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.

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Going deeper with convolutions

Deep learning is a form of machine learning that enables computers to learn from experience and understand the world in terms of a hierarchy of concepts. Because the computer gathers knowledge from experience, there is no need for a human computer operator to formally specify all the knowledge that the computer needs. The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones; a graph of these hierarchies would be many layers deep. This book introduces a broad range of topics in deep learning. The text offers mathematical and conceptual background, covering relevant concepts in linear algebra, probability theory and information theory, numerical computation, and machine learning. It describes deep learning techniques used by practitioners in industry, including deep feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling, and practical methodology; and it surveys such applications as natural language processing, speech recognition, computer vision, online recommendation systems, bioinformatics, and videogames. Finally, the book offers research perspectives, covering such theoretical topics as linear factor models, autoencoders, representation learning, structured probabilistic models, Monte Carlo methods, the partition function, approximate inference, and deep generative models. Deep Learning can be used by undergraduate or graduate students planning careers in either industry or research, and by software engineers who want to begin using deep learning in their products or platforms. A website offers supplementary material for both readers and instructors.

Deep Learning

In supervised learning, the estimation of prediction error on unlabeled test data 1 is an important task. Existing methods are usually built on the assumption that 2 the training and test data are sampled from the same distribution, which is often 3 violated in practice. As a result, traditional estimators like cross-validation (CV) 4 will be biased and this may result in poor model selection. In this paper, we 5 assume that we have a test dataset in which the feature values are available but 6 not the outcome labels, and focus on a particular form of distributional shift of 7 covariate shift. We propose an alternative method based on parametric bootstrap of 8 the target of conditional error Err X [2]. Empirically our method outperforms CV 9 for both simulation and real data example across different modeling tasks, and is 10 comparable to state-of-the-art methods for image classification. 11

Estimation of prediction error with known covariate shift

Standard regression adjustment gives inconsistent estimates of causal effects when there are time-varying treatment effects and time-varying covariates. Loosely speaking, the issue is that some covariates are post-treatment variables because they may be affected by prior treatment status, and regressing out post-treatment variables causes bias. More precisely, the bias is due to certain non-confounding latent variables that create colliders in the causal graph. These latent variables, which we call phantoms, do not harm the identifiability of the causal effect, but they render naive regression estimates inconsistent. Motivated by this, we ask: how can we modify regression methods so that they hold up even in the presence of phantoms? We develop an estimator for this setting based on regression modeling (linear, log-linear, probit and Cox regression), proving that it is consistent for the causal effect of interest. In particular, the estimator is a regression model fit with a simple adjustment for collinearity, making it easy to understand and implement with standard regression software. From a causal point of view, the proposed estimator is an instance of the parametric g-formula. Importantly, we show that our estimator is immune to the null paradox that plagues most other parametric g-formula methods.

Causal Inference with Orthogonalized Regression Adjustment: Taming the Phantom

More complicated data structures

Glmnet in Python

Identifying heterogeneous treatment effects (HTEs) in randomized controlled trials is an important step toward understanding and acting on trial results. However, HTEs are often small and difficult to identify, and HTE modeling methods which are very general can suffer from low power. We present a method that exploits any existing relationship between illness severity and treatment effect, and identifies the "sweet spot", the contiguous range of illness severity where the estimated treatment benefit is maximized. We further compute a bias-corrected estimate of the conditional average treatment effect (CATE) in the sweet spot, and a $p$-value. Because we identify a single sweet spot and $p$-value, we believe our method to be straightforward to interpret and actionable: results from our method can inform future clinical trials and help clinicians make personalized treatment recommendations.

Robert Tibshirani

Papers

Estimation of prediction error with known covariate shift

Causal Inference with Orthogonalized Regression Adjustment: Taming the Phantom

More complicated data structures

Glmnet in Python

Finding and assessing treatment effect sweet spots in clinical trial data.