Clustering, cont. Genome 373 Genomic Informatics Elhanan Borenstein. Some slides adapted from Jacques van Helden
|
|
|
- Roberta Peters
- 5 years ago
- Views:
Transcription
1 Clustering, cont Genome 373 Genomic Informatics Elhanan Borenstein Some slides adapted from Jacques van Helden
2 Improving the search heuristic: Multiple starting points Simulated annealing Genetic algorithms A quick review Branch confidence and bootstrap support
3 Clustering: The clustering problem: homogeneity vs. separation Why clustering A quick review The number of possible clustering solutions gene x [0.1, 0.0, 0.6, 1.0, 2.1, 0.4, 0.2, 0.3, 0.5, 0.1, 2.1] gene y [0.2, 1.0, 0.8, 0.4, 1.4, 0.5, 0.3, 2.1, 1.2, 3.4, 0.1]
4 One problem, numerous solutions Many algorithms: Hierarchical clustering k-means self-organizing maps (SOM) Knn PCC CLICK There are many formulations of the clustering problem; most of them are NP-hard The results (i.e., obtained clusters) can vary drastically depending on: Clustering method Parameters specific to each clustering method
5 Different views of clustering
6 Different views of clustering
7 Different views of clustering
8 Different views of clustering
9 Different views of clustering
10 Different views of clustering
11 Measuring similarity/distance An important step in many clustering methods is the selection of a distance measure (metric), defining the distance between 2 data points (e.g., 2 genes) Point 1 : [ ] Point 2 : [ ] Genes are points in the multi-dimensional space R n (where n denotes the number of conditions)
12 Measuring similarity/distance So how do we measure the distance between two point in a multi-dimensional space? B A
13 Measuring similarity/distance So how do we measure the distance between two point in a multi-dimensional space? p-norm Common distance functions: The Euclidean distance (a.k.a distance as the crow flies or distance). The Manhattan distance (a.k.a taxicab distance) The maximum norm (a.k.a infinity distance) 2-norm 1-norm infinity-norm Correlation (Pearson, Spearman, Absolute Value of Correlation, etc.)
14 Metric matters! The metric of choice has a marked impact on the shape of the resulting clusters: Some elements may be close to one another in one metric and far from one anther in a different metric. Consider, for example, the point (x=1,y=1) and the origin. What s their distance using the 2-norm (Euclidean distance )? What s their distance using the 1-norm (a.k.a. taxicab/ Manhattan norm)? What s their distance using the infinity-norm?
15 Hierarchical clustering
16 object 1 object 2 object 3 object 4 object 5 Hierarchical clustering Hierarchical clustering is an agglomerative clustering method Takes as input a distance matrix Progressively regroups the closest objects/groups Tree representation Distance matrix branch node c3 c1 object 1 object 5 object object object object object root c4 c2 object 4 object 2 object 3 leaf nodes
17 mmm Déjà vu anyone?
18 Hierarchical clustering algorithm 1. Assign each object to a separate cluster. 2. Find the pair of clusters with the shortest distance, and regroup them into a single cluster. 3. Repeat 2 until there is a single cluster. The result is a tree, whose intermediate nodes represent clusters Branch lengths represent distances between clusters
19 Hierarchical clustering algorithm 1. Assign each object to a separate cluster. 2. Find the pair of clusters with the shortest distance, and regroup them into a single cluster. 3. Repeat 2 until there is a single cluster.
20 Linkage (agglomeration) methods 1. Assign each object to a separate cluster. 2. Find the pair of clusters with the shortest distance, and regroup them into a single cluster. 3. Repeat 2 until there is a single cluster. One needs to define a (dis)similarity metric between two groups. There are several possibilities Average linkage: the average distance between objects from groups A and B Single linkage: the distance between the closest objects from groups A and B Complete linkage: the distance between the most distant objects from groups A and B
21 Impact of the agglomeration rule These four trees were built from the same distance matrix, using 4 different agglomeration rules. Single-linkage typically creates nesting clusters Complete linkage create more balanced trees. Note: these trees were computed from a matrix of random numbers. The impression of structure is thus a complete artifact.
22 Hierarchical clustering result Five clusters
23 The philosophy of clustering Unsupervised learning problem No single solution is necessarily the true/correct! There is usually a tradeoff between homogeneity and separation: More clusters increased homogeneity but decreased separation Less clusters Increased separation but reduced homogeneity Method matters; metric matters; definitions matter; In most cases, heuristic methods or approximations are used.
24
Contents. ! Data sets. ! Distance and similarity metrics. ! K-means clustering. ! Hierarchical clustering. ! Evaluation of clustering results
Statistical Analysis of Microarray Data Contents Data sets Distance and similarity metrics K-means clustering Hierarchical clustering Evaluation of clustering results Clustering Jacques van Helden Jacques.van.Helden@ulb.ac.be
Clustering Jacques van Helden
Statistical Analysis of Microarray Data Clustering Jacques van Helden Jacques.van.Helden@ulb.ac.be Contents Data sets Distance and similarity metrics K-means clustering Hierarchical clustering Evaluation
Clustering. k-mean clustering. Genome 559: Introduction to Statistical and Computational Genomics Elhanan Borenstein
Clustering k-mean clustering Genome 559: Introduction to Statistical and Computational Genomics Elhanan Borenstein A quick review The clustering problem: homogeneity vs. separation Different representations
Clustering k-mean clustering
Clustering k-mean clustering Genome 373 Genomic Informatics Elhanan Borenstein The clustering problem: partition genes into distinct sets with high homogeneity and high separation Clustering (unsupervised)
Distances, Clustering! Rafael Irizarry!
Distances, Clustering! Rafael Irizarry! Heatmaps! Distance! Clustering organizes things that are close into groups! What does it mean for two genes to be close?! What does it mean for two samples to
9/29/13. Outline Data mining tasks. Clustering algorithms. Applications of clustering in biology
9/9/ I9 Introduction to Bioinformatics, Clustering algorithms Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Outline Data mining tasks Predictive tasks vs descriptive tasks Example
What is Unsupervised Learning?
Clustering What is Unsupervised Learning? Unlike in supervised learning, in unsupervised learning, there are no labels We simply a search for patterns in the data Examples Clustering Density Estimation
Gene Clustering & Classification
BINF, Introduction to Computational Biology Gene Clustering & Classification Young-Rae Cho Associate Professor Department of Computer Science Baylor University Overview Introduction to Gene Clustering
Measure of Distance. We wish to define the distance between two objects Distance metric between points:
Measure of Distance We wish to define the distance between two objects Distance metric between points: Euclidean distance (EUC) Manhattan distance (MAN) Pearson sample correlation (COR) Angle distance
Cluster Analysis for Microarray Data
Cluster Analysis for Microarray Data Seventh International Long Oligonucleotide Microarray Workshop Tucson, Arizona January 7-12, 2007 Dan Nettleton IOWA STATE UNIVERSITY 1 Clustering Group objects that
CSE 5243 INTRO. TO DATA MINING
CSE 5243 INTRO. TO DATA MINING Cluster Analysis: Basic Concepts and Methods Huan Sun, CSE@The Ohio State University Slides adapted from UIUC CS412, Fall 2017, by Prof. Jiawei Han 2 Chapter 10. Cluster
Cluster Analysis: Agglomerate Hierarchical Clustering
Cluster Analysis: Agglomerate Hierarchical Clustering Yonghee Lee Department of Statistics, The University of Seoul Oct 29, 2015 Contents 1 Cluster Analysis Introduction Distance matrix Agglomerative Hierarchical
Hierarchical Clustering
What is clustering Partitioning of a data set into subsets. A cluster is a group of relatively homogeneous cases or observations Hierarchical Clustering Mikhail Dozmorov Fall 2016 2/61 What is clustering
Unsupervised learning: Clustering & Dimensionality reduction. Theo Knijnenburg Jorma de Ronde
Unsupervised learning: Clustering & Dimensionality reduction Theo Knijnenburg Jorma de Ronde Source of slides Marcel Reinders TU Delft Lodewyk Wessels NKI Bioalgorithms.info Jeffrey D. Ullman Stanford
10601 Machine Learning. Hierarchical clustering. Reading: Bishop: 9-9.2
161 Machine Learning Hierarchical clustering Reading: Bishop: 9-9.2 Second half: Overview Clustering - Hierarchical, semi-supervised learning Graphical models - Bayesian networks, HMMs, Reasoning under
High throughput Data Analysis 2. Cluster Analysis
High throughput Data Analysis 2 Cluster Analysis Overview Why clustering? Hierarchical clustering K means clustering Issues with above two Other methods Quality of clustering results Introduction WHY DO
Midterm Examination CS 540-2: Introduction to Artificial Intelligence
Midterm Examination CS 54-2: Introduction to Artificial Intelligence March 9, 217 LAST NAME: FIRST NAME: Problem Score Max Score 1 15 2 17 3 12 4 6 5 12 6 14 7 15 8 9 Total 1 1 of 1 Question 1. [15] State
Clustering. Robert M. Haralick. Computer Science, Graduate Center City University of New York
Clustering Robert M. Haralick Computer Science, Graduate Center City University of New York Outline K-means 1 K-means 2 3 4 5 Clustering K-means The purpose of clustering is to determine the similarity
Uninformed Search Methods. Informed Search Methods. Midterm Exam 3/13/18. Thursday, March 15, 7:30 9:30 p.m. room 125 Ag Hall
Midterm Exam Thursday, March 15, 7:30 9:30 p.m. room 125 Ag Hall Covers topics through Decision Trees and Random Forests (does not include constraint satisfaction) Closed book 8.5 x 11 sheet with notes
Hierarchical clustering
Aprendizagem Automática Hierarchical clustering Ludwig Krippahl Hierarchical clustering Summary Hierarchical Clustering Agglomerative Clustering Divisive Clustering Clustering Features 1 Aprendizagem Automática
Chapter DM:II. II. Cluster Analysis
Chapter DM:II II. Cluster Analysis Cluster Analysis Basics Hierarchical Cluster Analysis Iterative Cluster Analysis Density-Based Cluster Analysis Cluster Evaluation Constrained Cluster Analysis DM:II-1
Unsupervised Learning and Clustering
Unsupervised Learning and Clustering Selim Aksoy Department of Computer Engineering Bilkent University saksoy@cs.bilkent.edu.tr CS 551, Spring 2009 CS 551, Spring 2009 c 2009, Selim Aksoy (Bilkent University)
Hard clustering. Each object is assigned to one and only one cluster. Hierarchical clustering is usually hard. Soft (fuzzy) clustering
An unsupervised machine learning problem Grouping a set of objects in such a way that objects in the same group (a cluster) are more similar (in some sense or another) to each other than to those in other
Hierarchical Clustering Lecture 9
Hierarchical Clustering Lecture 9 Marina Santini Acknowledgements Slides borrowed and adapted from: Data Mining by I. H. Witten, E. Frank and M. A. Hall 1 Lecture 9: Required Reading Witten et al. (2011:
CSE 5243 INTRO. TO DATA MINING
CSE 5243 INTRO. TO DATA MINING Cluster Analysis: Basic Concepts and Methods Huan Sun, CSE@The Ohio State University 09/25/2017 Slides adapted from UIUC CS412, Fall 2017, by Prof. Jiawei Han 2 Chapter 10.
How do microarrays work
Lecture 3 (continued) Alvis Brazma European Bioinformatics Institute How do microarrays work condition mrna cdna hybridise to microarray condition Sample RNA extract labelled acid acid acid nucleic acid
10701 Machine Learning. Clustering
171 Machine Learning Clustering What is Clustering? Organizing data into clusters such that there is high intra-cluster similarity low inter-cluster similarity Informally, finding natural groupings among
A quick review. The clustering problem: Hierarchical clustering algorithm: Many possible distance metrics K-mean clustering algorithm:
The clustering problem: partition genes into distinct sets with high homogeneity and high separation Hierarchical clustering algorithm: 1. Assign each object to a separate cluster.. Regroup the pair of
Clustering Gene Expression Data: Acknowledgement: Elizabeth Garrett-Mayer; Shirley Liu; Robert Tibshirani; Guenther Walther; Trevor Hastie
Clustering Gene Expression Data: Acknowledgement: Elizabeth Garrett-Mayer; Shirley Liu; Robert Tibshirani; Guenther Walther; Trevor Hastie Data from Garber et al. PNAS (98), 2001. Clustering Clustering
ECLT 5810 Clustering
ECLT 5810 Clustering What is Cluster Analysis? Cluster: a collection of data objects Similar to one another within the same cluster Dissimilar to the objects in other clusters Cluster analysis Grouping
Lesson 3. Prof. Enza Messina
Lesson 3 Prof. Enza Messina Clustering techniques are generally classified into these classes: PARTITIONING ALGORITHMS Directly divides data points into some prespecified number of clusters without a hierarchical
Hierarchical clustering
Hierarchical clustering Based in part on slides from textbook, slides of Susan Holmes December 2, 2012 1 / 1 Description Produces a set of nested clusters organized as a hierarchical tree. Can be visualized
CS7267 MACHINE LEARNING NEAREST NEIGHBOR ALGORITHM. Mingon Kang, PhD Computer Science, Kennesaw State University
CS7267 MACHINE LEARNING NEAREST NEIGHBOR ALGORITHM Mingon Kang, PhD Computer Science, Kennesaw State University KNN K-Nearest Neighbors (KNN) Simple, but very powerful classification algorithm Classifies
Exploratory data analysis for microarrays
Exploratory data analysis for microarrays Jörg Rahnenführer Computational Biology and Applied Algorithmics Max Planck Institute for Informatics D-66123 Saarbrücken Germany NGFN - Courses in Practical DNA
Cluster Analysis. Angela Montanari and Laura Anderlucci
Cluster Analysis Angela Montanari and Laura Anderlucci 1 Introduction Clustering a set of n objects into k groups is usually moved by the aim of identifying internally homogenous groups according to a
Working with Unlabeled Data Clustering Analysis. Hsiao-Lung Chan Dept Electrical Engineering Chang Gung University, Taiwan
Working with Unlabeled Data Clustering Analysis Hsiao-Lung Chan Dept Electrical Engineering Chang Gung University, Taiwan chanhl@mail.cgu.edu.tw Unsupervised learning Finding centers of similarity using
Olmo S. Zavala Romero. Clustering Hierarchical Distance Group Dist. K-means. Center of Atmospheric Sciences, UNAM.
Center of Atmospheric Sciences, UNAM November 16, 2016 Cluster Analisis Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster)
Clustering & Bootstrapping
Clustering & Bootstrapping Jelena Prokić University of Groningen The Netherlands March 25, 2009 Groningen Overview What is clustering? Various clustering algorithms Bootstrapping Application in dialectometry
Gene expression & Clustering (Chapter 10)
Gene expression & Clustering (Chapter 10) Determining gene function Sequence comparison tells us if a gene is similar to another gene, e.g., in a new species Dynamic programming Approximate pattern matching
An Unsupervised Technique for Statistical Data Analysis Using Data Mining
International Journal of Information Sciences and Application. ISSN 0974-2255 Volume 5, Number 1 (2013), pp. 11-20 International Research Publication House http://www.irphouse.com An Unsupervised Technique
Clustering algorithms
Clustering algorithms Machine Learning Hamid Beigy Sharif University of Technology Fall 1393 Hamid Beigy (Sharif University of Technology) Clustering algorithms Fall 1393 1 / 22 Table of contents 1 Supervised
Unsupervised Learning and Clustering
Unsupervised Learning and Clustering Selim Aksoy Department of Computer Engineering Bilkent University saksoy@cs.bilkent.edu.tr CS 551, Spring 2008 CS 551, Spring 2008 c 2008, Selim Aksoy (Bilkent University)
Introduction to Clustering
Introduction to Clustering Ref: Chengkai Li, Department of Computer Science and Engineering, University of Texas at Arlington (Slides courtesy of Vipin Kumar) What is Cluster Analysis? Finding groups of
Data Mining: Concepts and Techniques. Chapter March 8, 2007 Data Mining: Concepts and Techniques 1
Data Mining: Concepts and Techniques Chapter 7.1-4 March 8, 2007 Data Mining: Concepts and Techniques 1 1. What is Cluster Analysis? 2. Types of Data in Cluster Analysis Chapter 7 Cluster Analysis 3. A
Bioinformatics - Lecture 07
Bioinformatics - Lecture 07 Bioinformatics Clusters and networks Martin Saturka http://www.bioplexity.org/lectures/ EBI version 0.4 Creative Commons Attribution-Share Alike 2.5 License Learning on profiles
Hierarchical Clustering
Hierarchical Clustering Produces a set of nested clusters organized as a hierarchical tree Can be visualized as a dendrogram A tree like diagram that records the sequences of merges or splits 0 0 0 00
ECLT 5810 Clustering
ECLT 5810 Clustering What is Cluster Analysis? Cluster: a collection of data objects Similar to one another within the same cluster Dissimilar to the objects in other clusters Cluster analysis Grouping
Tree Models of Similarity and Association. Clustering and Classification Lecture 5
Tree Models of Similarity and Association Clustering and Lecture 5 Today s Class Tree models. Hierarchical clustering methods. Fun with ultrametrics. 2 Preliminaries Today s lecture is based on the monograph
Clustering Part 3. Hierarchical Clustering
Clustering Part Dr Sanjay Ranka Professor Computer and Information Science and Engineering University of Florida, Gainesville Hierarchical Clustering Two main types: Agglomerative Start with the points
Cluster Analysis. Ying Shen, SSE, Tongji University
Cluster Analysis Ying Shen, SSE, Tongji University Cluster analysis Cluster analysis groups data objects based only on the attributes in the data. The main objective is that The objects within a group
Hierarchical Clustering 4/5/17
Hierarchical Clustering 4/5/17 Hypothesis Space Continuous inputs Output is a binary tree with data points as leaves. Useful for explaining the training data. Not useful for making new predictions. Direction
Cluster Analysis. Mu-Chun Su. Department of Computer Science and Information Engineering National Central University 2003/3/11 1
Cluster Analysis Mu-Chun Su Department of Computer Science and Information Engineering National Central University 2003/3/11 1 Introduction Cluster analysis is the formal study of algorithms and methods
Clustering. Lecture 6, 1/24/03 ECS289A
Clustering Lecture 6, 1/24/03 What is Clustering? Given n objects, assign them to groups (clusters) based on their similarity Unsupervised Machine Learning Class Discovery Difficult, and maybe ill-posed
Biological Networks Analysis
Biological Networks Analysis Introduction and Dijkstra s algorithm Genome 559: Introduction to Statistical and Computational Genomics Elhanan Borenstein The clustering problem: partition genes into distinct
TELCOM2125: Network Science and Analysis
School of Information Sciences University of Pittsburgh TELCOM2125: Network Science and Analysis Konstantinos Pelechrinis Spring 2015 2 Part 4: Dividing Networks into Clusters The problem l Graph partitioning
CS570: Introduction to Data Mining
CS570: Introduction to Data Mining Scalable Clustering Methods: BIRCH and Others Reading: Chapter 10.3 Han, Chapter 9.5 Tan Cengiz Gunay, Ph.D. Slides courtesy of Li Xiong, Ph.D., 2011 Han, Kamber & Pei.
Unsupervised Learning
Outline Unsupervised Learning Basic concepts K-means algorithm Representation of clusters Hierarchical clustering Distance functions Which clustering algorithm to use? NN Supervised learning vs. unsupervised
3. Cluster analysis Overview
Université Laval Analyse multivariable - mars-avril 2008 1 3.1. Overview 3. Cluster analysis Clustering requires the recognition of discontinuous subsets in an environment that is sometimes discrete (as
Comparisons and validation of statistical clustering techniques for microarray gene expression data. Outline. Microarrays.
Comparisons and validation of statistical clustering techniques for microarray gene expression data Susmita Datta and Somnath Datta Presented by: Jenni Dietrich Assisted by: Jeffrey Kidd and Kristin Wheeler
Clustering and The Expectation-Maximization Algorithm
Clustering and The Expectation-Maximization Algorithm Unsupervised Learning Marek Petrik 3/7 Some of the figures in this presentation are taken from An Introduction to Statistical Learning, with applications
EECS730: Introduction to Bioinformatics
EECS730: Introduction to Bioinformatics Lecture 15: Microarray clustering http://compbio.pbworks.com/f/wood2.gif Some slides were adapted from Dr. Shaojie Zhang (University of Central Florida) Microarray
Chapter 6: Cluster Analysis
Chapter 6: Cluster Analysis The major goal of cluster analysis is to separate individual observations, or items, into groups, or clusters, on the basis of the values for the q variables measured on each
INF4820. Clustering. Erik Velldal. Nov. 17, University of Oslo. Erik Velldal INF / 22
INF4820 Clustering Erik Velldal University of Oslo Nov. 17, 2009 Erik Velldal INF4820 1 / 22 Topics for Today More on unsupervised machine learning for data-driven categorization: clustering. The task
Data Mining. Dr. Raed Ibraheem Hamed. University of Human Development, College of Science and Technology Department of Computer Science
Data Mining Dr. Raed Ibraheem Hamed University of Human Development, College of Science and Technology Department of Computer Science 06 07 Department of CS - DM - UHD Road map Cluster Analysis: Basic
10. Clustering. Introduction to Bioinformatics Jarkko Salojärvi. Based on lecture slides by Samuel Kaski
10. Clustering Introduction to Bioinformatics 30.9.2008 Jarkko Salojärvi Based on lecture slides by Samuel Kaski Definition of a cluster Typically either 1. A group of mutually similar samples, or 2. A
Clustering CS 550: Machine Learning
Clustering CS 550: Machine Learning This slide set mainly uses the slides given in the following links: http://www-users.cs.umn.edu/~kumar/dmbook/ch8.pdf http://www-users.cs.umn.edu/~kumar/dmbook/dmslides/chap8_basic_cluster_analysis.pdf
Hierarchical Clustering
Hierarchical Clustering Hierarchical Clustering Produces a set of nested clusters organized as a hierarchical tree Can be visualized as a dendrogram A tree-like diagram that records the sequences of merges
Multivariate Methods
Multivariate Methods Cluster Analysis http://www.isrec.isb-sib.ch/~darlene/embnet/ Classification Historically, objects are classified into groups periodic table of the elements (chemistry) taxonomy (zoology,
Based on Raymond J. Mooney s slides
Instance Based Learning Based on Raymond J. Mooney s slides University of Texas at Austin 1 Example 2 Instance-Based Learning Unlike other learning algorithms, does not involve construction of an explicit
Clustering. Chapter 10 in Introduction to statistical learning
Clustering Chapter 10 in Introduction to statistical learning 16 14 12 10 8 6 4 2 0 2 4 6 8 10 12 14 1 Clustering ² Clustering is the art of finding groups in data (Kaufman and Rousseeuw, 1990). ² What
Cluster analysis. Agnieszka Nowak - Brzezinska
Cluster analysis Agnieszka Nowak - Brzezinska Outline of lecture What is cluster analysis? Clustering algorithms Measures of Cluster Validity What is Cluster Analysis? Finding groups of objects such that
INF4820, Algorithms for AI and NLP: Hierarchical Clustering
INF4820, Algorithms for AI and NLP: Hierarchical Clustering Erik Velldal University of Oslo Sept. 25, 2012 Agenda Topics we covered last week Evaluating classifiers Accuracy, precision, recall and F-score
Clustering: K-means and Kernel K-means
Clustering: K-means and Kernel K-means Piyush Rai Machine Learning (CS771A) Aug 31, 2016 Machine Learning (CS771A) Clustering: K-means and Kernel K-means 1 Clustering Usually an unsupervised learning problem
CLUSTERING IN BIOINFORMATICS
CLUSTERING IN BIOINFORMATICS CSE/BIMM/BENG 8 MAY 4, 0 OVERVIEW Define the clustering problem Motivation: gene expression and microarrays Types of clustering Clustering algorithms Other applications of
BCLUST -- A program to assess reliability of gene clusters from expression data by using consensus tree and bootstrap resampling method
BCLUST -- A program to assess reliability of gene clusters from expression data by using consensus tree and bootstrap resampling method Introduction This program is developed in the lab of Hongyu Zhao
Oliver Dürr. Statistisches Data Mining (StDM) Woche 5. Institut für Datenanalyse und Prozessdesign Zürcher Hochschule für Angewandte Wissenschaften
Statistisches Data Mining (StDM) Woche 5 Oliver Dürr Institut für Datenanalyse und Prozessdesign Zürcher Hochschule für Angewandte Wissenschaften oliver.duerr@zhaw.ch Winterthur, 17 Oktober 2017 1 Multitasking
Classification. Vladimir Curic. Centre for Image Analysis Swedish University of Agricultural Sciences Uppsala University
Classification Vladimir Curic Centre for Image Analysis Swedish University of Agricultural Sciences Uppsala University Outline An overview on classification Basics of classification How to choose appropriate
Forestry Applied Multivariate Statistics. Cluster Analysis
1 Forestry 531 -- Applied Multivariate Statistics Cluster Analysis Purpose: To group similar entities together based on their attributes. Entities can be variables or observations. [illustration in Class]
Data Mining Cluster Analysis: Basic Concepts and Algorithms. Slides From Lecture Notes for Chapter 8. Introduction to Data Mining
Data Mining Cluster Analysis: Basic Concepts and Algorithms Slides From Lecture Notes for Chapter 8 Introduction to Data Mining by Tan, Steinbach, Kumar Tan,Steinbach, Kumar Introduction to Data Mining
Clustering. RNA-seq: What is it good for? Finding Similarly Expressed Genes. Data... And Lots of It!
RNA-seq: What is it good for? Clustering High-throughput RNA sequencing experiments (RNA-seq) offer the ability to measure simultaneously the expression level of thousands of genes in a single experiment!
Unsupervised Learning
Harvard-MIT Division of Health Sciences and Technology HST.951J: Medical Decision Support, Fall 2005 Instructors: Professor Lucila Ohno-Machado and Professor Staal Vinterbo 6.873/HST.951 Medical Decision
INF4820 Algorithms for AI and NLP. Evaluating Classifiers Clustering
INF4820 Algorithms for AI and NLP Evaluating Classifiers Clustering Erik Velldal & Stephan Oepen Language Technology Group (LTG) September 23, 2015 Agenda Last week Supervised vs unsupervised learning.
Midterm Examination CS540-2: Introduction to Artificial Intelligence
Midterm Examination CS540-2: Introduction to Artificial Intelligence March 15, 2018 LAST NAME: FIRST NAME: Problem Score Max Score 1 12 2 13 3 9 4 11 5 8 6 13 7 9 8 16 9 9 Total 100 Question 1. [12] Search
CS7267 MACHINE LEARNING
S7267 MAHINE LEARNING HIERARHIAL LUSTERING Ref: hengkai Li, Department of omputer Science and Engineering, University of Texas at Arlington (Slides courtesy of Vipin Kumar) Mingon Kang, Ph.D. omputer Science,
Task Description: Finding Similar Documents. Document Retrieval. Case Study 2: Document Retrieval
Case Study 2: Document Retrieval Task Description: Finding Similar Documents Machine Learning for Big Data CSE547/STAT548, University of Washington Sham Kakade April 11, 2017 Sham Kakade 2017 1 Document
3. Cluster analysis Overview
Université Laval Multivariate analysis - February 2006 1 3.1. Overview 3. Cluster analysis Clustering requires the recognition of discontinuous subsets in an environment that is sometimes discrete (as
Case-Based Reasoning. CS 188: Artificial Intelligence Fall Nearest-Neighbor Classification. Parametric / Non-parametric.
CS 188: Artificial Intelligence Fall 2008 Lecture 25: Kernels and Clustering 12/2/2008 Dan Klein UC Berkeley Case-Based Reasoning Similarity for classification Case-based reasoning Predict an instance
CS 188: Artificial Intelligence Fall 2008
CS 188: Artificial Intelligence Fall 2008 Lecture 25: Kernels and Clustering 12/2/2008 Dan Klein UC Berkeley 1 1 Case-Based Reasoning Similarity for classification Case-based reasoning Predict an instance
BBS654 Data Mining. Pinar Duygulu. Slides are adapted from Nazli Ikizler
BBS654 Data Mining Pinar Duygulu Slides are adapted from Nazli Ikizler 1 Classification Classification systems: Supervised learning Make a rational prediction given evidence There are several methods for
Cluster Analysis. Prof. Thomas B. Fomby Department of Economics Southern Methodist University Dallas, TX April 2008 April 2010
Cluster Analysis Prof. Thomas B. Fomby Department of Economics Southern Methodist University Dallas, TX 7575 April 008 April 010 Cluster Analysis, sometimes called data segmentation or customer segmentation,
Unsupervised Learning
Unsupervised Learning A review of clustering and other exploratory data analysis methods HST.951J: Medical Decision Support Harvard-MIT Division of Health Sciences and Technology HST.951J: Medical Decision
Clustering. CE-717: Machine Learning Sharif University of Technology Spring Soleymani
Clustering CE-717: Machine Learning Sharif University of Technology Spring 2016 Soleymani Outline Clustering Definition Clustering main approaches Partitional (flat) Hierarchical Clustering validation
ECS 234: Data Analysis: Clustering ECS 234
: Data Analysis: Clustering What is Clustering? Given n objects, assign them to groups (clusters) based on their similarity Unsupervised Machine Learning Class Discovery Difficult, and maybe ill-posed
Clustering. Content. Typical Applications. Clustering: Unsupervised data mining technique
Content Clustering Examples Cluster analysis Partitional: K-Means clustering method Hierarchical clustering methods Data preparation in clustering Interpreting clusters Cluster validation Clustering: Unsupervised
11/2/2017 MIST.6060 Business Intelligence and Data Mining 1. Clustering. Two widely used distance metrics to measure the distance between two records
11/2/2017 MIST.6060 Business Intelligence and Data Mining 1 An Example Clustering X 2 X 1 Objective of Clustering The objective of clustering is to group the data into clusters such that the records within
CISC 4631 Data Mining
CISC 4631 Data Mining Lecture 03: Nearest Neighbor Learning Theses slides are based on the slides by Tan, Steinbach and Kumar (textbook authors) Prof. R. Mooney (UT Austin) Prof E. Keogh (UCR), Prof. F.
An Efficient Optimal Leaf Ordering for Hierarchical Clustering in Microarray Gene Expression Data Analysis
An Efficient Optimal Leaf Ordering for Hierarchical Clustering in Microarray Gene Expression Data Analysis Jianting Zhang Le Gruenwald School of Computer Science The University of Oklahoma Norman, Oklahoma,
GS Analysis of Microarray Data
GS01 0163 Analysis of Microarray Data Keith Baggerly and Bradley Broom Department of Bioinformatics and Computational Biology UT MD Anderson Cancer Center kabagg@mdanderson.org bmbroom@mdanderson.org 19
COMP33111: Tutorial and lab exercise 7
COMP33111: Tutorial and lab exercise 7 Guide answers for Part 1: Understanding clustering 1. Explain the main differences between classification and clustering. main differences should include being unsupervised
Biological Networks Analysis
iological Networks nalysis Introduction and ijkstra s algorithm Genome 559: Introduction to Statistical and omputational Genomics Elhanan orenstein The clustering problem: partition genes into distinct