Scikit-learn: Machine Learning in Python

International audienceScikit-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

Array programming with NumPy.

Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis

Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Identification of novel prognostic markers of survival time in high-risk neuroblastoma using gene expression profiles

Neuroblastoma is the most common extracranial solid tumor in childhood. Patients in high-risk group often have poor outcomes with low survival rates despite several treatment options. This study aimed to identify a genetic signature from gene expression profiles that can serve as prognostic indicators of survival time in patients of high-risk neuroblastoma, and that could be potential therapeutic targets. RNA-seq count data was downloaded from UCSC Xena browser and samples grouped into Short Survival (SS) and Long Survival (LS) groups. Differential gene expression (DGE) analysis, enrichment analyses, regulatory network analysis and machine learning (ML) prediction of survival group were performed. Forty differentially expressed genes (DEGs) were identified including genes involved in molecular function activities essential for tumor proliferation. DEGs used as features for prediction of survival groups included EVX2, NHLH2, PRSS12, POU6F2, HOXD10, MAPK15, RTL1, LGR5, CYP17A1, OR10AB1P, MYH14, LRRTM3, GRIN3A, HS3ST5, CRYAB and NXPH3. An accuracy score of 82% was obtained by the ML classification models. SMIM28 was revealed to possibly have a role in tumor proliferation and aggressiveness. Our results indicate that these DEGs can serve as prognostic indicators of survival in high-risk neuroblastoma patients and will assist clinicians in making better therapeutic and patient management decisions. © 2020 Giwa et al

SciPy 1.0: fundamental algorithms for scientific computing in Python.

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments

Online Unsupervised Classification with Model Comparison in the Variational Bayes Framework for Voice Activity Detection

A new online, unsupervised method for Voice Activity Detection (VAD) is proposed. The conventional VAD methods often rely on heuristics to adapt the decision threshold to the estimated SNR. The proposed VAD method is based on the Variational Bayes (VB) approach to the online Expectation Maximization (EM), so that it can automatically adapt the decision level and the statistical model at the same time. We consider two parallel classifiers, one for the noise-only case, and the other for speech-and-noise case. Both models are trained concurrently and online using the VB framework. The VB framework also provides an explicit approximation of the log evidence called free energy. It is used to assess the reliability of the classifier in an online fashion, and to decide which model is more appropriate at a given time frame. Experimental evaluations were conducted on the CENSREC-1-C database designed for VAD evaluations. With the effect of the model comparison, the proposed scheme outperforms the conventional VAD algorithms, especially in the remote recording condition. It is also shown to be more robust with respect to changes of the noise type

オンライン キョウシ ナシ ブンルイ オ モチイタ オンセイ クカン ケンシュツ

京都大学0048新制・課程博士博士(情報学)甲第14881号情博第361号新制||情||67(附属図書館)27303UT51-2009-K677京都大学大学院情報学研究科知能情報学専攻(主査)教授 河原 達也, 教授 奥乃 博, 教授 田中 利幸学位規則第4条第1項該当Doctor of InformaticsKyoto UniversityDA

Scikit-learn: Machine Learning in Python

peer reviewedScikit-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.org