Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

/pdf/integrating-single-cell-transcriptomic-data-across-different-3dtsi5w7ob.pdf

Integrating single-cell transcriptomic data across different conditions, technologies, and species.

We present VOSviewer, a freely available computer program that we have developed for constructing and viewing bibliometric maps. Unlike most computer programs that are used for bibliometric mapping, VOSviewer pays special attention to the graphical representation of bibliometric maps. The functionality of VOSviewer is especially useful for displaying large bibliometric maps in an easy-to-interpret way. The paper consists of three parts. In the first part, an overview of VOSviewer’s functionality for displaying bibliometric maps is provided. In the second part, the technical implementation of specific parts of the program is discussed. Finally, in the third part, VOSviewer’s ability to handle large maps is demonstrated by using the program to construct and display a co-citation map of 5,000 major scientific journals.

/pdf/software-survey-vosviewer-a-computer-program-for-505jc6bwmd.pdf

Software survey: VOSviewer, a computer program for bibliometric mapping.

Evolutionary psychology is one of many biologically informed approaches to the study of human behavior. Along with cognitive psychologists, evolutionary psychologists propose that much, if not all, of our behavior can be explained by appeal to internal psychological mechanisms. What distinguishes evolutionary psychologists from many cognitive psychologists is the proposal that the relevant internal mechanisms are adaptations—products of natural selection—that helped our ancestors get around the world, survive and reproduce. To understand the central claims of evolutionary psychology we require an understanding of some key concepts in evolutionary biology, cognitive psychology, philosophy of science and philosophy of mind. Philosophers are interested in evolutionary psychology for a number of reasons. For philosophers of science —mostly philosophers of biology—evolutionary psychology provides a critical target. There is a broad consensus among philosophers of science that evolutionary psychology is a deeply flawed enterprise. For philosophers of mind and cognitive science evolutionary psychology has been a source of empirical hypotheses about cognitive architecture and specific components of that architecture. Philosophers of mind are also critical of evolutionary psychology but their criticisms are not as all-encompassing as those presented by philosophers of biology. Evolutionary psychology is also invoked by philosophers interested in moral psychology both as a source of empirical hypotheses and as a critical target.

/pdf/stanford-encyclopedia-of-philosophy-1wqoykisq0.pdf

Stanford Encyclopedia of Philosophy

bibliometrix: An R-tool for comprehensive science mapping analysis

This chapter provides an introduction to the topic of visualizing bibliometric networks. First, the most commonly studied types of bibliometric networks (i.e., citation, co-citation, bibliographic coupling, keyword co-occurrence, and coauthorship networks) are discussed, and three popular visualization approaches (i.e., distance-based, graph-based, and timeline-based approaches) are distinguished. Next, an overview is given of a number of software tools that can be used for visualizing bibliometric networks. In the second part of the chapter, the focus is specifically on two software tools: VOSviewer and CitNetExplorer. The techniques used by these tools to construct, analyze, and visualize bibliometric networks are discussed. In addition, tutorials are offered that demonstrate in a step-by-step manner how both tools can be used. Finally, the chapter concludes with a discussion of the limitations and the proper use of bibliometric network visualizations and with a summary of some ongoing and future developments.

/pdf/visualizing-bibliometric-networks-22tv7965er.pdf

Visualizing Bibliometric Networks

https://scholarlypublications.universiteitleiden.nl/access/item%3A2885478/view

A unified approach to mapping and clustering of bibliometric networks

Clustering scientific publications in an important problem in bibliometric research. We demonstrate how two software tools, CitNetExplorer and VOSviewer, can be used to cluster publications and to analyze the resulting clustering solutions. CitNetExplorer is used to cluster a large set of publications in the field of astronomy and astrophysics. The publications are clustered based on direct citation relations. CitNetExplorer and VOSviewer are used together to analyze the resulting clustering solutions. Both tools use visualizations to support the analysis of the clustering solutions, with CitNetExplorer focusing on the analysis at the level of individual publications and VOSviewer focusing on the analysis at an aggregate level. The demonstration provided in this paper shows how a clustering of publications can be created and analyzed using freely available software tools. Using the approach presented in this paper, bibliometricians are able to carry out sophisticated cluster analyses without the need to have a deep knowledge of clustering techniques and without requiring advanced computer skills.

/pdf/citation-based-clustering-of-publications-using-4m219pricf.pdf

Citation-based clustering of publications using CitNetExplorer and VOSviewer

We introduce a new algorithm for modularity-based community detection in large networks. The algorithm, which we refer to as a smart local moving algorithm, takes advantage of a well-known local moving heuristic that is also used by other algorithms. Compared with these other algorithms, our proposed algorithm uses the local moving heuristic in a more sophisticated way. Based on an analysis of a diverse set of networks, we show that our smart local moving algorithm identifies community structures with higher modularity values than other algorithms for large-scale modularity optimization, among which the popular “Louvain algorithm”. The computational efficiency of our algorithm makes it possible to perform community detection in networks with tens of millions of nodes and hundreds of millions of edges. Our smart local moving algorithm also performs well in small and medium-sized networks. In short computing times, it identifies community structures with modularity values equally high as, or almost as high as, the highest values reported in the literature, and sometimes even higher than the highest values found in the literature.

/pdf/a-smart-local-moving-algorithm-for-large-scale-modularity-1blamxmllx.pdf

Nees Jan van Eck

Papers

Software survey: VOSviewer, a computer program for bibliometric mapping.

Visualizing Bibliometric Networks

A unified approach to mapping and clustering of bibliometric networks

Citation-based clustering of publications using CitNetExplorer and VOSviewer

A smart local moving algorithm for large-scale modularity-based community detection