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.

/pdf/scikit-learn-machine-learning-in-python-23clfh9q83.pdf

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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/pdf/moderated-estimation-of-fold-change-and-dispersion-for-rna-3ywnbkcan0.pdf

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.

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

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.

We consider the situation in semi-supervised learning, where the "label sampling" mechanism stochastically depends on the true response (as well as potentially on the features). We suggest a method of moments for estimating this stochastic dependence using the unlabeled data. This is potentially useful for two distinct purposes: a. As an input to a supervised learning procedure which can be used to "de-bias" its results using labeled data only and b. As a potentially interesting learning task in itself. We present several examples to illustrate the practical usefulness of our method.

/pdf/a-method-for-inferring-label-sampling-mechanisms-in-semi-tr0jd4n5zp.pdf

A Method for Inferring Label Sampling Mechanisms in Semi-Supervised Learning

Patient-derived health state utilities for gastroesophageal reflux disease

https://www.annalsthoracicsurgery.org/article/S0003-4975(10)60788-6/pdf

Closed Mitral Valvotomy: Actuarial Analysis of Results in 654 Patients over 12 Years and Analysis of Preoperative Predictors of Long-Term Survival

Ischemia in three left ventricular regions: Insights into the pathogenesis of acute ischemic mitral regurgitation ☆ ☆☆ ★

/pdf/flexible-discriminant-and-mixture-models-1iq50iaslh.pdf

Trevor Hastie

Papers

A Method for Inferring Label Sampling Mechanisms in Semi-Supervised Learning

Patient-derived health state utilities for gastroesophageal reflux disease

Closed Mitral Valvotomy: Actuarial Analysis of Results in 654 Patients over 12 Years and Analysis of Preoperative Predictors of Long-Term Survival

Ischemia in three left ventricular regions: Insights into the pathogenesis of acute ischemic mitral regurgitation ☆ ☆☆ ★

Flexible discriminant and mixture models