MCL FAQ(7)                      MISCELLANEOUS                       MCL FAQ(7)



  NAME
          mclfaq - faqs and facts about the MCL cluster algorithm.

          MCL refers to the generic MCL algorithm and the MCL process on which
          the algorithm is based. mcl refers to the implementation.  This  FAQ
          answers  questions  related  to  both. In some places MCL is written
          where MCL or mcl can be read. This is the case for example  in  sec-
          tion  3, What  kind of graphs.  It should in general be obvious from
          the context.

          This FAQ does not begin to attempt to  explain  the  motivation  and
          mathematics  behind  the  MCL  algorithm  -  the  internals  are not
          explained. A broad view is given in faq 1.2, and  see  also  faq 1.5
          and section REFERENCES.

          Some  additional  sections  preceed the actual faq entries.  The TOC
          section contains a listing of all questions.

  RESOURCES
          The manual pages for all the utilities that come with mcl; refer  to
          mclfamily(7) for an overview.

          mcl  development is discussed on mcl-devel@micans.org, list informa-
          tion is at https://lists.micans.org:446/listinfo/mcl-devel.

          See the REFERENCES Section for publications detailing the  mathemat-
          ics behind the MCL algorithm.

  TOC
  1...... General questions
   1.1... For whom is mcl and for whom is this FAQ?
   1.2... What is the relationship between the MCL process, the MCL algorithm,
          and the 'mcl' implementation?
   1.3... What do the letters MCL stand for?
   1.4... How could you be so feebleminded to use MCL as abbreviation? Why  is
          it labeled 'Markov cluster' anyway?
   1.5... Where can I learn about the innards of the MCL algorithm/process?
   1.6... For which platforms is mcl available?
   1.7... How does mcl's versioning scheme work?

  2...... Input format
   2.1... How can I get my data into the MCL matrix format?

  3...... What kind of graphs
   3.1... What is legal input for MCL?
   3.2... What is sensible input for MCL?
   3.3... Does MCL work for weighted graphs?
   3.4... Does MCL work for directed graphs?
   3.5... Can MCL work for lattices / directed acyclic graphs / DAGs?
   3.6... Does MCL work for tree graphs?
   3.7... For  what  kind  of  graphs does MCL work well and for which does it
          not?
   3.8... What makes a good input graph?  How do I construct the similarities?
          How to make them satisfy this Markov condition?
   3.9... My input graph is directed. Is that bad?
   3.10.. Why  does  mcl  like  undirected graphs and why does it dislike uni-
          directed graphs so much?
   3.11.. How do I check that my graph/matrix is symmetric/undirected?

  4...... Speed and complexity
   4.1... How fast is mcl/MCL?
   4.2... What statistics are available?
   4.3... Does this implementation need to sort vectors?
   4.4... mcl does not compute the ideal MCL process!
   4.5... I've read elsewhere that MCL is slow [compared with XYZ]

  5...... Resource tuning / accuracy
   5.1... What do you mean by resource tuning?
   5.2... How do I compute the maximum amount of RAM needed by mcl?
   5.3... How much does the mcl clustering differ from the clustering  result-
          ing from a perfectly computed MCL process?
   5.4... How do I know that I am using enough resources?
   5.5... Where is the mathematical analysis of this mcl pruning strategy?
   5.6... What qualitative statements can be made about the effect of pruning?
   5.7... At different high resource levels my clusterings are not  identical.
          How can I trust the output clustering?

  6...... Tuning cluster granularity
   6.1... How do I tune cluster granularity?
   6.2... The effect of inflation on cluster granularity.
   6.3... The  effect of similarity distribution homogeneity on cluster granu-
          larity.
   6.4... The effect of initial centering on cluster granularity.

  7...... Implementing the MCL algorithm
   7.1... How easy is it to implement the MCL algorithm?

  8...... Cluster overlap / MCL iterand cluster interpretation
   8.1... Introduction
   8.2... Can the clusterings returned by mcl contain overlap?
   8.3... How do I obtain the clusterings associated with MCL iterands?

  9...... Miscellaneous
   9.1... How do I find the default settings of mcl?
   9.2... What's next?

  FAQ
                                   General questions

   1.1    For whom is mcl and for whom is this FAQ?

          For everybody with an appetite for graph clustering.  Regarding  the
          FAQ,  I  have  kept the amount of mathematics as low as possible, as
          far as matrix analysis is concerned.  Inevitably,  some  terminology
          pops up and some references are made to the innards of the MCL algo-
          rithm, especially in the section on resources  and  accuracy.  Graph
          terminology  is  used  somewhat  more  carelessly though. The future
          might bring definition entries, right now you have  to  do  without.
          Mathematically  inclined  people  may  be interested in the pointers
          found in the REFERENCES section.

          Given this mention of mathematics, let me point out  this  one  time
          only  that  using  mcl is extremely straightforward anyway. You need
          only mcl and an input graph (refer to the mcl manual page), and many
          people trained in something else than mathematics are using mcl hap-
          pily.

   1.2    What is the relationship between the MCL process, the MCL algorithm,
          and the 'mcl' implementation?

          mcl is what you use for clustering. It implements the MCL algorithm,
          which is a cluster algorithm for graphs. The MCL algorithm is  basi-
          cally  a shell in which the MCL process is computed and interpreted.
          I will describe them in the natural, reverse, order.

          The MCL process generates a row of stochastic  matrices  given  some
          initial stochastic matrix. The elements with even index are obtained
          by expanding the previous element, and the elements with  odd  index
          are  obtained by inflating the previous element given some inflation
          constant. Expansion is  nothing  but  normal  matrix  squaring,  and
          inflation is a particular way of rescaling the entries of a stochas-
          tic matrix such that it remains stochastic.

          The row of MCL elements (from the MCL process) is in principle with-
          out end, but what happens is that the elements converge to some spe-
          cific kind of matrix, called the limit of the process. The heuristic
          underlying  MCL  predicts  that  the  interaction  of expansion with
          inflation will lead to a limit exhibiting cluster structure  in  the
          graph  associated  with the initial matrix. This is indeed the case,
          and several mathematical results tie MCL iterands and limits and the
          MCL interpretation together (REFERENCES).

          The  MCL algorithm is simply a shell around the MCL process in which
          an input graph is transformed into an initial  matrix  suitable  for
          starting  the process, in which inflation parameters are set, and in
          which the MCL process is stopped once the limit is reached,  and  in
          which the result is interpreted as a clustering.

          The  mcl  implementation supplies the functionality of the MCL algo-
          rithm, with some extra facilities  for  manipulation  of  the  input
          graph, interpreting the result, manipulating resources while comput-
          ing the process, and monitoring the state of these manipulations.

   1.3    What do the letters MCL stand for?

          For Markov Cluster. The MCL algorithm is a cluster algorithm that is
          basically  a  shell in which an algebraic process is computed.  This
          process iteratively generates stochastic  matrices,  also  known  as
          Markov matrices, named after the famous Russian mathematician Andrei
          Markov.

   1.4    How could you be so feebleminded to use MCL as abbreviation? Why  is
          it labeled 'Markov cluster' anyway?

          Sigh.  It  is a widely known fact that a TLA or Three-Letter-Acronym
          is the canonical self-describing abbreviation  for  the  name  of  a
          species  with  which  computing terminology is infested (quoted from
          the Free Online Dictionary of Computing). Back when I  was  thinking
          of  a  nice  tag  for  this cute algorithm, I was totally unaware of
          this. I naturally dismissed MC (and would still do that today). Then
          MCL  occurred  to  me,  and without giving it much thought I started
          using it.  A Google search (or was I  still  using  Alta-Vista  back
          then?)  might have kept me from going astray.

          Indeed,  MCL  is  used  as  a tag for Macintosh Common Lisp, Mission
          Critical Linux, Monte Carlo  Localization,  MUD  Client  for  Linux,
          Movement for Canadian Literacy, and a gazillion other things - refer
          to the file mclmcl.txt. Confusing. It seems that the  three  charac-
          ters  MCL possess otherworldly magical powers making them an ever so
          strange and strong attractor in the space of TLAs. It probably helps
          that Em-See-Ell (Em-Say-Ell in Dutch) has some rhythm to it as well.
          Anyway MCL stuck, and it's here to stay.

          On a more general level, the label Markov Cluster is not an entirely
          fortunate  choice  either.  Although  phrased  in  the  language  of
          stochastic matrices, MCL theory bears very little relation to Markov
          theory,  and  is much closer to matrix analysis (including Hilbert's
          distance) and the theory of dynamical systems. No results have  been
          derived  in the latter framework, but many conjectures are naturally
          posed in the language of dynamical systems.

   1.5    Where can I learn about the innards of the MCL algorithm/process?

          Currently, the most basic explanation of the MCL algorithm is  found
          in  the  technical report [2]. It contains sections on several other
          (related) subjects though, and it assumes some working knowledge  on
          graphs, matrix arithmetic, and stochastic matrices.

   1.6    For which platforms is mcl available?

          It  should compile and run on virtually any flavour of UNIX (includ-
          ing Linux and the BSD variants of course).  Following  the  instruc-
          tions in the INSTALL file shipped with mcl should be straightforward
          and sufficient. Courtesy to Joost van Baal who completely autofooled
          mcl.

          Building  MCL  on Wintel (Windows on Intel chip) should be straight-
          forward if you use the full suite of cygwin tools. Install cygwin if
          you  do  not have it yet. In the cygwin shell, unpack mcl and simply
          issue the commands ./configure, make, make install, i.e. follow  the
          instructions in INSTALL.

          This MCL implementation has not yet been reported to run on MAC. For
          the latest Mac OS X one would expect that it is  certainly  possible
          to make this happen.

          If you have further questions or news about this issue, contact mcl-
          devel <at> lists <dot> micans <dot> org.

   1.7    How does mcl's versioning scheme work?

          The current setup, which I hope to continue, is this.  All  releases
          are identified by a date stamp. For example 02-095 denotes day 95 in
          the year 2002. This date stamp agrees (as of April  2000)  with  the
          (differently  presented) date stamp used in all manual pages shipped
          with that release.  For example, the date stamp of the FAQ  you  are
          reading is 27 Feb 2006, which corresponds with the MCL stamp 06-058.
          The Changelog file contains a list of what's changed/added with each
          release. Currently, the date stamp is the primary way of identifying
          an mcl release. When asked for its version by using  --version,  mcl
          outputs both the date stamp and a version tag (see below).

          In early 2002 it occurred to me that mcl should, in addition to time
          stamps, also have something like version  numbers,  wanting  to  use
          those  to  indicate  noteworthy  changes. The April 2002 release got
          version tag 1.001, in order to celebrate the then-recent addition of
          this  FAQ,  mcl's new logging facility --log, and clmimac to the MCL
          distribution. The January 2003 release had its version number bumped
          to  1.002,  marking  MCL's ability to directly deal with a much more
          general type of graph encoding.  1.003 brought  mclpipeline,  mcxde-
          blast,  mclblastline,  mcxassemble,  clmformat  and automatic output
          naming. 1.004 revived binary format, improved  mcxsubs,  and  had  a
          host  of  other additions. 1.005 removed an IO bottleneck, consider-
          ably speeding up matrix  reads.  1.006  featured  mcl's  ability  to
          directly  read  and produce label output. Currently, the version tag
          is not used in the mcl distribution name - only the  date  stamp  is
          used for that.

                                      Input format

   2.1    How can I get my data into the MCL matrix format?

          One  of  the  easiest ways is if you have a list of label pairs with
          similarities attached to the pairs.  Put  this  information  into  a
          file  with  each  pair  of labels and the associated similarity on a
          single line separated by whitespace. Example:

          apples    oranges    2.14
          oranges   pears      0.78
          oranges   apples     1.57
          pears     apples     1.01

          Suppose the file is called mydata.  You can simply cluster  it  like
          this:

             mcl mydata --abc -I 2.0 -o mydata.cls-I20
             mcl mydata --abc -I 2.4 -o mydata.cls-I24
             mcl mydata --abc -I 2.8 -o mydata.cls-I28

          In  this  example  a  few  runs  were shown with different inflation
          parameters.  This is nonsensical with this particular  4-node  input
          but  a  good idea in general. mcl provides many options to cache the
          intermediate matrix input and the intermediate tab  file.  Refer  to
          the  mcl  manual  page,  specifically  look  for  the -cache-tab and
          -cache-graph options.

          Alternatively, use mcxload(1) to save label input as an  mcl  matrix
          and  one  or more tab files, then apply mcl to the matrix file using
          the -use-tab option.

          NOTE
          Simply doing

             mcl mydata --abc -I 2.0
             mcl mydata --abc -I 2.4
             mcl mydata --abc -I 2.8

          will result in the output files out.mydata.I20s6,  out.mydata.I24s6,
          and  out.mydata.I28s6. The s6 bit indicates the resource scheme used
          by mcl. The automatic naming facility is very convenient -  try  it.
          If  you  need  to  script mcl use the -az option to capture the name
          that mcl would generate given the rest of the command-line.

                                  What kind of graphs

   3.1    What is legal input for MCL?

          Any graph (encoded as a matrix of similarities) that is nonnegative,
          i.e. all similarities are greater than or equal to zero.

   3.2    What is sensible input for MCL?

          It  is  ok  for graphs to be weighted, and they should preferably be
          symmetric.   They  should  certainly  not  contain  parts  that  are
          (almost)  cyclic, although nothing stops you from experimenting with
          such input.

   3.3    Does MCL work for weighted graphs?

          Yes, unequivocally. They should preferably  be  symmetric/undirected
          though.  See entries 3.7 and 3.8.

   3.4    Does MCL work for directed graphs?

          Maybe, with a big caveat. See entries 3.8 and 3.9.

   3.5    Can MCL work for lattices / directed acyclic graphs / DAGs?

          Such  graphs  [term]  can surely exhibit clear cluster structure. If
          they do, there is only one way for mcl to  find  out.  You  have  to
          change  all  arcs to edges, i.e. if there is an arc from i to j with
          similarity s(i,j) - by the DAG property this implies s(j,i)  =  0  -
          then make s(j,i) equal to s(i,j).

          This  may feel like throwing away valuable information, but in truth
          the information that is thrown away (direction) is  not  informative
          with  respect  to  the  presence of cluster structure. This may well
          deserve a longer discussion than would be justified here.

   3.6    Does MCL work for tree graphs?

          Nah, I don't think so. More info at entry 3.7.

   3.7    For what kind of graphs does MCL work well and  for  which  does  it
          not?

          Graphs  in which the diameter [term] of (subgraphs induced by) natu-
          ral clusters is not too large. Additionally, graphs  should  prefer-
          ably be (almost) undirected (see entry below) and not so sparse that
          the cardinality of the edge set is close to the number of nodes.

          A class of such very sparse graphs is that of tree graphs. You might
          look  into  graph  visualization  software  and  research if you are
          interested in decomposing trees into 'tight' subtrees.

          The diameter criterion could be  violated  by  neighbourhood  graphs
          derived  from  vector  data.  In the specific case of 2 and 3 dimen-
          sional data, you might  be  interested  in  image  segmentation  and
          boundary  detection,  and  for  the  general case there is a host of
          other algorithms out there. [add]

          In case of weighted graphs, the notion of diameter is sometimes  not
          applicable.  Generalizing this notion requires inspecting the mixing
          properties of a subgraph induced by a natural cluster  in  terms  of
          its  spectrum. However, the diameter statement is something grounded
          on heuristic considerations (confirmed by practical evidence [4]) to
          begin with, so you should probably forget about mixing properties.

   3.8    What makes a good input graph?  How do I construct the similarities?
          How to make them satisfy this Markov condition?

          To begin with the last one: you need not and must not make the input
          graph such that it is stochastic aka Markovian [term]. What you need
          to do is make a graph that is preferably symmetric/undirected,  i.e.
          where  s(i,j)  =  s(j,i)  for all nodes i and j. It need not be per-
          fectly undirected, see the following faq for a discussion  of  that.
          mcl will work with the graph of random walks that is associated with
          your input graph, and that is the natural state of affairs.

          The input graph should preferably be honest in  the  sense  that  if
          s(x,y)=N  and  s(x,z)=200N (i.e. the similarities differ by a factor
          200), then this should really reflect that the similarity of y to  x
          is neglectible compared with the similarity of z to x.

          For  the rest, anything goes. Try to get a feeling by experimenting.
          Sometimes it is a good idea to filter out high-frequency and/or low-
          frequency  data,  i.e.  nodes  with  either  very many neighbours or
          extremely few neighbours.

   3.9    My input graph is directed. Is that bad?

          It depends. The class of directed graphs can be viewed as a spectrum
          going from undirected graphs to uni-directed graphs. Uni-directed is
          terminology I am inventing here, which I define as the property that
          for  all  node pairs i, j, at least one of s(i,j) or s(j,i) is zero.
          In other words, if there is an arc going from  i  to  j  in  a  uni-
          directed  graph,  then  there  is no arc going from j to i. I call a
          node pair i, j, almost uni-directed if  s(i,j)  <<  s(j,i)  or  vice
          versa, i.e. if the similarities differ by an order of magnitude.

          If  a  graph  does  not have (large) subparts that are (almost) uni-
          directed, have a go with mcl. Otherwise, try to make your graph less
          uni-directed.   You are in charge, so do anything with your graph as
          you see fit, but preferably abstain from  feeding  mcl  uni-directed
          graphs.

   3.10   Why  does  mcl  like  undirected graphs and why does it dislike uni-
          directed graphs so much?

          Mathematically, the mcl iterands will be nice when the  input  graph
          is  symmetric,  where nice is in this case diagonally symmetric to a
          semi-positive definite matrix (ignore as  needed).  For  one  thing,
          such  nice  matrices can be interpreted as clusterings in a way that
          generalizes the interpretation of the mcl limit as a clustering  (if
          you   are   curious  to  these  intermediate  clusterings,  see  faq
          entry 8.3).  See the REFERENCES section for pointers to mathematical
          publications.

          The  reason  that  mcl  dislikes uni-directed graphs is not very mcl
          specific, it has more to do  with  the  clustering  problem  itself.
          Somehow,  directionality  thwarts  the  notion of cluster structure.
          [add].

   3.11   How do I check that my graph/matrix is symmetric/undirected?

          Whether your graph is created by third-party software or  by  custom
          sofware written by someone you know (e.g. yourself), it is advisable
          to test whether the software generates symmetric matrices. This  can
          be  done as follows using the mcx utility, assuming that you want to
          test the matrix stored in file matrix.mci. The mcx utility should be
          available on your system if mcl was installed in the normal way.

          mcx /matrix.mci lm tp -1 mul add /check wm

          This  loads  the graph/matrix stored in matrix.mci into mcx's memory
          with the mcx lm primitive. - the leading slash is  how  strings  are
          introduced  in  the stack language interpreted by mcx. The transpose
          of that matrix is then pushed on the stack with the tp primitive and
          multiplied  by minus one. The two matrices are added, and the result
          is written to the file check.  The transposed matrix is the mirrored
          version   of   the  original  matrix  stored  in  matrix.mci.  If  a
          graph/matrix is undirected/symmetric, the mirrored image  is  neces-
          sarily  the  same,  so  if you subtract one from the other it should
          yield an all zero matrix.

          Thus, the file check should look like this:

          (mclheader
          mcltype matrix
          dimensions <num>x<num>
          )
          (mclmatrix
          begin
          )

          Where <num> is the same as in the file matrix.mci. If  this  is  not
          the case, find out what's prohibiting you from feeding mcl symmetric
          matrices. Note that any nonzero entries found in the  matrix  stored
          as check correspond to node pairs for which the arcs in the two pos-
          sible directions have different weight.

                                  Speed and complexity

   4.1    How fast is mcl/MCL?

          It's fast - here is how and why. Let N be the number of nodes in the
          input  graph.  A straigtforward implementation of MCL will have time
          and space complexity respecively O(N^3) (i.e. cubic in N) and O(N^2)
          (quadratic in N).  So you don't want one of those.

          mcl  implements  a slightly perturbed version of the MCL process, as
          discussed in section Resource tuning / accuracy.  Refer to that sec-
          tion  for  a  more extensive discussion of all the aspects involved.
          This section is only concerned with the high-level  view  of  things
          and the nitty gritty complexity details.

          While  computing  the square of a matrix (the product of that matrix
          with itself), mcl keeps the matrix sparse by allowing a certain max-
          imum number of nonzero entries per stochastic column. The maximum is
          one of the mcl parameters, and it is typically set somewhere between
          500 and 1000.  Call the maximum K.

          mcl's time complexity is governed by the complexity of matrix squar-
          ing.  There are two sub-algorithms to consider.  The  first  is  the
          algorithm responsible for assembling a new vector during matrix mul-
          tiplication. This algorithm has worst case  complexity  O(K^2).  The
          pruning  algorithm  (which  uses heap selection) has worst case com-
          plexity O(L*log(K)), where L is how large a  newly  computed  matrix
          column can get before it is reduced to at most K entries. L is bound
          by the smallest of the two numbers N and K^2 (the square of K),  but
          on  average  L  will  be  much smaller than that, as the presence of
          cluster structure aids in keeping the factor L low. [Related to this
          is  the fact that clustering algorithms are actually used to compute
          matrix splittings that minimize  the  number  of  cross-computations
          when  carrying out matrix multiplication among multiple processors.]
          In actual cases of heavy usage, L is of order in the tens  of  thou-
          sands, and K is in the order of several hundreds up to a thousand.

          It  is  safe to say that in general the worst case complexity of mcl
          is of order O(N*K^2); for extremely  tight  and  dense  graphs  this
          might  become  O(N*N*log(K)). Still, these are worst case estimates,
          and observed running times for actual usage  are  much  better  than
          that.  (refer to faq 4.2).

          In  this  analysis, the number of iterations required by mcl was not
          included. It is nearly always far below  100.  Only  the  first  few
          iterations  are  genuinely  time consuming; the first few iterations
          (some number below 10) are usually responsible for more than 95 per-
          cent of the running time.

          The  process  of removing the smallest entries of a vector is called
          pruning. mcl provides extensive facilities for monitoring  and  con-
          trolling  the effect of pruning, and it will output statistics and a
          summary once it is done. More information is provided in the pruning
          section of the mcl manual and Section 5 in this FAQ.

          The space complexity is of order O(N*K).

   4.2    What statistics are available?

          Few.  Some  experiments are described in [4], and [5] mentions large
          graphs being clustered in very reasonable time. In protein  cluster-
          ing,  mcl  has  been applied to graphs with up to one million nodes,
          and on high-end hardware such graphs can be clustered within  a  few
          hours.

   4.3    Does this implementation need to sort vectors?

          No, it does not. You might expect that one needs to sort a vector in
          order to obtain the K  largest  entries,  but  a  simpler  mechanism
          called  heap selection does the job nicely.  Selecting the K largest
          entries from a set of L by sorting would require O(L*log(L))  opera-
          tions; heap selection requires O(L*log(K)) operations.

   4.4    mcl does not compute the ideal MCL process!

          Indeed  it  does not. What are the ramifications? Several entries in
          section Resource tuning / accuracy discuss this issue. For a  synop-
          sis, consider two ends of a spectrum.

          On the one end, a graph that has very strong cluster structure, with
          clearly (and not necessarity fully)  separated  clusters.  This  mcl
          implementation  will certainly retrieve those clusters if the graphs
          falls into the category of graphs for which mcl is  applicable.   On
          the other end, consider a graph that has only weak cluster structure
          superimposed on a background of a more or less random  graph.  There
          might sooner be a difference between the clustering that should ide-
          ally result and the one computed by mcl. Such a graph  will  have  a
          large  number  of  whimsical  nodes that might end up either here or
          there, nodes that are of a peripheral  nature,  and  for  which  the
          (cluster)  destination  is  very  sensitive to fluctutations in edge
          weights or algorithm parametrizations (any algorithm, not just mcl).

          One  can  say  that  the  perturbation effect of the pruning process
          applied by mcl is just a small source of noise. Additionally, graphs
          at  the noisy end of the spectrum will generally be very susceptible
          to changes in parametrization of the MCL algorithm and process,  and
          the  perturbation caused by computing an imperfect process will gen-
          erally be small compared with the effect  of  changing  parametriza-
          tions.

          Of  course,  there is the issue of very large and very dense graphs.
          The act of pruning will have a larger impact as graphs  grow  larger
          and denser.  Obviously, mcl will have trouble dealing with such very
          large and very dense graphs - so will other methods.

          Finally, there is the engineering approach, which offers the  possi-
          bility  of  pruning  a  whole lot of speculation. Do the experiments
          with mcl, try it out, and see what's there to like and dislike.

   4.5    I've read elsewhere that MCL is slow [compared with XYZ]

          Presumably, they did not know mcl, and did not read the parts in [1]
          and  [2]  that discuss implementation. Perhaps they assume or insist
          that the only way to implement MCL is to implement  the  ideal  pro-
          cess. And there is always the genuine possibility of a really stupi-
          fyingly fast algorithm.  [One such  publication  is  Ulrik  Brandes,
          Marco Gaertler, and Dorothea Wagner: Experiments on Graph Clustering
          Algorithms. Proc. 11th Europ. Symp. Algorithms (ESA  '03),  Springer
          LNCS].

                               Resource tuning / accuracy

   5.1    What do you mean by resource tuning?

          mcl  computes a process in which stochastic matrices are alternately
          expanded and inflated. Expansion is nothing but standard matrix mul-
          tiplication,  inflation  is a particular way of rescaling the matrix
          entries.

          Expansion causes problems in terms of both time and space. mcl works
          with  matrices of dimension N, where N is the number of nodes in the
          input graph.  If no precautions are taken, the number of entries  in
          the  mcl iterands (which are stochastic matrices) will soon approach
          the square of N. The time it takes to compute such a matrix will  be
          proportional  to  the  cube  of  N.  If your input graph has 100.000
          nodes, the  memory  requirements  become  infeasible  and  the  time
          requirements become impossible.

          What  mcl  does  is  perturbing  the process it computes a little by
          removing the smallest entries - it keeps its matrices sparse.   This
          is  a  natural  thing  to  do,  because the matrices are sparse in a
          weighted sense (a very high proportion of  the  stochastic  mass  is
          contained  in  relatively few entries), and the process converges to
          matrices that are extremely sparse, with  usually  no  more  than  N
          entries.   It  is  thus  known that the MCL iterands are sparse in a
          weighted sense and are usually very close to truly sparse  matrices.
          The  way  mcl  perturbs  its matrices is by the strategy of pruning,
          selection, and recovery that is extensively  described  in  the  mcl
          manual  page.  The question then is: What is the effect of this per-
          turbation on the resulting clustering, i.e. how would the clustering
          resulting  from  a  perfectly  computed mcl process compare with the
          clustering I have on disk?  Faq entry 5.3 discusses this issue.

          The amount of resources used by mcl is bounded in terms of the maxi-
          mum number of neighbours a node is allowed to have during all compu-
          tations.  Equivalently,  this  is  the  maximum  number  of  nonzero
          entries  a matrix column can possibly have. This number, finally, is
          the maximum of the the values  corresponding  with  the  -S  and  -R
          options.   The  latter  two are listed when using the -z option (see
          faq 9.1).

   5.2    How do I compute the maximum amount of RAM needed by mcl?

          It is rougly equal to

          2 * s * K * N

          bytes, where 2 is the number of matrices held in memory by mcl, s is
          the  size of a single cell (c.q. matrix entry or node/arc specifica-
          tion), N is the number of nodes in the input graph, and where  K  is
          the  maximum  of the values corresponding with the -S and -R options
          (and this assumes that the average node degree in  the  input  graph
          does  not exceed K either). The value of s can be found by using the
          -z option. It is listed in one of the first lines of  the  resulting
          output.  s equals the size of an int plus the size of a float, which
          will be 8 on most systems.  The estimate above will in most cases be
          way too pessimistic (meaning you do not need that amount of memory).

          The -how-much-ram option is provided by mcl for computing the  bound
          given  above.  This options takes as argument the number of nodes in
          the input graph.

          The theoretically more precise upper bound is slightly larger due to
          overhead. It is something like

          ( 2 * s * (K + c)) * N

          where c is 5 or so, but one should not pay attention to such a small
          difference anyway.

   5.3    How much does the mcl clustering differ from the clustering  result-
          ing from a perfectly computed MCL process?

          For  graphs  with up until a few thousand nodes a perfectly computed
          MCL process can be achieved by abstaining  from  pruning  and  doing
          full-blown matrix arithmetic. Of course, this still leaves the issue
          of machine precision, but let us wholeheartedly ignore that.

          Such experiments give evidence (albeit incidental) that  pruning  is
          indeed  really  what  it is thought to be - a small perturbation. In
          many cases,  the  'approximated'  clustering  is  identical  to  the
          'exact'  clustering.  In  other  cases,  they are very close to each
          other in terms of the metric  split/join  distance  as  computed  by
          clmdist(1).   Some  experiments with randomly generated test graphs,
          clustering, and pruning are described in [4].

          On a different level of abstraction, note that perturbations of  the
          inflation parameter will also lead to perturbations in the resulting
          clusterings, and surely, large changes in  the  inflation  parameter
          will  in general lead to large shifts in the clusterings. Node/clus-
          ter pairs that are different for  the  approximated  and  the  exact
          clustering  will  very  likely  correspond  with nodes that are in a
          boundary region between two or more clusters anyway, as the  pertur-
          bation  is  not likely to move a node from one core of attraction to
          another.

          Faq entry 5.6 has more to say about this subject.

   5.4    How do I know that I am using enough resources?

          In mcl parlance, this becomes how do I know that my -scheme  parame-
          ter is high enough or more elaborately how do I know that the values
          of the {-P, -S, -R, -pct} combo are high enough?

          There are several aspects. First, watch the jury marks  reported  by
          mcl  when  it's  done.  The jury marks are three grades, each out of
          100. They indicate how well pruning went. If the marks  are  in  the
          seventies,  eighties,  or  nineties,  mcl is probably doing fine. If
          they are in the eighties or lower, try to see if  you  can  get  the
          marks higher by spending more resources (e.g. increase the parameter
          to the -scheme option).

          Second, you can do multiple mcl runs for different resource schemes,
          and  compare  the  resulting  clusterings  using clmdist(1). See the
          clmdist manual for a case study.

   5.5    Where is the mathematical analysis of this mcl pruning strategy?

          There is none. [add]

          Ok, the next entry gives an engineer's rule of thumb.

   5.6    What qualitative statements can be made about the effect of pruning?

          The  more severe pruning is, the more the computed process will tend
          to converge prematurely. This will generally lead  to  finer-grained
          clusterings.   In cases where pruning was severe, the mcl clustering
          will likely be closer to a clustering ideally resulting from another
          MCL process with higher inflation value, than to the clustering ide-
          ally resulting from the same MCL process. Strong support for this is
          found in a general observation illustrated by the following example.
          Suppose u is a stochastic vector resulting from expansion:

          u   =  0.300 0.200 0.200 0.100 0.050 0.050 0.050 0.050

          Applying inflation with inflation value 2.0 to u gives

          v   =  0.474 0.211 0.211 0.053 0.013 0.013 0.013 0.013

          Now suppose we first apply pruning to u  such  that  the  3  largest
          entries  0.300, 0.200 and 0.200 survive, throwing away 30 percent of
          the stochastic mass (which is quite a lot by all means).  We rescale
          those three entries and obtain

          u'  =  0.429 0.286 0.286 0.000 0.000 0.000 0.000 0.000

          Applying inflation with inflation value 2.0 to u' gives

          v'  =  0.529 0.235 0.235 0.000 0.000 0.000 0.000 0.000

          If  we had applied inflation with inflation value 2.5 to u, we would
          have obtained

          v'' =  0.531 0.201 0.201 0.038 0.007 0.007 0.007 0.007

          The vectors v' and v'' are much closer to each other than  the  vec-
          tors v' and v, illustrating the general idea.

          In  practice,  mcl  should  (on average) do much better than in this
          example.

   5.7    At different high resource levels my clusterings are not  identical.
          How can I trust the output clustering?

          Did  you  read  all  other entries in this section? That should have
          reassured you somewhat, except perhaps for Faq answer 5.5.

          You need not feel uncomfortable with  the  clusterings  still  being
          different at high resource levels, if ever so slightly. In all like-
          lihood, there are anyway nodes which are not in any core of  attrac-
          tion,  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.

          By the way, you do know all about clmdist(1), don't you? Because the
          statement  that  clusterings are not identical should be quantified:
          How much do they differ? This issue is discussed in  the  clmdist(1)
          manual  page  -  clmdist gives you a robust measure for the distance
          (dissimilarity) between two clusterings.

          There are other means of gaining trust in a  clustering,  and  there
          are  different issues at play. There is the matter of how accurately
          this mcl computed the mcl process, and there is the  matter  of  how
          well  the chosen inflation parameter fits the data. The first can be
          judged by looking at the jury marks (faq 5.4) and  applying  clmdist
          to  different  clusterings.  The second can be judged by measurement
          (e.g. use clminfo(1)) and/or inspection (use your judgment).

                               Tuning cluster granularity

   6.1    How do I tune cluster granularity?

          There are several ways for influencing  cluster  granularity.  These
          ways and their relative merits are successively discussed below. The
          clmdist(1) manual contains an example of doing multiple mcl runs for
          finding  granularily  different  clusterings,  using the most common
          approach, namely that of varying inflation.

   6.2    The effect of inflation on cluster granularity.

          The main handle for changing inflation is the  -I  option.  This  is
          also the principal handle for regulating cluster granularity. Unless
          you are mangling huge graphs it could be the  only  mcl  option  you
          ever need besides the output redirection option -o.

          Increasing  the value of -I will increase cluster granularity.  Con-
          ceivable values are from 1.1 to 5.0 or so, but the range of suitable
          values  will  certainly depend on your input graph. For many graphs,
          1.1 will be far too low, and for many other graphs, 5.0 will be  far
          too  high.  You will have to find the right value or range of values
          by experimenting, using your judgment, and using  measurement  tools
          such  as  clmdist(1) and clminfo(1). The default 2.0 is a good value
          to begin the experimental stage with.

          For experiments that are more subtle with respect to inflation,  mcl
          provides the -i option in conjunction with the -l (small letter ell)
          option. Do this only if you have the  intention  of  playing  around
          with  mcl  in order to study the characteristics of the process that
          it computes, and maybe, just maybe, use it in a production  environ-
          ment if you find it useful. In the first vein, you may be interested
          to know that mcx(1) is a stack  language/interpreter  in  which  the
          entire  MCL algorithm can be written in three lines of code. It pro-
          vides comprehensive access to the MCL graph  and  matrix  libraries.
          However,  the mcx interface to the MCL pruning facilities is not yet
          satisfactory at this time.

   6.3    The effect of similarity distribution homogeneity on cluster  granu-
          larity.

          How  similarities  in  the  input  graph  were derived, constructed,
          adapted, filtered (et cetera) will affect cluster  granularity.   It
          is important that the similarities are honest; refer to faq 3.8.

          Another  issue  is  that  homogeneous similarities tend to result in
          more coarse-grained clusterings. You can make a set of  similarities
          more  homogeneous by applying some function to all of them, e.g. for
          all pairs of nodes (x y) replace S(x,y) by the square root, the log-
          arithm,  or some other convex function. Note that you need not worry
          about scaling, i.e. the possibly large changes in magnitude  of  the
          similarities. MCL is not affected by absolute magnitudes, it is only
          affected by magnitudes taken relative to each other.

          As of version 03-154, mcl supports the pre-inflation  -pi f  option.
          Make a graph more homogeneous with respect to the weight function by
          using -pi with argument f somewhere in the interval [0,1] - 0.5  can
          be  considered  a reasonable first try.  Make it less homogeneous by
          setting f somewhere in the interval [1,10].  In this  case  5  is  a
          reasonable starting point.

   6.4    The effect of initial centering on cluster granularity.

          This  refers  to  the  -c  parameter,  which adds loops to the input
          graph. Its default value is 1.0, which results in loops of a somehow
          'neutral' weight to be added. If you need to really fine-tune granu-
          larity, this option can be of use, otherwise you should abstain from
          using it.  Increasing its value will increase cluster granularity.

          Conceivable/normal  values  are in the range 1.0 to 5.0, but nothing
          stops you from going higher or slightly lower. Going lower than  0.5
          is definitely not a good idea.

          If  you  are into clustering at high levels of granularity, there is
          the issue whether to  further  increase  -I,  or  whether  to  start
          increasing  or  further  increase  -c.  It will really depend on the
          characteristics of the graph you are working with, and at this point
          in  time I cannot even give advice in terms of a general categoriza-
          tion. Experiment, learn, and let me know the results if you like.

                             Implementing the MCL algorithm

   7.1    How easy is it to implement the MCL algorithm?

          Very easy, if you will be doing small graphs only, say up to  a  few
          thousand entries at most. These are the basic ingredients:

          o  Adding  loops  to  the  input  graph,  conversion to a stochastic
             matrix.
          o  Matrix multiplication and matrix inflation.
          o  The interpretation function mapping MCL limits onto  clusterings.

          These must be wrapped in a program that does graph input and cluster
          output, alternates multiplication (i.e. expansion) and inflation  in
          a loop, monitors the matrix iterands thus found, quits the loop when
          convergence is detected, and interprets the last iterand.

          Implementing matrix muliplication is a standard exercise. Implement-
          ing  inflation  is  nearly trivial. The hardest part may actually be
          the interpretation function, because you need to  cover  the  corner
          cases  of  overlap and attractor systems of cardinality greater than
          one.

          In Mathematica or Maple, this should be doable in at most  50  lines
          of  code.   For perl you may need 50 more lines - note that MCL does
          not use intricate and expensive operations such as matrix  inversion
          or matrix reductions. In lower level languages such as C a basic MCL
          program may need a few hundred lines,  but  the  largest  part  will
          probably be input/output and interpretation.

          To  illustrate all these points, mcl now ships with minimcl, a small
          perl script that implements mcl for educational purposes.  Both  its
          line  and statement count well exceed the estimation made above - it
          was not coded to be maximally succint. Its structure is very  simple
          though and should be easy to follow.

          Implementing  the basic MCL algorithm makes a nice programming exer-
          cise. However, if you need an implementation that scales to  several
          hundreds of thousands of nodes and possibly beyond, then your duties
          become much heavier. This is because one needs to prune MCL iterands
          (c.q.  matrices)  such  that  they  remain sparse. This must be done
          carefully and preferably in such a  way  that  a  trade-off  between
          speed,  memory  usage, and potential losses or gains in accuracy can
          be controlled via monitoring and logging  of  relevant  characteris-
          tics.   Some other points are i) support for threading via pthreads,
          openMP, or some other parallel programming API.  ii)  a  robust  and
          generic  interpretation  function is written in terms of weakly con-
          nected components.

                  Cluster overlap / MCL iterand cluster interpretation

   8.1    Introduction

          A natural mapping exists of MCL iterands to DAGs  (directed  acyclic
          graphs). This is because MCL iterands are generally diagonally posi-
          tive semi-definite - see [3].  Such a DAG can be  interpreted  as  a
          clustering,  simply  by  taking as cores all endnodes (sinks) of the
          DAG, and by attaching to each core all the nodes that reach it. This
          procedure may result in clusterings containing overlap.

          In  the MCL limit, the associated DAG has in general a very degener-
          ated form, which induces overlap only on very  rare  occasions  (see
          faq entry 8.2).

          Interpreting  mcl  iterands  as clusterings may well be interesting.
          Few experiments have been done so far. It is clear though that early
          iterands  generally  contain  the  most overlap (when interpreted as
          clusterings).  Overlap  dissappears  soon  as  the   iterand   index
          increases.  For  more information, consult the other entries in this
          section and the clmimac manual page.

   8.2    Can the clusterings returned by mcl contain overlap?

          No. Clusterings resulting from the abstract  MCL  algorithm  may  in
          theory  contain  overlap,  but  the  default  behaviour in mcl is to
          remove it should it occur, by allocating the nodes in overlap to the
          first  cluster  in  which  they  are seen. mcl will warn you if this
          occurs. This behaviour is switched  off  by  supplying  --keep-over-
          lap=yes.

          Do  note  that  overlap  is mostly a theoretical possibility.  It is
          conjectured that it requires the presence of very strong  symmetries
          in  the input graph, to the extent that there exists an automorphism
          of the input graph mapping the overlapping part onto itself.

          It is possible to construct (highly symmetric) input graphs  leading
          to  cluster  overlap.  Examples  of overlap in which a few nodes are
          involved are easy to construct; examples with many nodes are  excep-
          tionally hard to construct.

          Clusterings associated with intermediate/early MCL iterands may very
          well contain overlap, see the introduction in this section and other
          entries.

   8.3    How do I obtain the clusterings associated with MCL iterands?

          There are two options. If you are interested in clusterings contain-
          ing overlap, you should go for the second. If not,  use  the  first,
          but beware that the resulting clusterings may contain overlap.

          The first solution is to use -dump cls (probably in conjunction with
          either -L or -dumpi in order to limit the number of  matrices  writ-
          ten).  This will cause mcl to write the clustering generically asso-
          ciated with each iterand to file. The -dumpstem option may be conve-
          nient as well.

          The  second  solution  is  to  use  the -dump ite option (-dumpi and
          -dumpstem may be of use again). This will cause  mcl  to  write  the
          intermediate  iterands  to  file.  After that, you can apply clmimac
          (interpret matrix as clustering) to those iterands.  clmimac  has  a
          -tight  parameter  which affects the mapping of matrices to cluster-
          ings. It takes a value between 0 and 100 as argument. The default is
          100  and  corresponds  with  the strict mapping. Lowering the -tight
          value will generally result in clusterings containing more  overlap.
          This  will  have  the  largest effect for early iterands; its effect
          will diminish as the iterand index increases.

          When set to 0, the -tight parameter results in the clustering  asso-
          ciated  with  the DAG associated with an MCL iterand as described in
          [3]. This DAG is pruned (thus possibly resulting in less overlap  in
          the clustering) by increasing the -tight parameter. [add]

                                     Miscellaneous

   9.1    How do I find the default settings of mcl?

          Use  -z  to  find out the actual settings - it shows the settings as
          resulting from the command line options (e.g. the  default  settings
          if no other options are given).

   9.2    What's next?

          I'd  like  to  port  MCL to cluster computing, using one of the PVM,
          MPI, or openMP frameworks.  For the 1.002 release,  mcl's  internals
          were  rewritten  to  allow  more  general matrix computations. Among
          other things, mcl's data structures and primitive operations are now
          more  suited  to be employed in a distributed computing environment.
          However, much remains to be done before mcl can operate in  such  an
          environment.

          At  some  point in the future a second, xml-based, interchange input
          format may be introduced.

          If you feel that mcl should support some other standard matrix  for-
          mat, let us know.

  BUGS
          This  FAQ  tries  to compromise between being concise and comprehen-
          sive. The collection of answers should preferably cover the universe
          of questions at a pleasant level of semantic granularity without too
          much overlap. It should offer value to people interested in cluster-
          ing  but without sound mathematical training. Therefore, if this FAQ
          has not failed somewhere, it must have failed.

          Send criticism and missing questions for consideration to mcl-faq at
          micans.org.

  AUTHOR
          Stijn van Dongen.

  SEE ALSO
          mclfamily(7) for an overview of all the documentation and the utili-
          ties in the mcl family.

          mcl's home at http://micans.org/mcl/.

  REFERENCES
          [1] Stijn van Dongen. Graph Clustering by Flow Simulation.  PhD the-
          sis, University of Utrecht, May 2000.
          http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm

          [2]  Stijn  van  Dongen.  A cluster algorithm for graphs.  Technical
          Report INS-R0010, National Research Institute  for  Mathematics  and
          Computer Science in the Netherlands, Amsterdam, May 2000.
          http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z

          [3]  Stijn  van  Dongen. A stochastic uncoupling process for graphs.
          Technical Report INS-R0011, National Research Institute  for  Mathe-
          matics and Computer Science in the Netherlands, Amsterdam, May 2000.
          http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z

          [4] 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

          [5]  Enright  A.J., Van Dongen S., Ouzounis C.A.  An efficient algo-
          rithm for large-scale detection of protein families,  Nucleic  Acids
          Research 30(7):1575-1584 (2002).

  NOTES
          This    page    was    generated    from    ZOEM    manual   macros,
          http://micans.org/zoem. Both html and roff pages can be created from
          the  same source without having to bother with all the usual conver-
          sion problems, while keeping some level  of  sophistication  in  the
          typesetting.



  MCL FAQ 1.006, 06-058             27 Feb 2006                       MCL FAQ(7)
