Sorry, my error in my first post. I've since re-checked my large dataset and although there are partial duplications between some vectors output from maximal.cliques(), there are no cases where the entire contents of one vector is the subset of another. So no bug - just a bug in my understanding!!
But I'm still scratching my head in how to solve my problem. I need to extract clusters where all within-cluster members are completely connected and a member can only exist in one cluster. Maybe it's a community detection solution ? On 18 November 2013 17:54, Gábor Csárdi <[email protected]> wrote: > On Mon, Nov 18, 2013 at 12:46 PM, Tony Larson <[email protected]> > wrote: > > Hmmm - I think I am misunderstanding fundamentally what > maximal.cliques() is > > doing - I assumed there should be no overlap but of course there will be > as > > vertices can be shared amongst cliques! What I am trying to achieve is > > effectively clustering by pulling out complete subgraphs, but vertices > > should appear uniquely in the final set of clusters. Can you suggest a > way > > of doing this? > > I guess what makes sense depends on your application. In general > cliques will overlap, so just taking the maximal or largest cliques is > definitely not good. > > Overlap is one thing, but in your first email you had a reported > maximal clique that was a subset of another reported maximal clique. > If this happens, then it is a bug. So if you could reproduce it, that > would be great, even if the maximal clique finder was rewritten from > scratch in our development version, and it is unlikely that we'll have > the same error form version 0.7. > > Gabor > > > One thought I had was to recursively calculate the largest.cliques(), > > delete the associated vertices, and continue until there are no vertices > > left. However, I am still stuck with the problem that largest.cliques() > > can return more than one clique (if vector lengths are equal) and these > can > > contain overlapping vertices, so there still has to be a choice made of > > which vertices to use... > > > > > > On 18 November 2013 17:23, Gábor Csárdi <[email protected]> wrote: > >> > >> On Mon, Nov 18, 2013 at 11:57 AM, Tony Larson <[email protected]> > >> wrote: > >> > OK, > >> > Here's a toy example (and on the latest igraph) - still not behaving > as > >> > expected?? > >> > >> You need to set the random seed to make this example reproducible. > >> > >> >> mat <- matrix(sample(c(0,1), 100 * 100, replace = TRUE, prob = c(0.8, > >> >> 0.2)), 100, 100) > >> >> g <- graph.adjacency(mat, mode = "undirected", weighted = TRUE, diag > = > >> >> FALSE) > >> >> mc <- maximal.cliques(g) > >> >> any(duplicated(unlist(mc))) > >> > >> No, this is not good, you just create a long vector from all clique > >> vertices, and there will be duplicates if there is overlap.... you > >> need to check whether one is a subset of any of the others. > >> > >> G. > >> > >> [...] > >> > >> _______________________________________________ > >> igraph-help mailing list > >> [email protected] > >> https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > > > > > > > -- > > *************************************** > > Dr. Tony R. Larson > > CNAP > > Department of Biology, Area 7 > > University of York > > Wentworth Way > > Heslington > > York YO10 5DD > > UK > > > > Tel: +44(0)1904 328 826 (office) > > Tel: +44(0)7833 471 685 (mobile) > > Fax: +44(0)1904 328 762 > > E-mail: [email protected] > > *************************************** > > > > Times Higher Education University of the Year 2010 > > > > > > Disclaimer: This email and any > > attachment(s) are strictly confidential > > and contain information intended only > > for the use of the individual(s) named > > above. If you are not the intended > > recipients please delete this message > > from your system, do not use or > > disclose the information in any way and > > notify us by return e-mail. > > > > > > _______________________________________________ > > igraph-help mailing list > > [email protected] > > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > -- *************************************** Dr. Tony R. Larson CNAP Department of Biology, Area 7 University of York Wentworth Way Heslington York YO10 5DD UK Tel: +44(0)1904 328 826 (office) Tel: +44(0)7833 471 685 (mobile) Fax: +44(0)1904 328 762 E-mail: [email protected] *************************************** Times Higher Education University of the Year 2010 Disclaimer: This email and any attachment(s) are strictly confidential and contain information intended only for the use of the individual(s) named above. If you are not the intended recipients please delete this message from your system, do not use or disclose the information in any way and notify us by return e-mail.
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