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

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.

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.

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XGBoost: A Scalable Tree Boosting System

We present SpaceNet, a multivariate method for brain decoding and segmentation. SpaceNet uses priors like TV (Total Variation). SpaceNet uses priors like TV (Total Variation) [Michel et al. 2011], TV-L1 [Baldassarre et al. 2012, Gramfort et al. 2013], and GraphNet / Smooth-Lasso [Hebiri et al. 2011, Grosenick et al. 2013] to regularize / penalize classification and regression problems in brain imaging. The result are brain maps which are both sparse (i.e regression coefficients are zero everywhere, except at predictive voxels) and structured (blobby). The superiority of such priors over methods without structured priors like the Lasso, SVM, ANOVA, Ridge, etc. for yielding more interpretable maps and improved classification / prediction scores is now well-established [Baldassarre et al. 2012, Gramfort et al. 2013, Grosenick et al. 2013]. In addition, such priors lead to state-of-the-art methods for extracting brain atlases [Abraham et al. 2013].

https://hal.inria.fr/hal-01187230/document

SpaceNet: Multivariate brain decoding and segmentation

Extracting activation patterns from functional Magnetic Resonance Images (fMRI) datasets remains challenging in rapid-event designs due to the inherent delay of blood oxygen level-dependent (BOLD) signal. The general linear model (GLM) allows to estimate the activation from a design matrix and a fixed hemodynamic response function (HRF). However, the HRF is known to vary substantially between subjects and brain regions. In this paper, we propose a model for jointly estimating the hemodynamic response function (HRF) and the activation patterns via a low-rank representation of task effects.This model is based on the linearity assumption behind the GLM and can be computed using standard gradient-based solvers. We use the activation patterns computed by our model as input data for encoding and decoding studies and report performance improvement in both settings.

HRF estimation improves sensitivity of fMRI encoding and decoding models

High-quality data accumulation is now becoming ubiquitous in the health domain. There is increasing opportunity to exploit rich data from normal subjects to improve supervised estimators in specific diseases with notorious data scarcity. We demonstrate that low-dimensional embedding spaces can be derived from the UK Biobank population dataset and used to enhance data-scarce prediction of health indicators, lifestyle and demographic characteristics. Phenotype predictions facilitated by Variational Autoencoder manifolds typically scaled better with increasing unlabeled data than dimensionality reduction by PCA or Isomap. Performances gains from semisupervison approaches will probably become an important ingredient for various medical data science applications.

Label scarcity in biomedicine: Data-rich latent factor discovery enhances phenotype prediction.

Inter-subject variability is a major hurdle for neuroimaging group-level inference, as it creates complex image patterns that are not captured by standard analysis models and jeopardizes the sensitivity of statistical procedures. A solution to this problem is to model random subjects effects by using the redundant information conveyed by multiple imaging contrasts. In this paper, we introduce a novel analysis framework, where we estimate the amount of variance that is fit by a random effects subspace learned on other images; we show that a principal component regression estimator outperforms other regression models and that it fits a significant proportion (10% to 25%) of the between-subject variability. This proves for the first time that the accumulation of contrasts in each individual can provide the basis for more sensitive neuroimaging group analyzes.

New Results - Principal Component Regression predicts functional responses across individuals

This chapter proposes a review of the most prominent issues in analysing brain functional Magnetic Resonance data. It introduces the domain for readers with no or little knowledge in the field. The introduction places the context and orients the reader in the many questions put to the data, and summarizes the currently most commonly applied approach. The second section deals with intra subject data analysis, emphasizing hemodynamic response estimation issues. The third section describes current approaches and advances in analysing group data in a standard coordinate system. The last section proposes new spatial models for group analyses. Overall, the chapter gives a brief overview of the field and details some specific advances that are important for application studies in cognitive neurosciences.

Bertrand Thirion

Papers

SpaceNet: Multivariate brain decoding and segmentation

HRF estimation improves sensitivity of fMRI encoding and decoding models

Label scarcity in biomedicine: Data-rich latent factor discovery enhances phenotype prediction.

New Results - Principal Component Regression predicts functional responses across individuals

Intra and inter subject analyses of brain functional Magnetic Resonance Images (fMRI)