Hierarchical clustering for gene expression data analysis

Size: px
Start display at page:

Download "Hierarchical clustering for gene expression data analysis"

Transcription

1 Herarchcal clusterng for gene expresson data analyss Gorgo Valentn e-mal:

2 Clusterng of Mcroarray Data. Clusterng of gene expresson profles (rows) => dscovery of co-regulated and functonally related genes(or unrelated genes: dfferent clusters) 2. Clusterng of samples (columns) => dentfcaton of sub-types of related samples 3. Two-way clusterng => combned sample clusterng wth gene clusterng to dentfy whch genes are the most mportant forsample clusterng

3 Herarchcal Clusterng Herarchcal Clusterng Dendrogram

4 Dendrograms - The root represents the whole data set - A leaf represents a sngle obect n the data set - An nternal node represent the unon of all obects n ts subtree - The heght of an nternal node represents the dstance between ts two chld nodes

5 Herarchcal Clusterng Two man types of herarchcal clusterng. Agglomeratve: Start wth the ponts as ndvdual clusters At each step, merge the closest par of clusters. Untl only one cluster (or k clusters) left Ths requres defnng the noton of cluster proxmty. Dvsve: Start wth one, all-nclusve cluster At each step, splt a cluster Untl each cluster contans a pont (or there are k clusters) Need to decde whch cluster to splt at each step.

6 Basc Agglomeratve Herarchcal Clusterng Algorthm. Intally, each obect forms ts own cluster 2. Compute all parwse dstances between the ntal clusters (obects) repeat 3. Merge the closest par (A, B) n the set of the current clusters nto a new cluster C = A B 4. Remove A and B from the set of current clusters; nsert C nto the set of current clusters 5. Determne the dstance between the new cluster C and all other clusters n the set of current clusters untl only a sngle cluster remans

7 Agglomeratve Herarchcal Clusterng: Startng Stuaton For agglomeratve herarchcal clusterng we start wth clusters of ndvdual ponts and a proxmty matrx. p p2 p3 p4 p5.. p p2 p3 p4 p5.... Proxmty Matrx

8 Agglomeratve Herarchcal Clusterng: Intermedate Stuaton After some mergng steps, we have some clusters. C C2 C3 C4 C5 C3 C4 C C2 C3 C C4 C5 C2 C5 Proxmty Matrx

9 Agglomeratve Herarchcal Clusterng: Intermedate Stuaton We want to merge the two closest clusters (C2 and C5) and update the proxmty matrx. C C2 C3 C4 C5 C3 C4 C C2 C3 C C4 C5 C2 C5 Proxmty Matrx

10 Agglomeratve Herarchcal Clusterng: after Mergng The queston s How do we update the proxmty matrx? C3 C4 C C2 U C5 C3 C4 C C C2 U C5 C3?????? C2 U C5 C4? Dstance Matrx Key operaton s the computaton of the dstance of two clusters. Dfferent approaches to defnng the dstance between clusters dstngushes the dfferent algorthms

11 Inter-cluster dstances Four wdely used ways of defnng the nter-cluster dstance,.e., the dstance between two separate clusters C and C, are o sngle lnkage method (nearest neghbor): d( C, C ) = mn, { d( x, y) } x C o complete lnkage method (furthest neghbor): d( C, C ) = max x C, { d( x, y) } y C o average lnkage method (unweghted par-group average): d( C, C ) = avg, { d( x, y) } o centrod lnkage method (dstance between cluster centrods c and c ): x C y C y C d ( C, C ) = d( c, c )

12 Sngle lnkage (mnmum dstance) method Dstance (dssmlarty) of two clusters s based on the two most smlar (closest) ponts n the dfferent clusters C and C : Determned by one par of ponts,.e., by one lnk n the proxmty graph. Can handle non-ellptcal shapes. Senstve to nose and outlers. { d( x, )} d( C, C ) = mn, y x C y C Smlarty matrx I I2 I3 I4 I5 I I I I I

13 Sngle lnkage { (, )} d( C, C ) = mn d x y, x C y C

14 Herarchcal Clusterng: mnmum dstance Nested Clusters Dendrogram

15 Strength of mnmum dstance Orgnal Ponts Two Clusters

16 Lmtaton of mnmum dstance Orgnal Ponts Two Clusters

17 Complete Lnkage (maxmum dstance) method Dstance of two clusters s based on the two least smlar (most dstant) ponts n the dfferent clusters C and C : Determned by all pars of ponts n the two clusters. Tends to break large clusters. Less susceptble to nose and outlers. { d( x, )} d( C, C ) = max, y x C y C Smlarty matrx I I2 I3 I4 I5 I I I I I

18 Complete lnkage { d( x, )} d( C, C ) = max, y x C y C

19 Cluster Smlarty: maxmum dstance or Complete Lnkage Smlarty of two clusters s based on the two most dstant ponts n the dfferent clusters. Tends to break large clusters. Less susceptble to nose and outlers. Based towards globular clusters.

20 Herarchcal Clusterng: maxmum dstance Nested Clusters Dendrogram

21 Strength of maxmum dstance Orgnal Ponts Two Clusters

22 Lmtatons of maxmum dstance Orgnal Ponts Two Clusters

23 Average lnkage (average dstance) method Dstance of two clusters s the average of parwse dstances between ponts n the two clusters C and C : Compromse between Sngle and Complete Lnk. Need to use average connectvty for scalablty snce total connectvty favors large clusters. Less susceptble to nose and outlers. Based towards globular clusters. Smlarty matrx d ( C =, C ) d( x, y) C C x y C C I I2 I3 I4 I5 I I I I I

24 Average lnkage d ( C =, C ) d( x, y) C C x y C C

25 Herarchcal Clusterng: Average dstance Nested Clusters Dendrogram

26 Centrod lnkage (centrod dstance) method Dstance of two clusters s dstance of the two centrods c and c of the two clusters C and C : d ( C, C ) = d( c, c ) c = C x C x c = C x C x Compromse between Sngle and Complete Lnk. Less computatonally ntensve wth respect to average lnkage.

27 Centrod lnkage d ( C, C ) = d( c, c ) c = C x C x c = C x C x

28 Cluster Smlarty: Ward s Method Smlarty of two clusters s based on the ncrease n squared error when two clusters are merged. Smlar to group average f dstance between ponts s dstance squared. Less susceptble to nose and outlers. Based towards globular clusters. Herarchcal analogue of K-means But Ward s method does not correspond to a local mnmum Can be used to ntalze K-means

29 Herarchcal Clusterng: Ward s method Nested Clusters Dendrogram

30 Herarchcal Clusterng: comparson Average Ward s Method MIN MAX

31 Comparson of mnmum, maxmum, average and centrod dstance Mnmum dstance When d mn s used to measure dstance between clusters, the algorthm s called the nearestneghbor or sngle- lnkage clusterng algorthm If the algorthm s allowed to run untl only one cluster remans, the result s a mnmum spannng tree (MST) Ths algorthm favors elongated classes Maxmum dstance When d max s used to measure dstance between clusters, the algorthm s called the farthestneghbor or complete- lnkage clusterng algorthm From a graph- theoretc pont of vew, each cluster consttutes a complete sub- graph Ths algorthm favors compact classes Average and centrod dstance The mnmum and maxmum dstance are extremely senstve to outlers snce ther measurement of between- cluster dstance nvolves mnma or maxma The average and centrod dstance approaches are more robust to outlers Of the two, the centrod dstance s computatonally more attractve Notce that the average dstance approach nvolves the computaton of C C dstances for each par of clusters

32 Herarchcal Clusterng: Tme and Space requrements O(N 2 ) space snce t uses the proxmty matrx. N s the number of ponts. O(N 3 ) tme n many cases. There are N steps and at each step the sze, N 2, proxmty matrx must be updated and searched. By beng careful, the complexty can be reduced to O(N 2 log(n) ) tme for some approaches.

33 Herarchcal Clusterng: problems and lmtatons Once a decson s made to combne two clusters, t cannot be undone. No obectve functon s drectly mnmzed. Dfferent schemes have problems wth one or more of the followng: Senstvty to nose and outlers. Dffculty handlng dfferent szed clusters and convex shapes. Breakng large clusters.

34 Advantages and dsadvantages of Herarchcal clusterng Advantages Does not requre the number of clusters to be known n advance No nput parameters (besdes the choce of the (ds)smlarty) Computes a complete herarchy of clusters Good result vsualzatons ntegrated nto the methods Dsadvantages May not scale well: runtme for the standard methods: O(n 2 log n) No explct clusters: a flat partton can be derved afterwards (e.g. va a cut through the dendrogram or termnaton condton n the constructon) No automatc dscoverng of optmal clusters

35 Herarchcal clusterng of tssues and genes: Alzadeh et al. 2000, Dstnct types of dffuse large B-cell lymphoma dentfed by gene expresson proflng, Nature 403:3.

Machine Learning: Algorithms and Applications

Machine Learning: Algorithms and Applications 14/05/1 Machne Learnng: Algorthms and Applcatons Florano Zn Free Unversty of Bozen-Bolzano Faculty of Computer Scence Academc Year 011-01 Lecture 10: 14 May 01 Unsupervsed Learnng cont Sldes courtesy of

More information

Outline. Type of Machine Learning. Examples of Application. Unsupervised Learning

Outline. Type of Machine Learning. Examples of Application. Unsupervised Learning Outlne Artfcal Intellgence and ts applcatons Lecture 8 Unsupervsed Learnng Professor Danel Yeung danyeung@eee.org Dr. Patrck Chan patrckchan@eee.org South Chna Unversty of Technology, Chna Introducton

More information

Subspace clustering. Clustering. Fundamental to all clustering techniques is the choice of distance measure between data points;

Subspace clustering. Clustering. Fundamental to all clustering techniques is the choice of distance measure between data points; Subspace clusterng Clusterng Fundamental to all clusterng technques s the choce of dstance measure between data ponts; D q ( ) ( ) 2 x x = x x, j k = 1 k jk Squared Eucldean dstance Assumpton: All features

More information

Hierarchical agglomerative. Cluster Analysis. Christine Siedle Clustering 1

Hierarchical agglomerative. Cluster Analysis. Christine Siedle Clustering 1 Herarchcal agglomeratve Cluster Analyss Chrstne Sedle 19-3-2004 Clusterng 1 Classfcaton Basc (unconscous & conscous) human strategy to reduce complexty Always based Cluster analyss to fnd or confrm types

More information

Unsupervised Learning

Unsupervised Learning Pattern Recognton Lecture 8 Outlne Introducton Unsupervsed Learnng Parametrc VS Non-Parametrc Approach Mxture of Denstes Maxmum-Lkelhood Estmates Clusterng Prof. Danel Yeung School of Computer Scence and

More information

Machine Learning. Topic 6: Clustering

Machine Learning. Topic 6: Clustering Machne Learnng Topc 6: lusterng lusterng Groupng data nto (hopefully useful) sets. Thngs on the left Thngs on the rght Applcatons of lusterng Hypothess Generaton lusters mght suggest natural groups. Hypothess

More information

Unsupervised Learning and Clustering

Unsupervised Learning and Clustering Unsupervsed Learnng and Clusterng Supervsed vs. Unsupervsed Learnng Up to now we consdered supervsed learnng scenaro, where we are gven 1. samples 1,, n 2. class labels for all samples 1,, n Ths s also

More information

CS434a/541a: Pattern Recognition Prof. Olga Veksler. Lecture 15

CS434a/541a: Pattern Recognition Prof. Olga Veksler. Lecture 15 CS434a/541a: Pattern Recognton Prof. Olga Veksler Lecture 15 Today New Topc: Unsupervsed Learnng Supervsed vs. unsupervsed learnng Unsupervsed learnng Net Tme: parametrc unsupervsed learnng Today: nonparametrc

More information

K-means and Hierarchical Clustering

K-means and Hierarchical Clustering Note to other teachers and users of these sldes. Andrew would be delghted f you found ths source materal useful n gvng your own lectures. Feel free to use these sldes verbatm, or to modfy them to ft your

More information

Outline. Self-Organizing Maps (SOM) US Hebbian Learning, Cntd. The learning rule is Hebbian like:

Outline. Self-Organizing Maps (SOM) US Hebbian Learning, Cntd. The learning rule is Hebbian like: Self-Organzng Maps (SOM) Turgay İBRİKÇİ, PhD. Outlne Introducton Structures of SOM SOM Archtecture Neghborhoods SOM Algorthm Examples Summary 1 2 Unsupervsed Hebban Learnng US Hebban Learnng, Cntd 3 A

More information

Unsupervised Learning and Clustering

Unsupervised Learning and Clustering Unsupervsed Learnng and Clusterng Why consder unlabeled samples?. Collectng and labelng large set of samples s costly Gettng recorded speech s free, labelng s tme consumng 2. Classfer could be desgned

More information

Cluster Analysis of Electrical Behavior

Cluster Analysis of Electrical Behavior Journal of Computer and Communcatons, 205, 3, 88-93 Publshed Onlne May 205 n ScRes. http://www.scrp.org/ournal/cc http://dx.do.org/0.4236/cc.205.350 Cluster Analyss of Electrcal Behavor Ln Lu Ln Lu, School

More information

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 or splits 0 0 0 00

More information

CSCI 104 Sorting Algorithms. Mark Redekopp David Kempe

CSCI 104 Sorting Algorithms. Mark Redekopp David Kempe CSCI 104 Sortng Algorthms Mark Redekopp Davd Kempe Algorthm Effcency SORTING 2 Sortng If we have an unordered lst, sequental search becomes our only choce If we wll perform a lot of searches t may be benefcal

More information

6.854 Advanced Algorithms Petar Maymounkov Problem Set 11 (November 23, 2005) With: Benjamin Rossman, Oren Weimann, and Pouya Kheradpour

6.854 Advanced Algorithms Petar Maymounkov Problem Set 11 (November 23, 2005) With: Benjamin Rossman, Oren Weimann, and Pouya Kheradpour 6.854 Advanced Algorthms Petar Maymounkov Problem Set 11 (November 23, 2005) Wth: Benjamn Rossman, Oren Wemann, and Pouya Kheradpour Problem 1. We reduce vertex cover to MAX-SAT wth weghts, such that the

More information

Graph-based Clustering

Graph-based Clustering Graphbased Clusterng Transform the data nto a graph representaton ertces are the data ponts to be clustered Edges are eghted based on smlarty beteen data ponts Graph parttonng Þ Each connected component

More information

Clustering Part 3. Hierarchical Clustering

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

More information

Clustering. A. Bellaachia Page: 1

Clustering. A. Bellaachia Page: 1 Clusterng. Obectves.. Clusterng.... Defntons... General Applcatons.3. What s a good clusterng?. 3.4. Requrements 3 3. Data Structures 4 4. Smlarty Measures. 4 4.. Standardze data.. 5 4.. Bnary varables..

More information

The Greedy Method. Outline and Reading. Change Money Problem. Greedy Algorithms. Applications of the Greedy Strategy. The Greedy Method Technique

The Greedy Method. Outline and Reading. Change Money Problem. Greedy Algorithms. Applications of the Greedy Strategy. The Greedy Method Technique //00 :0 AM Outlne and Readng The Greedy Method The Greedy Method Technque (secton.) Fractonal Knapsack Problem (secton..) Task Schedulng (secton..) Mnmum Spannng Trees (secton.) Change Money Problem Greedy

More information

Survey of Cluster Analysis and its Various Aspects

Survey of Cluster Analysis and its Various Aspects Harmnder Kaur et al, Internatonal Journal of Computer Scence and Moble Computng, Vol.4 Issue.0, October- 05, pg. 353-363 Avalable Onlne at www.csmc.com Internatonal Journal of Computer Scence and Moble

More information

Design and Analysis of Algorithms

Design and Analysis of Algorithms Desgn and Analyss of Algorthms Heaps and Heapsort Reference: CLRS Chapter 6 Topcs: Heaps Heapsort Prorty queue Huo Hongwe Recap and overvew The story so far... Inserton sort runnng tme of Θ(n 2 ); sorts

More information

Lecture Notes for Chapter 7. Introduction to Data Mining, 2 nd Edition. by Tan, Steinbach, Karpatne, Kumar

Lecture Notes for Chapter 7. Introduction to Data Mining, 2 nd Edition. by Tan, Steinbach, Karpatne, Kumar Data Mining Cluster Analysis: Basic Concepts and Algorithms Lecture Notes for Chapter 7 Introduction to Data Mining, 2 nd Edition by Tan, Steinbach, Karpatne, Kumar Hierarchical Clustering Produces a set

More information

Data Mining Concepts & Techniques

Data Mining Concepts & Techniques Data Mining Concepts & Techniques Lecture No 08 Cluster Analysis Naeem Ahmed Email: naeemmahoto@gmailcom Department of Software Engineering Mehran Univeristy of Engineering and Technology Jamshoro Outline

More information

Clustering validation

Clustering validation MOHAMMAD REZAEI Clusterng valdaton Publcatons of the Unversty of Eastern Fnland Dssertatons n Forestry and Natural Scences No 5 Academc Dssertaton To be presented by permsson of the Faculty of Scence and

More information

Module Management Tool in Software Development Organizations

Module Management Tool in Software Development Organizations Journal of Computer Scence (5): 8-, 7 ISSN 59-66 7 Scence Publcatons Management Tool n Software Development Organzatons Ahmad A. Al-Rababah and Mohammad A. Al-Rababah Faculty of IT, Al-Ahlyyah Amman Unversty,

More information

Lobachevsky State University of Nizhni Novgorod. Polyhedron. Quick Start Guide

Lobachevsky State University of Nizhni Novgorod. Polyhedron. Quick Start Guide Lobachevsky State Unversty of Nzhn Novgorod Polyhedron Quck Start Gude Nzhn Novgorod 2016 Contents Specfcaton of Polyhedron software... 3 Theoretcal background... 4 1. Interface of Polyhedron... 6 1.1.

More information

Course Introduction. Algorithm 8/31/2017. COSC 320 Advanced Data Structures and Algorithms. COSC 320 Advanced Data Structures and Algorithms

Course Introduction. Algorithm 8/31/2017. COSC 320 Advanced Data Structures and Algorithms. COSC 320 Advanced Data Structures and Algorithms Course Introducton Course Topcs Exams, abs, Proects A quc loo at a few algorthms 1 Advanced Data Structures and Algorthms Descrpton: We are gong to dscuss algorthm complexty analyss, algorthm desgn technques

More information

1 Dynamic Connectivity

1 Dynamic Connectivity 15-850: Advanced Algorthms CMU, Sprng 2017 Lecture #3: Dynamc Graph Connectvty algorthms 01/30/17 Lecturer: Anupam Gupta Scrbe: Hu Han Chn, Jacob Imola Dynamc graph algorthms s the study of standard graph

More information

APPLIED MACHINE LEARNING

APPLIED MACHINE LEARNING Methods for Clusterng K-means, Soft K-means DBSCAN 1 Objectves Learn basc technques for data clusterng K-means and soft K-means, GMM (next lecture) DBSCAN Understand the ssues and major challenges n clusterng

More information

This excerpt from. Foundations of Statistical Natural Language Processing. Christopher D. Manning and Hinrich Schütze The MIT Press.

This excerpt from. Foundations of Statistical Natural Language Processing. Christopher D. Manning and Hinrich Schütze The MIT Press. Ths excerpt from Foundatons of Statstcal Natural Language Processng. Chrstopher D. Mannng and Hnrch Schütze. 1999 The MIT Press. s provded n screen-vewable form for personal use only by members of MIT

More information

Insertion Sort. Divide and Conquer Sorting. Divide and Conquer. Mergesort. Mergesort Example. Auxiliary Array

Insertion Sort. Divide and Conquer Sorting. Divide and Conquer. Mergesort. Mergesort Example. Auxiliary Array Inserton Sort Dvde and Conquer Sortng CSE 6 Data Structures Lecture 18 What f frst k elements of array are already sorted? 4, 7, 1, 5, 1, 16 We can shft the tal of the sorted elements lst down and then

More information

Clustering is a discovery process in data mining.

Clustering is a discovery process in data mining. Cover Feature Chameleon: Herarchcal Clusterng Usng Dynamc Modelng Many advanced algorthms have dffculty dealng wth hghly varable clusters that do not follow a preconceved model. By basng ts selectons on

More information

cos(a, b) = at b a b. To get a distance measure, subtract the cosine similarity from one. dist(a, b) =1 cos(a, b)

cos(a, b) = at b a b. To get a distance measure, subtract the cosine similarity from one. dist(a, b) =1 cos(a, b) 8 Clusterng 8.1 Some Clusterng Examples Clusterng comes up n many contexts. For example, one mght want to cluster journal artcles nto clusters of artcles on related topcs. In dong ths, one frst represents

More information

Clustering Lecture 3: Hierarchical Methods

Clustering Lecture 3: Hierarchical Methods Clustering Lecture 3: Hierarchical Methods Jing Gao SUNY Buffalo 1 Outline Basics Motivation, definition, evaluation Methods Partitional Hierarchical Density-based Mixture model Spectral methods Advanced

More information

SCALABLE AND VISUALIZATION-ORIENTED CLUSTERING FOR EXPLORATORY SPATIAL ANALYSIS

SCALABLE AND VISUALIZATION-ORIENTED CLUSTERING FOR EXPLORATORY SPATIAL ANALYSIS SCALABLE AND VISUALIZATION-ORIENTED CLUSTERING FOR EXPLORATORY SPATIAL ANALYSIS J.H.Guan, F.B.Zhu, F.L.Ban a School of Computer, Spatal Informaton & Dgtal Engneerng Center, Wuhan Unversty, Wuhan, 430079,

More information

Support Vector Machines

Support Vector Machines Support Vector Machnes Decson surface s a hyperplane (lne n 2D) n feature space (smlar to the Perceptron) Arguably, the most mportant recent dscovery n machne learnng In a nutshell: map the data to a predetermned

More information

Sorting. Sorting. Why Sort? Consistent Ordering

Sorting. Sorting. Why Sort? Consistent Ordering Sortng CSE 6 Data Structures Unt 15 Readng: Sectons.1-. Bubble and Insert sort,.5 Heap sort, Secton..6 Radx sort, Secton.6 Mergesort, Secton. Qucksort, Secton.8 Lower bound Sortng Input an array A of data

More information

CSE 326: Data Structures Quicksort Comparison Sorting Bound

CSE 326: Data Structures Quicksort Comparison Sorting Bound CSE 326: Data Structures Qucksort Comparson Sortng Bound Steve Setz Wnter 2009 Qucksort Qucksort uses a dvde and conquer strategy, but does not requre the O(N) extra space that MergeSort does. Here s the

More information

Kent State University CS 4/ Design and Analysis of Algorithms. Dept. of Math & Computer Science LECT-16. Dynamic Programming

Kent State University CS 4/ Design and Analysis of Algorithms. Dept. of Math & Computer Science LECT-16. Dynamic Programming CS 4/560 Desgn and Analyss of Algorthms Kent State Unversty Dept. of Math & Computer Scence LECT-6 Dynamc Programmng 2 Dynamc Programmng Dynamc Programmng, lke the dvde-and-conquer method, solves problems

More information

Sorting Review. Sorting. Comparison Sorting. CSE 680 Prof. Roger Crawfis. Assumptions

Sorting Review. Sorting. Comparison Sorting. CSE 680 Prof. Roger Crawfis. Assumptions Sortng Revew Introducton to Algorthms Qucksort CSE 680 Prof. Roger Crawfs Inserton Sort T(n) = Θ(n 2 ) In-place Merge Sort T(n) = Θ(n lg(n)) Not n-place Selecton Sort (from homework) T(n) = Θ(n 2 ) In-place

More information

SLAM Summer School 2006 Practical 2: SLAM using Monocular Vision

SLAM Summer School 2006 Practical 2: SLAM using Monocular Vision SLAM Summer School 2006 Practcal 2: SLAM usng Monocular Vson Javer Cvera, Unversty of Zaragoza Andrew J. Davson, Imperal College London J.M.M Montel, Unversty of Zaragoza. josemar@unzar.es, jcvera@unzar.es,

More information

Clustering algorithms and validity measures

Clustering algorithms and validity measures Clusterng algorthms and valdty measures M. Hald, Y. Batstas, M. Vazrganns Department of Informatcs Athens Unversty of Economcs & Busness Emal: {mhal, yanns, mvazrg}@aueb.gr Abstract Clusterng ams at dscoverng

More information

Keyword-based Document Clustering

Keyword-based Document Clustering Keyword-based ocument lusterng Seung-Shk Kang School of omputer Scence Kookmn Unversty & AIrc hungnung-dong Songbuk-gu Seoul 36-72 Korea sskang@kookmn.ac.kr Abstract ocument clusterng s an aggregaton of

More information

Fuzzy C-Means Initialized by Fixed Threshold Clustering for Improving Image Retrieval

Fuzzy C-Means Initialized by Fixed Threshold Clustering for Improving Image Retrieval Fuzzy -Means Intalzed by Fxed Threshold lusterng for Improvng Image Retreval NAWARA HANSIRI, SIRIPORN SUPRATID,HOM KIMPAN 3 Faculty of Informaton Technology Rangst Unversty Muang-Ake, Paholyotn Road, Patumtan,

More information

CS 534: Computer Vision Model Fitting

CS 534: Computer Vision Model Fitting CS 534: Computer Vson Model Fttng Sprng 004 Ahmed Elgammal Dept of Computer Scence CS 534 Model Fttng - 1 Outlnes Model fttng s mportant Least-squares fttng Maxmum lkelhood estmaton MAP estmaton Robust

More information

TOWARDS FUZZY-HARD CLUSTERING MAPPING PROCESSES. MINYAR SASSI National Engineering School of Tunis BP. 37, Le Belvédère, 1002 Tunis, Tunisia

TOWARDS FUZZY-HARD CLUSTERING MAPPING PROCESSES. MINYAR SASSI National Engineering School of Tunis BP. 37, Le Belvédère, 1002 Tunis, Tunisia TOWARDS FUZZY-HARD CLUSTERING MAPPING PROCESSES MINYAR SASSI Natonal Engneerng School of Tuns BP. 37, Le Belvédère, 00 Tuns, Tunsa Although the valdaton step can appear crucal n the case of clusterng adoptng

More information

Sequential search. Building Java Programs Chapter 13. Sequential search. Sequential search

Sequential search. Building Java Programs Chapter 13. Sequential search. Sequential search Sequental search Buldng Java Programs Chapter 13 Searchng and Sortng sequental search: Locates a target value n an array/lst by examnng each element from start to fnsh. How many elements wll t need to

More information

For instance, ; the five basic number-sets are increasingly more n A B & B A A = B (1)

For instance, ; the five basic number-sets are increasingly more n A B & B A A = B (1) Secton 1.2 Subsets and the Boolean operatons on sets If every element of the set A s an element of the set B, we say that A s a subset of B, or that A s contaned n B, or that B contans A, and we wrte A

More information

On the Efficiency of Swap-Based Clustering

On the Efficiency of Swap-Based Clustering On the Effcency of Swap-Based Clusterng Pas Fränt and Oll Vrmaok Department of Computer Scence, Unversty of Joensuu, Fnland {frant, ovrma}@cs.oensuu.f Abstract. Random swap-based clusterng s very smple

More information

A new segmentation algorithm for medical volume image based on K-means clustering

A new segmentation algorithm for medical volume image based on K-means clustering Avalable onlne www.jocpr.com Journal of Chemcal and harmaceutcal Research, 2013, 5(12):113-117 Research Artcle ISSN : 0975-7384 CODEN(USA) : JCRC5 A new segmentaton algorthm for medcal volume mage based

More information

CSE 326: Data Structures Quicksort Comparison Sorting Bound

CSE 326: Data Structures Quicksort Comparison Sorting Bound CSE 326: Data Structures Qucksort Comparson Sortng Bound Bran Curless Sprng 2008 Announcements (5/14/08) Homework due at begnnng of class on Frday. Secton tomorrow: Graded homeworks returned More dscusson

More information

Collision Detection. Overview. Efficient Collision Detection. Collision Detection with Rays: Example. C = nm + (n choose 2)

Collision Detection. Overview. Efficient Collision Detection. Collision Detection with Rays: Example. C = nm + (n choose 2) Overvew Collson detecton wth Rays Collson detecton usng BSP trees Herarchcal Collson Detecton OBB tree, k-dop tree algorthms Multple object CD system Collson Detecton Fundamental to graphcs, VR applcatons

More information

Bidirectional Hierarchical Clustering for Web Mining

Bidirectional Hierarchical Clustering for Web Mining Bdrectonal Herarchcal Clusterng for Web Mnng ZHONGMEI YAO & BEN CHOI Computer Scence, College of Engneerng and Scence Lousana Tech Unversty, Ruston, LA 71272, USA zya001@latech.edu, pro@bencho.org Abstract

More information

CHAPTER 3 SEQUENTIAL MINIMAL OPTIMIZATION TRAINED SUPPORT VECTOR CLASSIFIER FOR CANCER PREDICTION

CHAPTER 3 SEQUENTIAL MINIMAL OPTIMIZATION TRAINED SUPPORT VECTOR CLASSIFIER FOR CANCER PREDICTION 48 CHAPTER 3 SEQUENTIAL MINIMAL OPTIMIZATION TRAINED SUPPORT VECTOR CLASSIFIER FOR CANCER PREDICTION 3.1 INTRODUCTION The raw mcroarray data s bascally an mage wth dfferent colors ndcatng hybrdzaton (Xue

More information

SHAPE RECOGNITION METHOD BASED ON THE k-nearest NEIGHBOR RULE

SHAPE RECOGNITION METHOD BASED ON THE k-nearest NEIGHBOR RULE SHAPE RECOGNITION METHOD BASED ON THE k-nearest NEIGHBOR RULE Dorna Purcaru Faculty of Automaton, Computers and Electroncs Unersty of Craoa 13 Al. I. Cuza Street, Craoa RO-1100 ROMANIA E-mal: dpurcaru@electroncs.uc.ro

More information

Analyzing Popular Clustering Algorithms from Different Viewpoints

Analyzing Popular Clustering Algorithms from Different Viewpoints 1000-9825/2002/13(08)1382-13 2002 Journal of Software Vol.13, No.8 Analyzng Popular Clusterng Algorthms from Dfferent Vewponts QIAN We-nng, ZHOU Ao-yng (Department of Computer Scence, Fudan Unversty, Shangha

More information

A Hierarchical Clustering and Validity Index for Mixed Data

A Hierarchical Clustering and Validity Index for Mixed Data Graduate Theses and Dssertatons Graduate College 2012 A Herarchcal Clusterng and Valdty Index for Mxed Data Ru Yang Iowa State Unversty Follow ths and addtonal works at: http://lb.dr.astate.edu/etd Part

More information

Web Mining: Clustering Web Documents A Preliminary Review

Web Mining: Clustering Web Documents A Preliminary Review Web Mnng: Clusterng Web Documents A Prelmnary Revew Khaled M. Hammouda Department of Systems Desgn Engneerng Unversty of Waterloo Waterloo, Ontaro, Canada 2L 3G1 hammouda@pam.uwaterloo.ca February 26,

More information

Hierarchical clustering

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

More information

A Deflected Grid-based Algorithm for Clustering Analysis

A Deflected Grid-based Algorithm for Clustering Analysis A Deflected Grd-based Algorthm for Clusterng Analyss NANCY P. LIN, CHUNG-I CHANG, HAO-EN CHUEH, HUNG-JEN CHEN, WEI-HUA HAO Department of Computer Scence and Informaton Engneerng Tamkang Unversty 5 Yng-chuan

More information

Agenda & Reading. Simple If. Decision-Making Statements. COMPSCI 280 S1C Applications Programming. Programming Fundamentals

Agenda & Reading. Simple If. Decision-Making Statements. COMPSCI 280 S1C Applications Programming. Programming Fundamentals Agenda & Readng COMPSCI 8 SC Applcatons Programmng Programmng Fundamentals Control Flow Agenda: Decsonmakng statements: Smple If, Ifelse, nested felse, Select Case s Whle, DoWhle/Untl, For, For Each, Nested

More information

EECS 730 Introduction to Bioinformatics Sequence Alignment. Luke Huan Electrical Engineering and Computer Science

EECS 730 Introduction to Bioinformatics Sequence Alignment. Luke Huan Electrical Engineering and Computer Science EECS 730 Introducton to Bonformatcs Sequence Algnment Luke Huan Electrcal Engneerng and Computer Scence http://people.eecs.ku.edu/~huan/ HMM Π s a set of states Transton Probabltes a kl Pr( l 1 k Probablty

More information

Today s Outline. Sorting: The Big Picture. Why Sort? Selection Sort: Idea. Insertion Sort: Idea. Sorting Chapter 7 in Weiss.

Today s Outline. Sorting: The Big Picture. Why Sort? Selection Sort: Idea. Insertion Sort: Idea. Sorting Chapter 7 in Weiss. Today s Outlne Sortng Chapter 7 n Wess CSE 26 Data Structures Ruth Anderson Announcements Wrtten Homework #6 due Frday 2/26 at the begnnng of lecture Proect Code due Mon March 1 by 11pm Today s Topcs:

More information

A Two-Stage Algorithm for Data Clustering

A Two-Stage Algorithm for Data Clustering A Two-Stage Algorthm for Data Clusterng Abdolreza Hatamlou 1 and Salwan Abdullah 2 1 Islamc Azad Unversty, Khoy Branch, Iran 2 Data Mnng and Optmsaton Research Group, Center for Artfcal Intellgence Technology,

More information

the nber of vertces n the graph. spannng tree T beng part of a par of maxmally dstant trees s called extremal. Extremal trees are useful n the mxed an

the nber of vertces n the graph. spannng tree T beng part of a par of maxmally dstant trees s called extremal. Extremal trees are useful n the mxed an On Central Spannng Trees of a Graph S. Bezrukov Unverstat-GH Paderborn FB Mathematk/Informatk Furstenallee 11 D{33102 Paderborn F. Kaderal, W. Poguntke FernUnverstat Hagen LG Kommunkatonssysteme Bergscher

More information

Programming in Fortran 90 : 2017/2018

Programming in Fortran 90 : 2017/2018 Programmng n Fortran 90 : 2017/2018 Programmng n Fortran 90 : 2017/2018 Exercse 1 : Evaluaton of functon dependng on nput Wrte a program who evaluate the functon f (x,y) for any two user specfed values

More information

Steps for Computing the Dissimilarity, Entropy, Herfindahl-Hirschman and. Accessibility (Gravity with Competition) Indices

Steps for Computing the Dissimilarity, Entropy, Herfindahl-Hirschman and. Accessibility (Gravity with Competition) Indices Steps for Computng the Dssmlarty, Entropy, Herfndahl-Hrschman and Accessblty (Gravty wth Competton) Indces I. Dssmlarty Index Measurement: The followng formula can be used to measure the evenness between

More information

Hierarchical Clustering

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

More information

CE 221 Data Structures and Algorithms

CE 221 Data Structures and Algorithms CE 1 ata Structures and Algorthms Chapter 4: Trees BST Text: Read Wess, 4.3 Izmr Unversty of Economcs 1 The Search Tree AT Bnary Search Trees An mportant applcaton of bnary trees s n searchng. Let us assume

More information

Data Mining Approaches to User Modeling for Adaptive Hypermedia: Survey and Future Directions

Data Mining Approaches to User Modeling for Adaptive Hypermedia: Survey and Future Directions > REPLACE THIS LINE WITH YOUR PAPER IDENTIFICATION NUMBER (DOUBLE-CLICK HERE TO EDIT) < Data Mnng Approaches to User Modelng for Adaptve Hypermeda: Survey and Future Drectons Enrque Fras-Martnez, Sherry

More information

An Optimal iterative Minimal Spanning tree Clustering Algorithm for images

An Optimal iterative Minimal Spanning tree Clustering Algorithm for images Internatonal Journal of Scentfc & Engneerng Research Volume 3, Issue, May-2012 1 An Optmal teratve Mnmal Spannng tree Clusterng Algorthm for mages S. Senthl, A. Sathya, Dr.R.Davd Chandrakumar Abstract:-Lmted

More information

Compiler Design. Spring Register Allocation. Sample Exercises and Solutions. Prof. Pedro C. Diniz

Compiler Design. Spring Register Allocation. Sample Exercises and Solutions. Prof. Pedro C. Diniz Compler Desgn Sprng 2014 Regster Allocaton Sample Exercses and Solutons Prof. Pedro C. Dnz USC / Informaton Scences Insttute 4676 Admralty Way, Sute 1001 Marna del Rey, Calforna 90292 pedro@s.edu Regster

More information

Clustering on antimatroids and convex geometries

Clustering on antimatroids and convex geometries Clusterng on antmatrods and convex geometres YULIA KEMPNER 1, ILYA MUCNIK 2 1 Department of Computer cence olon Academc Insttute of Technology 52 Golomb tr., P.O. Box 305, olon 58102 IRAEL 2 Department

More information

An Efficient Genetic Algorithm with Fuzzy c-means Clustering for Traveling Salesman Problem

An Efficient Genetic Algorithm with Fuzzy c-means Clustering for Traveling Salesman Problem An Effcent Genetc Algorthm wth Fuzzy c-means Clusterng for Travelng Salesman Problem Jong-Won Yoon and Sung-Bae Cho Dept. of Computer Scence Yonse Unversty Seoul, Korea jwyoon@sclab.yonse.ac.r, sbcho@cs.yonse.ac.r

More information

On the Two-level Hybrid Clustering Algorithm

On the Two-level Hybrid Clustering Algorithm On the Two-level Clusterng Algorthm ng Yeow Cheu, Chee Keong Kwoh, Zongln Zhou Bonformatcs Research Centre, School of Comuter ngneerng, Nanyang Technologcal Unversty, Sngaore 639798 ezlzhou@ntu.edu.sg

More information

Learning the Kernel Parameters in Kernel Minimum Distance Classifier

Learning the Kernel Parameters in Kernel Minimum Distance Classifier Learnng the Kernel Parameters n Kernel Mnmum Dstance Classfer Daoqang Zhang 1,, Songcan Chen and Zh-Hua Zhou 1* 1 Natonal Laboratory for Novel Software Technology Nanjng Unversty, Nanjng 193, Chna Department

More information

The Research of Support Vector Machine in Agricultural Data Classification

The Research of Support Vector Machine in Agricultural Data Classification The Research of Support Vector Machne n Agrcultural Data Classfcaton Le Sh, Qguo Duan, Xnmng Ma, Me Weng College of Informaton and Management Scence, HeNan Agrcultural Unversty, Zhengzhou 45000 Chna Zhengzhou

More information

5 The Primal-Dual Method

5 The Primal-Dual Method 5 The Prmal-Dual Method Orgnally desgned as a method for solvng lnear programs, where t reduces weghted optmzaton problems to smpler combnatoral ones, the prmal-dual method (PDM) has receved much attenton

More information

Outline. Discriminative classifiers for image recognition. Where in the World? A nearest neighbor recognition example 4/14/2011. CS 376 Lecture 22 1

Outline. Discriminative classifiers for image recognition. Where in the World? A nearest neighbor recognition example 4/14/2011. CS 376 Lecture 22 1 4/14/011 Outlne Dscrmnatve classfers for mage recognton Wednesday, Aprl 13 Krsten Grauman UT-Austn Last tme: wndow-based generc obect detecton basc ppelne face detecton wth boostng as case study Today:

More information

12. Segmentation. Computer Engineering, i Sejong University. Dongil Han

12. Segmentation. Computer Engineering, i Sejong University. Dongil Han Computer Vson 1. Segmentaton Computer Engneerng, Sejong Unversty Dongl Han Image Segmentaton t Image segmentaton Subdvdes an mage nto ts consttuent regons or objects - After an mage has been segmented,

More information

Data Mining: Model Evaluation

Data Mining: Model Evaluation Data Mnng: Model Evaluaton Aprl 16, 2013 1 Issues: Evaluatng Classfcaton Methods Accurac classfer accurac: predctng class label predctor accurac: guessng value of predcted attrbutes Speed tme to construct

More information

A PATTERN RECOGNITION APPROACH TO IMAGE SEGMENTATION

A PATTERN RECOGNITION APPROACH TO IMAGE SEGMENTATION 1 THE PUBLISHING HOUSE PROCEEDINGS OF THE ROMANIAN ACADEMY, Seres A, OF THE ROMANIAN ACADEMY Volume 4, Number 2/2003, pp.000-000 A PATTERN RECOGNITION APPROACH TO IMAGE SEGMENTATION Tudor BARBU Insttute

More information

A mathematical programming approach to the analysis, design and scheduling of offshore oilfields

A mathematical programming approach to the analysis, design and scheduling of offshore oilfields 17 th European Symposum on Computer Aded Process Engneerng ESCAPE17 V. Plesu and P.S. Agach (Edtors) 2007 Elsever B.V. All rghts reserved. 1 A mathematcal programmng approach to the analyss, desgn and

More information

Retrieval and Clustering from a 3D Human Database based on Body and Head Shape

Retrieval and Clustering from a 3D Human Database based on Body and Head Shape SAE 06DHM 57 Retreval and Clusterng from a 3D Human Database based on Body and Head Shape Afzal Godl, Sandy Ressler Natonal Insttute of Standards and Technology ABSTRACT In ths paper, we descrbe a framework

More information

Parallelism for Nested Loops with Non-uniform and Flow Dependences

Parallelism for Nested Loops with Non-uniform and Flow Dependences Parallelsm for Nested Loops wth Non-unform and Flow Dependences Sam-Jn Jeong Dept. of Informaton & Communcaton Engneerng, Cheonan Unversty, 5, Anseo-dong, Cheonan, Chungnam, 330-80, Korea. seong@cheonan.ac.kr

More information

Image Representation & Visualization Basic Imaging Algorithms Shape Representation and Analysis. outline

Image Representation & Visualization Basic Imaging Algorithms Shape Representation and Analysis. outline mage Vsualzaton mage Vsualzaton mage Representaton & Vsualzaton Basc magng Algorthms Shape Representaton and Analyss outlne mage Representaton & Vsualzaton Basc magng Algorthms Shape Representaton and

More information

Assignment # 2. Farrukh Jabeen Algorithms 510 Assignment #2 Due Date: June 15, 2009.

Assignment # 2. Farrukh Jabeen Algorithms 510 Assignment #2 Due Date: June 15, 2009. Farrukh Jabeen Algorthms 51 Assgnment #2 Due Date: June 15, 29. Assgnment # 2 Chapter 3 Dscrete Fourer Transforms Implement the FFT for the DFT. Descrbed n sectons 3.1 and 3.2. Delverables: 1. Concse descrpton

More information

Routing in Degree-constrained FSO Mesh Networks

Routing in Degree-constrained FSO Mesh Networks Internatonal Journal of Hybrd Informaton Technology Vol., No., Aprl, 009 Routng n Degree-constraned FSO Mesh Networks Zpng Hu, Pramode Verma, and James Sluss Jr. School of Electrcal & Computer Engneerng

More information

A Clustering Algorithm for Chinese Adjectives and Nouns 1

A Clustering Algorithm for Chinese Adjectives and Nouns 1 Clusterng lgorthm for Chnese dectves and ouns Yang Wen, Chunfa Yuan, Changnng Huang 2 State Key aboratory of Intellgent Technology and System Deptartment of Computer Scence & Technology, Tsnghua Unversty,

More information

FINDING IMPORTANT NODES IN SOCIAL NETWORKS BASED ON MODIFIED PAGERANK

FINDING IMPORTANT NODES IN SOCIAL NETWORKS BASED ON MODIFIED PAGERANK FINDING IMPORTANT NODES IN SOCIAL NETWORKS BASED ON MODIFIED PAGERANK L-qng Qu, Yong-quan Lang 2, Jng-Chen 3, 2 College of Informaton Scence and Technology, Shandong Unversty of Scence and Technology,

More information

APPLICATION OF IMPROVED K-MEANS ALGORITHM IN THE DELIVERY LOCATION

APPLICATION OF IMPROVED K-MEANS ALGORITHM IN THE DELIVERY LOCATION An Open Access, Onlne Internatonal Journal Avalable at http://www.cbtech.org/pms.htm 2016 Vol. 6 (2) Aprl-June, pp. 11-17/Sh Research Artcle APPLICATION OF IMPROVED K-MEANS ALGORITHM IN THE DELIVERY LOCATION

More information

CSE 347/447: DATA MINING

CSE 347/447: DATA MINING CSE 347/447: DATA MINING Lecture 6: Clustering II W. Teal Lehigh University CSE 347/447, Fall 2016 Hierarchical Clustering Definition Produces a set of nested clusters organized as a hierarchical tree

More information

Topics. Clustering. Unsupervised vs. Supervised. Vehicle Example. Vehicle Clusters Advanced Algorithmics

Topics. Clustering. Unsupervised vs. Supervised. Vehicle Example. Vehicle Clusters Advanced Algorithmics .0.009 Topcs Advanced Algorthmcs Clusterng Jaak Vlo 009 Sprng What s clusterng Herarchcal clusterng K means + K medods SOM Fuzzy EM Jaak Vlo MTAT.0.90 Text Algorthms Unsupervsed vs. Supervsed Clusterng

More information

Clustering Algorithm of Similarity Segmentation based on Point Sorting

Clustering Algorithm of Similarity Segmentation based on Point Sorting Internatonal onference on Logstcs Engneerng, Management and omputer Scence (LEMS 2015) lusterng Algorthm of Smlarty Segmentaton based on Pont Sortng Hanbng L, Yan Wang*, Lan Huang, Mngda L, Yng Sun, Hanyuan

More information

Data Mining MTAT (4AP = 6EAP)

Data Mining MTAT (4AP = 6EAP) Clusterng Data Mnng MTAT018 (AP = 6EAP) Clusterng Jaak Vlo 009 Fall Groupng objects by smlarty Take all data and ask what are typcal examples, groups n data Jaak Vlo and other authors UT: Data Mnng 009

More information

More on Sorting: Quick Sort and Heap Sort

More on Sorting: Quick Sort and Heap Sort More on Sortng: Quck Sort and Heap Sort Antono Carzanga Faculty of Informatcs Unversty of Lugano October 12, 2007 c 2006 Antono Carzanga 1 Another dvde-and-conuer sortng algorthm The heap Heap sort Outlne

More information

Angle-Independent 3D Reconstruction. Ji Zhang Mireille Boutin Daniel Aliaga

Angle-Independent 3D Reconstruction. Ji Zhang Mireille Boutin Daniel Aliaga Angle-Independent 3D Reconstructon J Zhang Mrelle Boutn Danel Alaga Goal: Structure from Moton To reconstruct the 3D geometry of a scene from a set of pctures (e.g. a move of the scene pont reconstructon

More information

Sorting and Algorithm Analysis

Sorting and Algorithm Analysis Unt 7 Sortng and Algorthm Analyss Computer Scence S-111 Harvard Unversty Davd G. Sullvan, Ph.D. Sortng an Array of Integers 0 1 2 n-2 n-1 arr 15 7 36 40 12 Ground rules: sort the values n ncreasng order

More information

NUMERICAL SOLVING OPTIMAL CONTROL PROBLEMS BY THE METHOD OF VARIATIONS

NUMERICAL SOLVING OPTIMAL CONTROL PROBLEMS BY THE METHOD OF VARIATIONS ARPN Journal of Engneerng and Appled Scences 006-017 Asan Research Publshng Network (ARPN). All rghts reserved. NUMERICAL SOLVING OPTIMAL CONTROL PROBLEMS BY THE METHOD OF VARIATIONS Igor Grgoryev, Svetlana

More information

Lecture 4: Principal components

Lecture 4: Principal components /3/6 Lecture 4: Prncpal components 3..6 Multvarate lnear regresson MLR s optmal for the estmaton data...but poor for handlng collnear data Covarance matrx s not nvertble (large condton number) Robustness

More information