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Statistical and machine learning approaches for network analysis
\"This book explores novel graph classes and presents novel methods to classify networks. It particularly addresses the following problems: exploration of novel graph classes and their relationships among each other; existing and classical methods to analyze networks; novel graph similarity and graph classification techniques based on machine learning methods; and applications of graph classification and graph mining. Key topics are addressed in depth including the mathematical definition of novel graph classes, i.e. generalized trees and directed universal hierarchical graphs, and the application areas in which to apply graph classes to practical problems in computational biology, computer science, mathematics, mathematical psychology, etc\"--
eBook
Statistics for library and information services
Statistics for Library and Information Services, written for non-statisticians, provides logical, user-friendly, and step-by-step instructions to make statistics more accessible for students and professionals in the field of Information Science.
eBook
Reality Mining
Big Data is made up of lots of little data: numbers entered into cell phones, addresses entered into GPS devices, visits to websites, online purchases, ATM transactions, and any other activity that leaves a digital trail. Although the abuse of Big Data -- surveillance, spying, hacking -- has made headlines, it shouldn't overshadow the abundant positive applications of Big Data. InReality Mining, Nathan Eagle and Kate Greene cut through the hype and the headlines to explore the positive potential of Big Data, showing the ways in which the analysis of Big Data (\"Reality Mining\") can be used to improve human systems as varied as political polling and disease tracking, while considering user privacy.Eagle, a recognized expert in the field, and Greene, an experienced technology journalist, describe Reality Mining at five different levels: the individual, the neighborhood and organization, the city, the nation, and the world. For each level, they first offer a nontechnical explanation of data collection methods and then describe applications and systems that have been or could be built. These include a mobile app that helps smokers quit smoking; a workplace \"knowledge system\"; the use of GPS, Wi-Fi, and mobile phone data to manage and predict traffic flows; and the analysis of social media to track the spread of disease. Eagle and Greene argue that Big Data, used respectfully and responsibly, can help people live better, healthier, and happier lives.
eBook
MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites
Quality control of MRI is essential for excluding problematic acquisitions and avoiding bias in subsequent image processing and analysis. Visual inspection is subjective and impractical for large scale datasets. Although automated quality assessments have been demonstrated on single-site datasets, it is unclear that solutions can generalize to unseen data acquired at new sites. Here, we introduce the MRI Quality Control tool (MRIQC), a tool for extracting quality measures and fitting a binary (accept/exclude) classifier. Our tool can be run both locally and as a free online service via the OpenNeuro.org portal. The classifier is trained on a publicly available, multi-site dataset (17 sites, N = 1102). We perform model selection evaluating different normalization and feature exclusion approaches aimed at maximizing across-site generalization and estimate an accuracy of 76%±13% on new sites, using leave-one-site-out cross-validation. We confirm that result on a held-out dataset (2 sites, N = 265) also obtaining a 76% accuracy. Even though the performance of the trained classifier is statistically above chance, we show that it is susceptible to site effects and unable to account for artifacts specific to new sites. MRIQC performs with high accuracy in intra-site prediction, but performance on unseen sites leaves space for improvement which might require more labeled data and new approaches to the between-site variability. Overcoming these limitations is crucial for a more objective quality assessment of neuroimaging data, and to enable the analysis of extremely large and multi-site samples.
Journal Article
Chemometric analysis in Raman spectroscopy from experimental design to machine learning–based modeling
Raman spectroscopy is increasingly being used in biology, forensics, diagnostics, pharmaceutics and food science applications. This growth is triggered not only by improvements in the computational and experimental setups but also by the development of chemometric techniques. Chemometric techniques are the analytical processes used to detect and extract information from subtle differences in Raman spectra obtained from related samples. This information could be used to find out, for example, whether a mixture of bacterial cells contains different species, or whether a mammalian cell is healthy or not. Chemometric techniques include spectral processing (ensuring that the spectra used for the subsequent computational processes are as clean as possible) as well as the statistical analysis of the data required for finding the spectral differences that are most useful for differentiation between, for example, different cell types. For Raman spectra, this analysis process is not yet standardized, and there are many confounding pitfalls. This protocol provides guidance on how to perform a Raman spectral analysis: how to avoid these pitfalls, and strategies to circumvent problematic issues. The protocol is divided into four parts: experimental design, data preprocessing, data learning and model transfer. We exemplify our workflow using three example datasets where the spectra from individual cells were collected in single-cell mode, and one dataset where the data were collected from a raster scanning–based Raman spectral imaging experiment of mice tissue. Our aim is to help move Raman-based technologies from proof-of-concept studies toward real-world applications.
Raman spectroscopy is increasingly being used in biological assays and studies. This protocol provides guidance for performing chemometric analysis to detect and extract information relating to the chemical differences between biological samples.
Journal Article
Statistical and Machine Learning forecasting methods: Concerns and ways forward
Machine Learning (ML) methods have been proposed in the academic literature as alternatives to statistical ones for time series forecasting. Yet, scant evidence is available about their relative performance in terms of accuracy and computational requirements. The purpose of this paper is to evaluate such performance across multiple forecasting horizons using a large subset of 1045 monthly time series used in the M3 Competition. After comparing the post-sample accuracy of popular ML methods with that of eight traditional statistical ones, we found that the former are dominated across both accuracy measures used and for all forecasting horizons examined. Moreover, we observed that their computational requirements are considerably greater than those of statistical methods. The paper discusses the results, explains why the accuracy of ML models is below that of statistical ones and proposes some possible ways forward. The empirical results found in our research stress the need for objective and unbiased ways to test the performance of forecasting methods that can be achieved through sizable and open competitions allowing meaningful comparisons and definite conclusions.
Journal Article