clm vol(1) USER COMMANDS clm vol(1)
NAME
clm vol - compute volatile nodes from a set of clusterings
clmvol is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode vol.
The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page.
SYNOPSIS
clm vol [-fraction num (nff factor)] [-o fname (output file)] <cl file>+
DESCRIPTION
clm vol computes a score for each node, which at a minimum is equal to one. The output is in the form of a matrix containing a single col-
umn. The score correlates with what is deemed to be volatile behaviour. For all pairs of clusterings the set of all intersections is com-
puted, and these are considered in turn. An intersection is deemed to be volatile if the size of the intersection is less than half the
size of the smallest of the two clusters. In that case, for each node in the intersection its volatility score is incremented by one over
the size of the intersection. The size comparison can be made more stringent by increasing the -fraction <frac> option, which is by default
set to 0.5. Volatility occurs if the size of the intersection is less than <frac> times the size of the smallest cluster. If the -fraction
value is increased all the way up to 1.0, the implication is that an intersection is considered volatile unless one of the two clusteres
considered is a subset of the other.
AUTHOR
Stijn van Dongen.
OPTIONS
-fraction num (nff factor)
See the discussion at DESCRIPTION.
-o fname (output file)
SEE ALSO
mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
clm vol 12-068 8 Mar 2012 clm vol(1)
Check Out this Related Man Page
clm mate(1) USER COMMANDS clm mate(1)
NAME
clm mate - compute best matches between two clusterings
clmmate is not in actual fact a program. This manual page documents the behaviour and options of the clm program when invoked in mode mate.
The options -h, --apropos, --version, -set, --nop are accessible in all clm modes. They are described in the clm manual page.
SYNOPSIS
clm mate [-o fname (output file name)] [-b (omit headers)] [--one-to-many (require multiple hits in <clfile1>)] [-h (print synopsis, exit)]
[--apropos (print synopsis, exit)] [--version (print version, exit)] <clfile1> <clfile2>
DESCRIPTION
clm mate computes for each cluster X in clfile1 all clusters Y in clfile2 that have non-empty intersection and outputs a line with the data
points listed below.
overlap(X,Y) # 2 * size(meet(X,Y)) / (size(X)+size(Y))
index(X) # name of cluster
index(Y) # name of cluster
size(meet(X,Y))
size(X-Y) # size of left difference
size(Y-X) # size of right difference
size(X)
size(Y)
projection(X, clfile2) # see below
projection(Y, clfile1) # see below
The projected size of a cluster X relative to a clustering K is simply the sum of all the nodes shared between any cluster Y in K and X,
duplications allowed. For example, the projected size of (0,1) relative to {(0,2,4), (1,4,9), (1,3,5)} equals 3.
The overlap between X and Y is exactly 1.0 if the two clusters are identical, and for nearly identical clusterings the score will be close
to 1.0.
All of this information can also be obtained from the contingency matrix defined for two clusterings. The [i,j] row-column entry in a con-
tigency matrix between to clusterings gives the number of entries in the intersection between cluster i and cluster j from the respective
clusterings. The other information is implicitly present; the total number of nodes in clusters i and j for example can be obtained as the
sum of entries in row i and column j respectively, and the difference counts can then be obtained by substracting the intersection count.
The contingency matrix can easily be computed using mcx; e.g.
mcx /clfile2 lm /clfile1 lm tp mul /ting wm
will create the contingency matrix in mcl matrix format in the file ting, where columns range over the clusters in clfile1.
The output can be put to good use by sorting it numerically on that first score field. It is advisable to use a stable sort routine (use the
-s option for UNIX sort) From this information one can quickly extract the closest clusters between two clusterings.
OPTIONS
-o fname (output file name)
Specify the name of the output file.
-b (omit headers)
Batch mode, omit column names.
--one-to-many (require multiple hits in <clfile1>)
Do not output information for clusters in the first file that are subset of a cluster in the second file.
AUTHOR
Stijn van Dongen.
SEE ALSO
mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.
clm mate 12-068 8 Mar 2012 clm mate(1)