those essential devices that any good data scientist needs to master for their craft

Ridge Regularizaton: an Essential Concept in Data Science

Cross-Validation and C p Estimates of Prediction Error

We consider rules for discarding predictors in lasso regression and related problems, for computational efficiency. El Ghaoui et al (2010) propose "SAFE" rules that guarantee that a coefficient will be zero in the solution, based on the inner products of each predictor with the outcome. In this paper we propose strong rules that are not foolproof but rarely fail in practice. These can be complemented with simple checks of the Karush- Kuhn-Tucker (KKT) conditions to provide safe rules that offer substantial speed and space savings in a variety of statistical convex optimization problems.

Trevor Hastie

Papers

Regularization Path Algorithms for Detecting Gene Interactions

Ridge Regularizaton: an Essential Concept in Data Science

Cross-Validation and C p Estimates of Prediction Error

Strong rules for discarding predictors in lasso-type problems

High-Dimensional Problems: p N