16 May 2014
**clm dist**
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clm dist — compute the distance between two or more partitions (clusterings).

The distance that is computed can be any of
*split/join distance*, *variance of information*,
or *Mirkin metric*.

clmdist is not in actual fact a program. This manual
page documents the behaviour and options of the clm program when
invoked in mode *dist*. The options **-h**, **--apropos**,
**--version**, **-set**, **--nop** are accessible
in all **clm** modes. They are described
in the clm manual page.

**clm dist** [options] <file name> <file name>+

**clm dist**
**[-mode** <sj|vi|mk|sc> (*distance type*)**]**
**[-o** fname (*output file*)**]**
**[--chain** (*only compare consecutive clusterings*)**]**
**[--one-to-many** (*compare first clustering to all others*)**]**
**[--sort** (*sort clusterings based on coarseness*)**]**
**[--index** (*output Rand, adjusted Rand and Jaccard indices*)**]**
**[-digits** k (*output decimals*)**]**
**[-h** (*print synopsis, exit*)**]**
**[--apropos** (*print synopsis, exit*)**]**
**[--version** (*print version, exit*)**]**
<file name> <file name>+

**clm dist** computes distances between clusterings. It can compute the
*split/join distance* (described below), the *variance of information
measure*, and the *Mirkin metric*. By default it computes the chosen distance
for all pairs of distances in the clusterings provided. Clusterings must be in
the mcl matrix format (cf. mcxio), and are supplied on the command
line as the names of the files in which they are stored.
It is possible to compare only consecutive clusterings by using
the **--chain** option.

Currently, **clm dist** cannot compute different distance types simultaneously.

The output is linewise, each line giving information about the distance between a pair of clusterings. A line has the following format:

d d1 d2 N v name1 name2 [v50,v75,v90,v95,v99]

where `dT` is the distance between the two clusterings, `d1` is the
distance from the first clustering to the greatest common subclustering
(alternatively called GCS, intersection, or meet) of the two clusterings,
`d2` is similarly the distance from the second clustering to the GCS,
`N` is the number of nodes in the set over which the clusterings are
defined, `name1` is the name of the file containing the first clustering,
`name2` is the name of the file containing the second clustering, and
`vXX` is the number of *volatile nodes* at stringency factor `0.XX`
(i.e. 0.5 for `v50`). Refer to clm vol for a definition of
*volatile node*.

Use **sj** for the *split/join distance* (described below), **vi** for
the *variance of information measure* and **mk** for the *Mirkin metric*.

This option can be used if you know that the clusterings are nested
clusterings (or appoximately so) and ordered from coarse to fine-grained
or vice versa. An example of this is the set of clusterings resulting
from applying **mcl** with a range of inflation parameters.

Use this option for example to compare a gold standard classification
to a collection of clusterings.
Bear in mind that sub-clustering and super-clustering are also
ways for a clustering to be compatible with a gold standard.
This means that the simple numerical criterion of distance between
clusters (by whatever method) is only partially informative.
For the Mirkin, variation of information and split/join metrics
it pays to take into account the constituent distances `d1`
and `d2` (see above). Assuming that the first clustering
given as argument represents a gold standard, a small value
for `d1` implies that the second clustering is (nearly) a superclustering,
and similarly a small value for `d2` implies that it is (nearly)
a subclustering.

This option can be useful in conjunction with the **--chain**
option, in case the list of clusterings supplied is not necessarily
ordered by granularity.

As described.

The number of decimals printed when using the variance of information measure.

For each pair of clusterings **C1**, **C2**, two numbers are given,
say **d1** and **d2**. Then **d1** + **d2** equals the number
of nodes that have to be exchanged in order to transform any of the two
clusterings into the other, and you can think of (**d1**+**d2**)/**2N**
as the percentage that the two clusterings differ. The split/join
distance has a linearity property with respect to the meet of **C1** and
**C2**, see below.

The split/join distance **sjd** is very handy in computing the consistency of
two or more clusterings of the same graph, or comparing clusterings made
with different resource (but otherwise identical) parameters. The latter is
for finding out whether you can settle for cheaper mcl settings, or whether
you need to switch to more expensive settings. The former is for finding out
whether clusterings are identical, conflicting, or whether one is (almost) a
subclustering of the other - mostly for comparing a set of clusterings of
different granularity, made by letting the mcl parameter **-I** vary.
The EXAMPLES section contains examples of all these **clm dist** uses,
and the use of **clm info** and **clm meet** is also discussed there.

**sjd** is a metric distance on the space of partitions of
a set of a given fixed cardinality. It has the following linearity
property. Let **P1** and **P2** be partitions, then

**sjd**(**P1**, **P2**) = **sjd**(**P1**, **D**) + **sjd**(**P2**, **D**)

where **D** (for Dutch Doorsnede)
is the intersection of **P1** and **P2**, i.e. the unique clustering
that is both a subclustering of **P1** and **P2** *and* a superclustering of
all other subclusterings of **P1** and **P2**. Sloppily worded, **D** is the largest
subclustering of both **P1** and **P2**. See the REFERENCES section for
a pointer to the technical report in which **sjd** was first defined (and in
which the non-trivial triangle inequality is proven).

Because it is useful to know whether one partition (or clustering)
is almost a subclustering of the other, **clm dist** returns the
two constituents **sjd**(**P1**,**D**) and **sjd**(**P2**,**D**).

Let **P1** and **P2** be two clusterings of a graph of cardinality **N**,
and suppose **clm dist** returns the integers **d1** and **d2**. You can think of
**100 * (d1 + d2) / N** as the percentage that **P1** and **P2** differ.
This interpretation is in fact slightly conservative.
The numerator is the number of nodes that need to be exchanged in order to
transform one into the other. This number may grow as large as
**2*N - 2*sqrt(N)**, so it would be justified to take 50 as a scaling
factor rather than 100.

For example, if **A** and **B** are both clusterings of a graph
on a set of 9058 nodes and **clm dist** returns [38, 2096], this conveys
that **A** is almost a subclustering of **B** (by splitting 38 nodes
in **A** we obtain a clustering **D** that is a subclustering of **B**),
and that **B** is much less granular than **A**. The latter is
because we can obtain **B** from **D** by *joining* 2096 nodes
in some way.

The following is an example of several mcl validation tools
applied to a set of clusterings on a protein graph of 9058 nodes.
In the first experiment, six
different clusterings were generated for different values of the inflation
parameter, which was respectively set to 1.2, 1.6, 2.0, 2.4, 2.8, and 3.2.
It should be noted that protein graphs seem somewhat special in that an
inflation parameter setting as low as 1.2 still produces a very acceptable
clustering. The six clusterings are scrutinized using **clm dist**,
**clm info**, and **clm meet**.
In the second experiment, four different clusterings were generated
with identical flow (i.e. inflation) parameter, but
with different resource parameters. **clm dist** is used to choose
a sufficient resource level.

High **-P/-S/-R** values make **mcl** more accurate but also
more time and memory consuming. Run **mcl** with different settings for these
parameters, holding other parameters fixed. If the expensive and supposedly
more accurate clusterings are very similar to the clusterings resulting from
cheaper settings, the cheaper setting is sufficient. If the distances
between cheaper clusterings and more expensive clusterings are large, this
is an indication that you need the expensive settings. In that case, you may
want to increase the **-P/-S/-R** parameters (or simply the
**-scheme** parameter) until associated
clusterings at nearby resource levels are very similar.

In this particular example, the validation tools do not reveal that one
clustering in particular can be chosen as 'best', because all clusterings
seem at least acceptable. They do aid however in showing the relative
merits of each clusterings. The most important issue in this respect is
cluster granularity. The table below shows the output of **clm info**.

Efficiency Mass frac Area frac Cl weight Mx link weight
1.2 0.42364 0.98690 0.02616 52.06002 50.82800
1.6 0.58297 0.95441 0.01353 55.40282 50.82800
2.0 0.63279 0.92386 0.01171 58.09409 50.82800
2.4 0.65532 0.90702 0.01091 59.58283 50.82800
2.8 0.66854 0.84954 0.00940 63.19183 50.82800
3.2 0.67674 0.82275 0.00845 66.10831 50.82800

This data shows that there is exceptionally strong cluster structure present in the input graph. The 1.2 clustering captures almost all edge mass using only 2.5 percent of 'area'. The 3.2 clustering still captures 82 percent of the mass using less than 1 percent of area. We continue with looking at the mutual consistency of the six clusterings. Below is a table that shows all pairwise distances between the clusterings.

| 1.6 | 2.0 | 2.4 | 2.8 | 3.2 | 3.6
-----------------------------------------------------------.
1.2 |2096,38 |2728,41 |3045,48 |3404,45 |3621,43 |3800, 42 |
-----------------------------------------------------------|
1.6 | | 797,72 |1204,76 |1638,78 |1919,70 |2167, 69 |
-----------------------------------------------------------|
2.0 | | | 477,68 | 936,78 |1235,85 |1504, 88 |
-----------------------------------------------------------|
2.4 | | | | 498,64 | 836,91 |1124,103 |
-----------------------------------------------------------|
2.8 | | | | | 384,95 | 688,119 |
-----------------------------------------------------------|
3.2 | | | | | | 350,110 |
-----------------------------------------------------------.

The table shows that the different clusterings are pretty consistent with each other, because for two different clusterings it is generally true that one is almost a subclustering of the other. The interpretation for the distance between the 1.6 and the 3.2 clustering for example, is that by rearranging 43 nodes in the 3.2 clustering, we obtain a subclustering of the 1.6 clustering. The table shows that for any pair of clusterings, at most 119 entries need to be rearranged in order to make one a subclustering of the other.

The overall consistency becomes all the more clear by looking at the meet of all the clusterings:

clm meet -o meet out12 out16 out20 out24 out28 out32
clm dist meet out12 out16 out20 out24 out28 out32

results in the following distances between the respective clusterings and their meet.

| 1.2 | 1.6 | 2.0 | 2.4 | 2.8 | 3.2 |
-------------- --------------------------------------------.
meet| 0,3663| 0,1972| 0,1321 | 0,958 | 0,559 | 0,283 |
-------------- --------------------------------------------.

This shows that by rearranging only 283 nodes in the 3.2 clustering, one obtains a subclustering of all other clusterings.

In the last experiment, **mcl** was run with inflation parameter 1.4,
for each of the four different preset pruning schemes `k=1,2,3,4`.
The **clm dist** distances between the different clusterings
are shown below.

| k=2 | k=3 | k=4 |
-------------------------------.
k=1 | 17,17 | 16,16 | 16,16 |
-------------------------------.
k=2 | | 3,3 | 5,5 |
-------------------------------.
k=3 | | | 4,4 |
-------------------------------.

This example is a little boring in that the cheapest scheme seems adequate.
If anything, the gaps between the `k=1` scheme and the rest are a little
larger than the three gaps between the `k=2`, `k=3`, and `k=4`
clusterings. Had all distances been much larger, then such an observation
would be reason to choose the `k=2` setting.

Note that you need not feel uncomfortable with the clusterings still being different at high resource levels, if ever so slightly. In all likelihood, there are anyway nodes which are not in any core of attraction, and that are on the boundary between two or more clusterings. They may go one way or another, and these are the nodes which will go different ways even at high resource levels. Such nodes may be stable in clusterings obtained for lower inflation values (i.e. coarser clusterings), in which the different clusters to which they are attracted are merged.

Stijn van Dongen.

mclfamily for an overview of all the documentation and the utilities in the mcl family.

Stijn van Dongen. *Performance criteria for graph clustering and Markov
cluster experiments*. Technical Report INS-R0012, National Research
Institute for Mathematics and Computer Science in the Netherlands,
Amsterdam, May 2000.

http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z

Marina Meila. *Comparing Clusterings — An Axiomatic View*.
In *Proceedings of the 22nd International Conference on Machine Learning*,
Bonn, Germany, 2005.

Marina Meila. *Comparing Clusterings*,
UW Statistics Technical Report 418.

http://www.stat.washington.edu/www/research/reports/2002/tr418.ps