Statistics::Gap(3) User Contributed Perl Documentation Statistics::Gap(3)
NNAAMMEE
Statistics::Gap - An adaptation of the "Gap Statistic"
SSYYNNOOPPSSIISS
use Statistics::Gap;
$predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4);
OR
use Statistics::Gap;
$predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4, 7);
IINNPPUUTTSS
1. Prefix: The string that should be used to as a prefix while naming
the intermediate files and the .dat files (plot files).
2. Space: Specifies the space in which the clustering should be per-
formed. Valid parameter values:
vec - vector space
sim - similarity space
3. InputMatrix: Path to input matrix file. (More details about the
input file-format below.)
4. ClusteringMethod: Specifies the clustering method to be used. (Learn
more about this at:
http://glaros.dtc.umn.edu/gkhome/cluto/cluto/overview)
Valid parameter values:
rb - Repeated Bisections
rbr - Repeated Bisections for by k-way refinement
direct - Direct k-way clustering
agglo - Agglomerative clustering
bagglo - Partitional biased Agglomerative clustering
NOTE: bagglo can be used only if space=vec
5. Crfun: Specifies the criterion function to be used for finding clus-
tering solutions. (Learn more about this at:
http://glaros.dtc.umn.edu/gkhome/cluto/cluto/overview)
Valid parameter values:
i1 - I1 Criterion function
i2 - I2 Criterion function
e1 - E1 Criterion function
h1 - H1 Criterion function
h2 - H2 Criterion function
6. K: This is an approximate upper bound for the number of clusters
that may be present in the dataset.
7. B: The number of replicates/references to be generated.
8. TypeRef: Specifies whether to generate B replicates from a reference
or to generate B references.
Valid parameter values:
rep - replicates
ref - references
9. Percentage: Specifies the percentage confidence to be reported in
the log file. Since Statistics::Gap uses parametric bootstrap method
for reference distribution generation, it is critical to understand the
interval around the sample mean that could contain the population
("true") mean and with what certainty.
10. Precision: Specifies the precision to be used while generating the
reference distribution.
11. Seed: The seed to be used with the random number generator. (This
is an optional parameter. By default no seed is set.)
DDeettaaiillss aabboouutt tthhee iinnppuutt mmaattrriixx ffoorrmmaatt::
The input matrix can be in either dense or sparse format. The cell val-
ues can be integer or real. Depending upon the value specified for the
space parameter the header in the input file (first line) changes.
Example of input matrix in dense format when space=vec:
The first line specifies the dimensions - #rows #cols
From the second line the actual matrix follows.
6 5
1.3 2 0 0 3
2.1 0 4 2.7 0
1.3 2 0 0 3
2.1 0 4 2.7 0
1.3 2 0 0 3
2.1 0 4 2.7 0
Example of input matrix in dense format when space=sim:
The matrix, when in similarity space, is square and symmetric.
The first line specifies the dimensions - #rows/#cols
From the second line the actual matrix follows.
5
1.0000 0.3179 0.5544 0.2541 0.4431
0.3179 1.0000 0.1386 0.4599 0.5413
0.5544 0.1386 1.0000 0.5143 0.2186
0.2541 0.4599 0.5143 1.0000 0.5148
0.4431 0.5413 0.2186 0.5148 1.0000
Example of input matrix in sparse format when space=vec:
The first line specifies the dimensions & number of non-zero elements
- #rows #cols #nonzeroElem
From the second line the matrix contents follow. Only non-zero elements
are specified. Thus the elements are specified as pairs of - #col elem.
The row number is implied by the (line number-1).
8 10 41
1 3 4 2 8 2 10 1
1 1 2 5 3 1 5 2 7 1 9 2
1 3 4 2 8 2 10 1
1 1 2 5 3 1 5 2 7 1 9 2
1 3 4 2 8 2 10 1
1 1 2 5 3 1 5 2 7 1 9 2
2 4 3 1 4 2 5 5 7 1 9 1
2 4 3 1 4 2 5 5 7 1 9 1
Example of input matrix in sparse format when space=sim:
The first line specifies the dimensions & number of non-zero elements
- #rows/#cols #nonzeroElem
The matrix format is same as explained above.
5 15
1 1.0000 3 0.5544 5 0.4431
2 1.0000 3 0.1386 4 0.4599 5 0.5413
1 0.5544 2 0.1386 3 1.0000
2 0.4599 4 1.0000
1 0.4431 2 0.5413 5 1.0000
OOUUTTPPUUTT
1. A single integer number at STDOUT which is the Gap Statistic's esti-
mate of number of clusters present in the input dataset.
2. The prefix.gap.log file contains the log of various values at dif-
ferent K values. The first table in the file gives values like Gap(k),
obs(crfun(k)) etc. for every k value experimented with.
3. The prefix.*.dat files are provided to facilitate generation of
plots of the observed distribution, expected distribution and gap(k),
if desired.
DDEESSCCRRIIPPTTIIOONN
Given a dataset how does one automatically find the optimal number of
clusters that the dataset should be grouped into? - is one of the pre-
vailing problems. Statisticians Robert Tibshirani, Guenther Walther and
Trevor Hastie propose a solution for this problem in a Techinal Report
named - "Estimating the number of clusters in a dataset via the Gap
Statistic". This perl module implements an adaptation of the approach
proposed in the above paper.
If one tries to cluster a dataset (i.e. numerous observations described
in terms of a feature space) into n groups/clusters and if we plot the
graph of within cluster disimilarity (error) or similarity along Y-axis
and Number of clusters along X-axis then this graph generally takes a
form of a elbow/knee depending upon the measure on the Y-axis. The Gap
Statistic seeks to locate this elbow/knee because the value on the
X-axis at this elbow is the optimal number of clusters for the
data.
To locate this elbow Gap Statistic standardizes the graph of error by
comparing it with the expected graph under appropriate null reference
distribution. The adopted null model is the case of single cluster
(k=1) which is rejected in favor of k (k>1) if sufficient evidence is
present. The predicted k is the k value for which the error graph
falls the farthest below the reference graph.
As we have seen above, the Gap Statistic uses the within cluster dis-
persion (error) measure to find the elbow/knee. In this adaptation, we
use clustering criterion functions (crfun) instead of within cluster
dispersion measure. The crfun are used by the clustering methods to
obtain an optimal clustering solution for a given data and number of
clusters.
We provide two types of reference generation methods:
1. One can choose to generate a random dataset over the observed dis-
tribution by holding the row and the column marginals fixed and then
generating B replicates from this random dataset using Monte Carlo sam-
pling.
2. Or to generate B random datasets over the observed distribution by
holding the row and the column marginals fixed.
Please refer to http://search.cpan.org/dist/Algorithm-RandomMatrixGen-
eration/ to learn more about generating random dataset over the
observed distribution by holding the row and the column marginals
fixed.
EEXXPPOORRTT
"gap" function by default.
PPRREE--RREEQQUUIISSIITTEESS
1. This module uses suite of C programs called CLUTO for clustering
purposes. Thus CLUTO needs to be installed for this module to be func-
tional. CLUTO can be downloaded from
http://www-users.cs.umn.edu/~karypis/cluto/
2. Following Perl Modules
Math::BigFloat (http://search.cpan.org/dist/Math-BigInt-1.77/)
Algorithm::RandomMatrixGeneration (http://search.cpan.org/dist/Algo-
rithm-RandomMatrixGeneration/)
SSEEEE AALLSSOO
http://citeseer.ist.psu.edu/tibshirani00estimating.html
http://www-users.cs.umn.edu/~karypis/cluto/
http://search.cpan.org/dist/Algorithm-RandomMatrixGeneration/
AAUUTTHHOORR
Anagha Kulkarni, University of Minnesota, Duluth
kulka020 d.umn.edu
Ted Pedersen, University of Minnesota, Duluth
tpederse d.umn.edu
CCOOPPYYRRIIGGHHTT AANNDD LLIICCEENNSSEE
Copyright (C) 2006-2008, Anagha Kulkarni and Ted Pedersen
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation; either version 2 of the License, or (at your
option) any later version. This program is distributed in the hope
that it will be useful, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PUR-
POSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
perl v5.8.5 2006-04-28 Statistics::Gap(3)