Cluster Analysis: Basic Concepts and Methods
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Text Mining Course for KNIME Analytics Platform
Text Mining Course for KNIME Analytics Platform KNIME AG Copyright © 2018 KNIME AG Table of Contents 1. The Open Analytics Platform 2. The Text Processing Extension 3. Importing Text 4. Enrichment 5. Preprocessing 6. Transformation 7. Classification 8. Visualization 9. Clustering 10. Supplementary Workflows Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 2 Noncommercial-Share Alike license 1 https://creativecommons.org/licenses/by-nc-sa/4.0/ Overview KNIME Analytics Platform Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 3 Noncommercial-Share Alike license 1 https://creativecommons.org/licenses/by-nc-sa/4.0/ What is KNIME Analytics Platform? • A tool for data analysis, manipulation, visualization, and reporting • Based on the graphical programming paradigm • Provides a diverse array of extensions: • Text Mining • Network Mining • Cheminformatics • Many integrations, such as Java, R, Python, Weka, H2O, etc. Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 4 Noncommercial-Share Alike license 2 https://creativecommons.org/licenses/by-nc-sa/4.0/ Visual KNIME Workflows NODES perform tasks on data Not Configured Configured Outputs Inputs Executed Status Error Nodes are combined to create WORKFLOWS Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 5 Noncommercial-Share Alike license 3 https://creativecommons.org/licenses/by-nc-sa/4.0/ Data Access • Databases • MySQL, MS SQL Server, PostgreSQL • any JDBC (Oracle, DB2, …) • Files • CSV, txt -
An Introduction to Psychometric Theory with Applications in R
What is psychometrics? What is R? Where did it come from, why use it? Basic statistics and graphics TOD An introduction to Psychometric Theory with applications in R William Revelle Department of Psychology Northwestern University Evanston, Illinois USA February, 2013 1 / 71 What is psychometrics? What is R? Where did it come from, why use it? Basic statistics and graphics TOD Overview 1 Overview Psychometrics and R What is Psychometrics What is R 2 Part I: an introduction to R What is R A brief example Basic steps and graphics 3 Day 1: Theory of Data, Issues in Scaling 4 Day 2: More than you ever wanted to know about correlation 5 Day 3: Dimension reduction through factor analysis, principal components analyze and cluster analysis 6 Day 4: Classical Test Theory and Item Response Theory 7 Day 5: Structural Equation Modeling and applied scale construction 2 / 71 What is psychometrics? What is R? Where did it come from, why use it? Basic statistics and graphics TOD Outline of Day 1/part 1 1 What is psychometrics? Conceptual overview Theory: the organization of Observed and Latent variables A latent variable approach to measurement Data and scaling Structural Equation Models 2 What is R? Where did it come from, why use it? Installing R on your computer and adding packages Installing and using packages Implementations of R Basic R capabilities: Calculation, Statistical tables, Graphics Data sets 3 Basic statistics and graphics 4 steps: read, explore, test, graph Basic descriptive and inferential statistics 4 TOD 3 / 71 What is psychometrics? What is R? Where did it come from, why use it? Basic statistics and graphics TOD What is psychometrics? In physical science a first essential step in the direction of learning any subject is to find principles of numerical reckoning and methods for practicably measuring some quality connected with it. -
A Survey of Clustering with Deep Learning: from the Perspective of Network Architecture
Received May 12, 2018, accepted July 2, 2018, date of publication July 17, 2018, date of current version August 7, 2018. Digital Object Identifier 10.1109/ACCESS.2018.2855437 A Survey of Clustering With Deep Learning: From the Perspective of Network Architecture ERXUE MIN , XIFENG GUO, QIANG LIU , (Member, IEEE), GEN ZHANG , JIANJING CUI, AND JUN LONG College of Computer, National University of Defense Technology, Changsha 410073, China Corresponding authors: Erxue Min ([email protected]) and Qiang Liu ([email protected]) This work was supported by the National Natural Science Foundation of China under Grant 60970034, Grant 61105050, Grant 61702539, and Grant 6097003. ABSTRACT Clustering is a fundamental problem in many data-driven application domains, and clustering performance highly depends on the quality of data representation. Hence, linear or non-linear feature transformations have been extensively used to learn a better data representation for clustering. In recent years, a lot of works focused on using deep neural networks to learn a clustering-friendly representation, resulting in a significant increase of clustering performance. In this paper, we give a systematic survey of clustering with deep learning in views of architecture. Specifically, we first introduce the preliminary knowledge for better understanding of this field. Then, a taxonomy of clustering with deep learning is proposed and some representative methods are introduced. Finally, we propose some interesting future opportunities of clustering with deep learning and give some conclusion remarks. INDEX TERMS Clustering, deep learning, data representation, network architecture. I. INTRODUCTION property of highly non-linear transformation. For the sim- Data clustering is a basic problem in many areas, such as plicity of description, we call clustering methods with deep machine learning, pattern recognition, computer vision, data learning as deep clustering1 in this paper. -
A Tree-Based Dictionary Learning Framework
A Tree-based Dictionary Learning Framework Renato Budinich∗ & Gerlind Plonka† June 11, 2020 We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method the data is organized into a binary partition tree representing a multiscale structure. The dictionary atoms are defined adaptively based on the data clusters in the partition tree. This approach can be interpreted as a generalization of a discrete Haar wavelet transform. Furthermore, any prior knowledge on the wanted structure of the dictionary elements can be simply incorporated. The computational complex- ity of our proposed algorithm depends on the employed clustering method and on the chosen similarity measure between data points. Thanks to the multi- scale properties of the partition tree, our dictionary is structured: when using Orthogonal Matching Pursuit to reconstruct patches from a natural image, dic- tionary atoms corresponding to nodes being closer to the root node in the tree have a tendency to be used with greater coefficients. Keywords. Multiscale dictionary learning, hierarchical clustering, binary partition tree, gen- eralized adaptive Haar wavelet transform, K-means, orthogonal matching pursuit 1 Introduction arXiv:1909.03267v2 [cs.LG] 9 Jun 2020 In many applications one is interested in sparsely approximating a set of N n-dimensional data points Y , columns of an n N real matrix Y = (Y1;:::;Y ). Assuming that the data j × N ∗R. Budinich is with the Fraunhofer SCS, Nordostpark 93, 90411 Nürnberg, Germany, e-mail: re- [email protected] †G. Plonka is with the Institute for Numerical and Applied Mathematics, University of Göttingen, Lotzestr. -
Cluster Analysis for Gene Expression Data: a Survey
Cluster Analysis for Gene Expression Data: A Survey Daxin Jiang Chun Tang Aidong Zhang Department of Computer Science and Engineering State University of New York at Buffalo Email: djiang3, chuntang, azhang @cse.buffalo.edu Abstract DNA microarray technology has now made it possible to simultaneously monitor the expres- sion levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremen- dous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. Cluster analysis seeks to partition a given data set into groups based on specified features so that the data points within a group are more similar to each other than the points in different groups. A very rich literature on cluster analysis has developed over the past three decades. Many conventional clustering algorithms have been adapted or directly applied to gene expres- sion data, and also new algorithms have recently been proposed specifically aiming at gene ex- pression data. These clustering algorithms have been proven useful for identifying biologically relevant groups of genes and samples. In this paper, we first briefly introduce the concepts of microarray technology and discuss the basic elements of clustering on gene expression data. -
Comparison of Dimensionality Reduction Techniques on Audio Signals
Comparison of Dimensionality Reduction Techniques on Audio Signals Tamás Pál, Dániel T. Várkonyi Eötvös Loránd University, Faculty of Informatics, Department of Data Science and Engineering, Telekom Innovation Laboratories, Budapest, Hungary {evwolcheim, varkonyid}@inf.elte.hu WWW home page: http://t-labs.elte.hu Abstract: Analysis of audio signals is widely used and this work: car horn, dog bark, engine idling, gun shot, and very effective technique in several domains like health- street music [5]. care, transportation, and agriculture. In a general process Related work is presented in Section 2, basic mathe- the output of the feature extraction method results in huge matical notation used is described in Section 3, while the number of relevant features which may be difficult to pro- different methods of the pipeline are briefly presented in cess. The number of features heavily correlates with the Section 4. Section 5 contains data about the evaluation complexity of the following machine learning method. Di- methodology, Section 6 presents the results and conclu- mensionality reduction methods have been used success- sions are formulated in Section 7. fully in recent times in machine learning to reduce com- The goal of this paper is to find a combination of feature plexity and memory usage and improve speed of following extraction and dimensionality reduction methods which ML algorithms. This paper attempts to compare the state can be most efficiently applied to audio data visualization of the art dimensionality reduction techniques as a build- in 2D and preserve inter-class relations the most. ing block of the general process and analyze the usability of these methods in visualizing large audio datasets. -
Reliability Engineering: Today and Beyond
Reliability Engineering: Today and Beyond Keynote Talk at the 6th Annual Conference of the Institute for Quality and Reliability Tsinghua University People's Republic of China by Professor Mohammad Modarres Director, Center for Risk and Reliability Department of Mechanical Engineering Outline – A New Era in Reliability Engineering – Reliability Engineering Timeline and Research Frontiers – Prognostics and Health Management – Physics of Failure – Data-driven Approaches in PHM – Hybrid Methods – Conclusions New Era in Reliability Sciences and Engineering • Started as an afterthought analysis – In enduing years dismissed as a legitimate field of science and engineering – Worked with small data • Three advances transformed reliability into a legitimate science: – 1. Availability of inexpensive sensors and information systems – 2. Ability to better described physics of damage, degradation, and failure time using empirical and theoretical sciences – 3. Access to big data and PHM techniques for diagnosing faults and incipient failures • Today we can predict abnormalities, offer just-in-time remedies to avert failures, and making systems robust and resilient to failures Seventy Years of Reliability Engineering – Reliability Engineering Initiatives in 1950’s • Weakest link • Exponential life model • Reliability Block Diagrams (RBDs) – Beyond Exp. Dist. & Birth of System Reliability in 1960’s • Birth of Physics of Failure (POF) • Uses of more proper distributions (Weibull, etc.) • Reliability growth • Life testing • Failure Mode and Effect Analysis -
Robust Hierarchical Clustering∗
Journal of Machine Learning Research 15 (2014) 4011-4051 Submitted 12/13; Published 12/14 Robust Hierarchical Clustering∗ Maria-Florina Balcan [email protected] School of Computer Science Carnegie Mellon University Pittsburgh, PA 15213, USA Yingyu Liang [email protected] Department of Computer Science Princeton University Princeton, NJ 08540, USA Pramod Gupta [email protected] Google, Inc. 1600 Amphitheatre Parkway Mountain View, CA 94043, USA Editor: Sanjoy Dasgupta Abstract One of the most widely used techniques for data clustering is agglomerative clustering. Such algorithms have been long used across many different fields ranging from computational biology to social sciences to computer vision in part because their output is easy to interpret. Unfortunately, it is well known, however, that many of the classic agglomerative clustering algorithms are not robust to noise. In this paper we propose and analyze a new robust algorithm for bottom-up agglomerative clustering. We show that our algorithm can be used to cluster accurately in cases where the data satisfies a number of natural properties and where the traditional agglomerative algorithms fail. We also show how to adapt our algorithm to the inductive setting where our given data is only a small random sample of the entire data set. Experimental evaluations on synthetic and real world data sets show that our algorithm achieves better performance than other hierarchical algorithms in the presence of noise. Keywords: unsupervised learning, clustering, agglomerative algorithms, robustness 1. Introduction Many data mining and machine learning applications ranging from computer vision to biology problems have recently faced an explosion of data. As a consequence it has become increasingly important to develop effective, accurate, robust to noise, fast, and general clustering algorithms, accessible to developers and researchers in a diverse range of areas. -
Space-Time Hierarchical Clustering for Identifying Clusters in Spatiotemporal Point Data
International Journal of Geo-Information Article Space-Time Hierarchical Clustering for Identifying Clusters in Spatiotemporal Point Data David S. Lamb 1,* , Joni Downs 2 and Steven Reader 2 1 Measurement and Research, Department of Educational and Psychological Studies, College of Education, University of South Florida, 4202 E Fowler Ave, Tampa, FL 33620, USA 2 School of Geosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL 33620, USA; [email protected] (J.D.); [email protected] (S.R.) * Correspondence: [email protected] Received: 2 December 2019; Accepted: 27 January 2020; Published: 1 February 2020 Abstract: Finding clusters of events is an important task in many spatial analyses. Both confirmatory and exploratory methods exist to accomplish this. Traditional statistical techniques are viewed as confirmatory, or observational, in that researchers are confirming an a priori hypothesis. These methods often fail when applied to newer types of data like moving object data and big data. Moving object data incorporates at least three parts: location, time, and attributes. This paper proposes an improved space-time clustering approach that relies on agglomerative hierarchical clustering to identify groupings in movement data. The approach, i.e., space–time hierarchical clustering, incorporates location, time, and attribute information to identify the groups across a nested structure reflective of a hierarchical interpretation of scale. Simulations are used to understand the effects of different parameters, and to compare against existing clustering methodologies. The approach successfully improves on traditional approaches by allowing flexibility to understand both the spatial and temporal components when applied to data. The method is applied to animal tracking data to identify clusters, or hotspots, of activity within the animal’s home range. -
Chapter G03 – Multivariate Methods
g03 – Multivariate Methods Introduction – g03 Chapter g03 – Multivariate Methods 1. Scope of the Chapter This chapter is concerned with methods for studying multivariate data. A multivariate data set consists of several variables recorded on a number of objects or individuals. Multivariate methods can be classified as those that seek to examine the relationships between the variables (e.g., principal components), known as variable-directed methods, and those that seek to examine the relationships between the objects (e.g., cluster analysis), known as individual-directed methods. Multiple regression is not included in this chapter as it involves the relationship of a single variable, known as the response variable, to the other variables in the data set, the explanatory variables. Routines for multiple regression are provided in Chapter g02. 2. Background 2.1. Variable-directed Methods Let the n by p data matrix consist of p variables, x1,x2,...,xp,observedonn objects or individuals. Variable-directed methods seek to examine the linear relationships between the p variables with the aim of reducing the dimensionality of the problem. There are different methods depending on the structure of the problem. Principal component analysis and factor analysis examine the relationships between all the variables. If the individuals are classified into groups then canonical variate analysis examines the between group structure. If the variables can be considered as coming from two sets then canonical correlation analysis examines the relationships between the two sets of variables. All four methods are based on an eigenvalue decomposition or a singular value decomposition (SVD)of an appropriate matrix. The above methods may reduce the dimensionality of the data from the original p variables to a smaller number, k, of derived variables that adequately represent the data. -
Biostatistics (BIOSTAT) 1
Biostatistics (BIOSTAT) 1 This course covers practical aspects of conducting a population- BIOSTATISTICS (BIOSTAT) based research study. Concepts include determining a study budget, setting a timeline, identifying study team members, setting a strategy BIOSTAT 301-0 Introduction to Epidemiology (1 Unit) for recruitment and retention, developing a data collection protocol This course introduces epidemiology and its uses for population health and monitoring data collection to ensure quality control and quality research. Concepts include measures of disease occurrence, common assurance. Students will demonstrate these skills by engaging in a sources and types of data, important study designs, sources of error in quarter-long group project to draft a Manual of Operations for a new epidemiologic studies and epidemiologic methods. "mock" population study. BIOSTAT 302-0 Introduction to Biostatistics (1 Unit) BIOSTAT 429-0 Systematic Review and Meta-Analysis in the Medical This course introduces principles of biostatistics and applications Sciences (1 Unit) of statistical methods in health and medical research. Concepts This course covers statistical methods for meta-analysis. Concepts include descriptive statistics, basic probability, probability distributions, include fixed-effects and random-effects models, measures of estimation, hypothesis testing, correlation and simple linear regression. heterogeneity, prediction intervals, meta regression, power assessment, BIOSTAT 303-0 Probability (1 Unit) subgroup analysis and assessment of publication -
Big Data for Reliability Engineering: Threat and Opportunity
Reliability, February 2016 Big Data for Reliability Engineering: Threat and Opportunity Vitali Volovoi Independent Consultant [email protected] more recently, analytics). It shares with the rest of the fields Abstract - The confluence of several technologies promises under this umbrella the need to abstract away most stormy waters ahead for reliability engineering. News reports domain-specific information, and to use tools that are mainly are full of buzzwords relevant to the future of the field—Big domain-independent1. As a result, it increasingly shares the Data, the Internet of Things, predictive and prescriptive lingua franca of modern systems engineering—probability and analytics—the sexier sisters of reliability engineering, both statistics that are required to balance the otherwise orderly and exciting and threatening. Can we reliability engineers join the deterministic engineering world. party and suddenly become popular (and better paid), or are And yet, reliability engineering does not wear the fancy we at risk of being superseded and driven into obsolescence? clothes of its sisters. There is nothing privileged about it. It is This article argues that“big-picture” thinking, which is at the rarely studied in engineering schools, and it is definitely not core of the concept of the System of Systems, is key for a studied in business schools! Instead, it is perceived as a bright future for reliability engineering. necessary evil (especially if the reliability issues in question are safety-related). The community of reliability engineers Keywords - System of Systems, complex systems, Big Data, consists of engineers from other fields who were mainly Internet of Things, industrial internet, predictive analytics, trained on the job (instead of receiving formal degrees in the prescriptive analytics field).