Scribd Logo
Upload

Welcome to Scribd!

  • 339 views

    Cluster Analysis: Biological Data Analysis and Chemometrics

    Uploaded by

    Deepthi Pakalapati
    This document provides an overview of cluster analysis methods and algorithms. It discusses two primary methods of cluster analysis (hierarchical and divisive clustering) and ordination. It also describes advantages of cluster analysis and different clustering algorithms like agglomerative clustering. Finally, it provides examples of calculating distances and similarities between objects and evaluating clustering results.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd

    Cluster Analysis: Biological Data Analysis and Chemometrics

    Uploaded by

    Deepthi Pakalapati
    339 views41 pages
    This document provides an overview of cluster analysis methods and algorithms. It discusses two primary methods of cluster analysis (hierarchical and divisive clustering) and ordination. It also describes advantages of cluster analysis and different clustering algorithms like agglomerative clustering. Finally, it provides examples of calculating distances and similarities between objects and evaluating clustering results.

    Original Title

    Cluster Analysis

    Copyright

    © Attribution Non-Commercial (BY-NC)

    Available Formats

    PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    This document provides an overview of cluster analysis methods and algorithms. It discusses two primary methods of cluster analysis (hierarchical and divisive clustering) and ordination. It also describes advantages of cluster analysis and different clustering algorithms like agglomerative clustering. Finally, it provides examples of calculating distances and similarities between objects and evaluating clustering results.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    339 views41 pages

    Cluster Analysis: Biological Data Analysis and Chemometrics

    Uploaded by

    Deepthi Pakalapati
    This document provides an overview of cluster analysis methods and algorithms. It discusses two primary methods of cluster analysis (hierarchical and divisive clustering) and ordination. It also describes advantages of cluster analysis and different clustering algorithms like agglomerative clustering. Finally, it provides examples of calculating distances and similarities between objects and evaluating clustering results.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 41

    Cluster analysis

    Based on H.C. Romesburg: Cluster analysis for researchers, Lifetime Learning Publications, Belmont, CA, 1984 P.H.A. Sneath and R.R. Sokal: Numericxal Taxonomy, Freeman, San Fransisco, CA, 1973

    Jens C. Frisvad BioCentrum-DTU

    Biological data analysis and chemometrics

    Two primary methods


    Cluster analysis (no projection)
    Hierarchical clustering Divisive clustering Fuzzy clustering

    Ordination (projection)
    Principal component analysis Correspondence analysis Multidimensional scaling

    Advantages of cluster analysis


    Good for a quick overview of data Good if there are many groups in data Good if unusual similarity measures are needed Can be added on ordination plots (often as a minimum spanning tree, however) Good for the nearest neighbours, ordination better for the deeper relationships

    Different clustering methods


    NCLAS: Agglomerative clustering by distance optimization HMCL: Agglomerative clustering by homogeneity optimization INFCL: Agglomerative clustering by information theory criteria MINGFC: Agglomerative clustering by global optimization ASSIN: Divisive monothetic clustering PARREL: Partitioning by global optimization FCM: Fuzzy c-means clustering MINSPAN: Minimum spanning tree REBLOCK: Block clustering (k-means clustering)

    SAHN clustering
    Sequential agglomerative hierarchic nonoverlapping clustering

    Single linkage
    Nearest neighbor, minimum method Close to minimum spanning tree Contracting space Chaining possible J = 0.5, K = 0.5, = 0, = -0.5 UJ,K = min Ujk

    U( J ,K ) L = JUJ ,L + KUK ,L + UJ ,K + UJ ,L UK ,L

    Complete linkage
    Furthest neighbor, maximum method Dilating space J = 0.5, K = 0.5, = 0, = 0.5 UJ,K = max Ujk

    Average linkage
    Aritmetic average
    Unweighted: UPGMA (group average) Weighted: WPGMA

    Centroid
    Unweighted centroid (Centroid) Weighted centroid (Median)

    From Sneath and Sokal, 1973, Numerical taxonomy

    Ordinary clustering
    Obtain the data matrix Transform or standardize the data matrix Select the best resemblance or distance measure Compute the resemblance matrix Execute the clustering method (often UPGMA = average linkage) Rearrange the data and resemblance matrices Compute the cophenetic correlation coefficient

    Binary similarity coefficients


    (between two objects i and j)

    j i 1

    Matches and mismatches


    m = a + b (number of matches) u = c + d (number of mismatches) n = m + u = a + b + c + d (total sample size) Similarity (often 0 to 1) Dissimilarity (distance) (often 0 to 1) Correlation (-1 to 1)

    Simple matching coefficient


    SM = (a + d) / (a + b + c + d) = m / n Euclidean distance for binary data: D = 1-SM = (b +c) / (a + b + c + d) = u / n

    Avoiding zero zero comparisons


    Jaccard = J = a / (a +b +c) Srensen or Dice: DICE = 2a / (2a + b + c)

    Correlation coefficients
    Yule: (ad bc) / (ad + bc)

    PHI = ( ad bc ) / ( a + b )(c + d )( a + c )(b + d )

    Other binary coefficients


    Hamann = H = (a + d b c) / (a + b + c + d) Rogers and Tanimoto = RT = (a + d) / (a + 2b + 2c + d) Russel and Rao = RR = a / (a + b + c + d) Kulzynski 1 = K1 = a / (b + c) UN1 = (2a + 2d) / (2a + b + c + 2d) UN2 = a / (a + 2b + 2c) UN3 = (a + d) / (b + c)

    Distances for quantitative (interval) data Euclidean and taxonomic distance

    EUCLID = Eij =
    DIST = d ij = 1 n

    ( xki + xkj )

    ( x ki + x kj ) 2 k

    Bray-Curtis and Canberra distance

    BRAYCURT = d ij = k xki xkj / k ( x ki + xkj )

    1 CANBERRA = k xki xkj / k ( xki + xkj ) n

    Average Manhattan distance (city block)

    1 MANHAT = M ij = k xki xkj n

    Chi-squared distance

    xki xkj x. x. j i CHISQ = d ij = k xk

    Cosine coefficient

    COSINE = cij = k xki xkj /

    k xki

    k xkj

    Step 1. Obtain the data matrix


    Object 1 1 Feature 2 2 3 4 5

    10 5

    20 20

    30 10

    30 15

    5 10

    Objects and features


    The five objects are plots of farm land The features are
    1. Water-holding capacity (%) 2. Weight % soil organic matter

    Objective: find the two most similar plots

    Resemblance matrix 1 1 2 18.0 3 4 2 3 4 5

    14.1 11.2 18.0

    5.00 25.0

    25.5

    20.6 22.4

    5 7.07

    Revised resemblance matrix 1 1 2 5 (34) 2 5 (34)

    18.0 7.07 21.5

    18.0 12.7

    25.3

    Revised resemblance matrix

    2 2

    (34)

    (15)

    12.7 18.0

    23.4

    (34)

    (15)

    Rvised resemblance matrix (15) (234)

    (15)

    21.6
    (234)

    Cophenetic correlation coefficient (Pearson product-moment correlation coefficient)


    A comparison of the similarities according to the similarity matrix and the similarities according to the dendrogram

    rX ,Y =

    xy (1/ n)(x)(y) (x (1/ n)(x) )(y (1/ n)( y) )


    2 2 2 2

    NTSYS
    Import matrix Transpose matrix if objects are rows (they are supposed to be columns in NTSYS) (transp in transformation / general) Consider log1 or autoscaling (standardization) Select similarity or distance measure (similarity) Produce similarity matrix

    NTSYS (continued)
    Select clustering procedure (often UPGMA) (clustering) Calculate cophenetic matrix (clustering) Compare similarity matrix with cophenetic matix (made from the dendrogram) and write down the cophenetic correlation (graphics, matrix comparison) Write dendrogram (graphics, treeplot)

    You might also like

    pFad - Phonifier reborn

    Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

    Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


    Alternative Proxies:

    Alternative Proxy

    pFad Proxy

    pFad v3 Proxy

    pFad v4 Proxy