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Re: [igraph] Re: igraph-help Digest, Vol 42, Issue 11
|
From: |
Gábor Csárdi |
|
Subject: |
Re: [igraph] Re: igraph-help Digest, Vol 42, Issue 11 |
|
Date: |
Fri, 15 Jan 2010 20:09:25 +0100 |
On Fri, Jan 15, 2010 at 6:40 PM, Vijaykumar Muley <address@hidden> wrote:
> Dear Gabor,
>
> Thanks for your help. I am confused as to how to determine the value for
> merges. Can you suggest me how to do this ?
Modularity value? See an example here:
http://igraph.sourceforge.net/screenshots2.html#10
You don't need the graphics stuff, only the calculation of the 'q' modularity.
> are there faster methods in
> igraph to determine the edge-betweenness.
No, there is no faster method.
> I have to do this operation for
> 500 graphs with similar interaction statistics (node 4000, edge 60,000).
This sounds pretty difficult, maybe impossible. You will need some
fine-tuned code and a computer cluster. And even then, it might be
impossible.
I suggest to use another community detection method, all of them are
faster than this one.
Best,
Gabor
> Thanks and Regards.
>
>
>
> On Fri, Jan 15, 2010 at 10:31 PM, <address@hidden> wrote:
>>
>> Send igraph-help mailing list submissions to
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>>
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>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of igraph-help digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Question about vector (zhengjun chen)
>> 2. Re: Question about vector (Tamas Nepusz)
>> 3. question about installing C packages (gunce orman)
>> 4. Re: question about installing C packages (Tamas Nepusz)
>> 5. Re: question about installing C packages (gunce orman)
>> 6. Re: question about installing C packages (Tamas Nepusz)
>> 7. Re: question about installing C packages (gunce orman)
>> 8. segfault in self-test (Neal Becker)
>> 9. Re: question about installing C packages (Tamas Nepusz)
>> 10. Re: question about installing C packages (gunce orman)
>> 11. Re: Question about vector (zhengjun chen)
>> 12. edge_betweenness community detection (zhengjun chen)
>> 13. Re: edge_betweenness community detection (G?bor Cs?rdi)
>> 14. Re: edge_betweenness community detection (Tamas Nepusz)
>> 15. Re: edge_betweenness community detection (G?bor Cs?rdi)
>> 16. Query regarding modularity calculations (Vijaykumar Muley)
>> 17. Re: Query regarding modularity calculations (G?bor Cs?rdi)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 14 Jan 2010 22:17:00 -0500
>> From: zhengjun chen <address@hidden>
>> Subject: [igraph] Question about vector
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>> I have a problem with vector data type. After using community structure
>> detection algorithm, I got the membership of vertices. This information is
>> written into file.
>> Then I want to calculate the modularity for this community division.
>> So I extract membership information from the file, and assign them to a
>> vector. The code is in the following:
>>
>> int member[12000] ;
>> ..........
>> for(j=0; j<nodes; j++) // nodes is the number of nodes in the graph
>> {
>> igraph_vector_set( &membership, j, (double) member [j] ); // member
>> array stores the membership of vertices
>> printf( "%f\n", (double)VECTOR(membership)[j] );
>> }
>> igraph_modularity( &graph, &membership, &modu, NULL );
>>
>> The vector membership is initialized correctly. But when running
>> igraph_modularity() function, it reports the following errors:
>>
>> *** glibc detected *** ./modularity: malloc(): memory corruption (fast):
>> 0x08084318 ***
>> ======= Backtrace: =========
>> /lib/i686/nosegneg/libc.so.6[0x45dbfc6e]
>> /lib/i686/nosegneg/libc.so.6(__libc_calloc+0x94)[0x45dc0874]
>> /usr/local/lib/libigraph.so.0(igraph_vector_init+0x33)[0xeb1143]
>> /usr/local/lib/libigraph.so.0(igraph_modularity+0x5f)[0xf0600f]
>> ./modularity[0x8048980]
>> /lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x45d6ddec]
>> ./modularity[0x8048691]
>>
>> So, I am a bit confused. Where is wrong?
>> --
>> Thanks
>> zhengjun
>>
>> Graduate research assistant
>> Dept of Computer Science and Engineering
>> Lehigh University
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 15 Jan 2010 10:30:52 +0000
>> From: Tamas Nepusz <address@hidden>
>> Subject: Re: [igraph] Question about vector
>> To: Help for igraph users <address@hidden>
>> Message-ID: <address@hidden>
>> Content-Type: text/plain; charset=us-ascii
>>
>> Hi,
>>
>> Please send a full code that reproduces the error. It might have
>> happened that your membership vector is not initialized properly for
>> instance. By the way, there is an easier way to treat a C array as an
>> igraph_vector_t, see:
>>
>> http://igraph.sourceforge.net/doc-0.5/html/ch06s02s05.html
>>
>> Make sure that you neither modify nor destroy vectors created this way.
>> Modifying the underlying array is fine.
>>
>> --
>> Tamas
>>
>>
>> > vector. The code is in the following:
>> >
>> > int member[12000] ;
>> > ..........
>> > for(j=0; j<nodes; j++) // nodes is the number of nodes in the
>> > graph
>> > {
>> > igraph_vector_set( &membership, j, (double) member [j] ); //
>> > member
>> > array stores the membership of vertices
>> > printf( "%f\n", (double)VECTOR(membership)[j] );
>> > }
>> > igraph_modularity( &graph, &membership, &modu, NULL );
>> >
>> > The vector membership is initialized correctly. But when running
>> > igraph_modularity() function, it reports the following errors:
>> >
>> > *** glibc detected *** ./modularity: malloc(): memory corruption (fast):
>> > 0x08084318 ***
>> > ======= Backtrace: =========
>> > /lib/i686/nosegneg/libc.so.6[0x45dbfc6e]
>> > /lib/i686/nosegneg/libc.so.6(__libc_calloc+0x94)[0x45dc0874]
>> > /usr/local/lib/libigraph.so.0(igraph_vector_init+0x33)[0xeb1143]
>> > /usr/local/lib/libigraph.so.0(igraph_modularity+0x5f)[0xf0600f]
>> > ./modularity[0x8048980]
>> > /lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x45d6ddec]
>> > ./modularity[0x8048691]
>> >
>> > So, I am a bit confused. Where is wrong?
>> > --
>> > Thanks
>> > zhengjun
>> >
>> > Graduate research assistant
>> > Dept of Computer Science and Engineering
>> > Lehigh University
>>
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 15 Jan 2010 12:47:30 +0200
>> From: gunce orman <address@hidden>
>> Subject: [igraph] question about installing C packages
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="utf-8"
>>
>> hello, I'm trying to install C packages of igraph for ubuntu 9.10, 64 bit
>> system... I've added the packages repository to my /etc/apt/source.list
>> as
>> mentioned your web page but I can't see any of the igraph packages in
>> synaptic manager... Is there something wrong?
>>
>> Thank you very much
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gnu.org/pipermail/igraph-help/attachments/20100115/d0507b28/attachment.html
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Fri, 15 Jan 2010 11:50:24 +0000
>> From: Tamas Nepusz <address@hidden>
>> Subject: Re: [igraph] question about installing C packages
>> To: Help for igraph users <address@hidden>
>> Message-ID: <address@hidden>
>> Content-Type: text/plain; charset=us-ascii
>>
>> > hello, I'm trying to install C packages of igraph for ubuntu 9.10, 64
>> > bit
>> > system... I've added the packages repository to my /etc/apt/source.list
>> > as
>> > mentioned your web page but I can't see any of the igraph packages in
>> > synaptic manager... Is there something wrong?
>> Did you run apt-get update after adding the repositories to
>> /etc/apt/sources.list?
>>
>> --
>> Tamas
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Fri, 15 Jan 2010 14:13:52 +0200
>> From: gunce orman <address@hidden>
>> Subject: Re: [igraph] question about installing C packages
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="utf-8"
>>
>> yes
>>
>> On Fri, Jan 15, 2010 at 1:50 PM, Tamas Nepusz <address@hidden> wrote:
>>
>> > > hello, I'm trying to install C packages of igraph for ubuntu 9.10, 64
>> > > bit
>> > > system... I've added the packages repository to my
>> > > /etc/apt/source.list
>> > as
>> > > mentioned your web page but I can't see any of the igraph packages in
>> > > synaptic manager... Is there something wrong?
>> > Did you run apt-get update after adding the repositories to
>> > /etc/apt/sources.list?
>> >
>> > --
>> > Tamas
>> >
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gnu.org/pipermail/igraph-help/attachments/20100115/45ceaaeb/attachment.html
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Fri, 15 Jan 2010 12:15:42 +0000
>> From: Tamas Nepusz <address@hidden>
>> Subject: Re: [igraph] question about installing C packages
>> To: Help for igraph users <address@hidden>
>> Message-ID: <address@hidden>
>> Content-Type: text/plain; charset=us-ascii
>>
>> > yes
>> In that case, I don't know what's wrong with Synaptic, but you can open
>> up a terminal and type:
>>
>> apt-get install libigraph libigraph-dev
>>
>> Does it work for you? If not, what's the error message?
>>
>> --
>> Tamas
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Fri, 15 Jan 2010 14:23:13 +0200
>> From: gunce orman <address@hidden>
>> Subject: Re: [igraph] question about installing C packages
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="utf-8"
>>
>> it is not working
>>
>> here the message:
>>
>> Reading package lists... Done
>> Building dependency tree
>> Reading state information... Done
>> E: Couldn't find package libigraph
>>
>>
>> On Fri, Jan 15, 2010 at 2:15 PM, Tamas Nepusz <address@hidden> wrote:
>>
>> > > yes
>> > In that case, I don't know what's wrong with Synaptic, but you can open
>> > up a terminal and type:
>> >
>> > apt-get install libigraph libigraph-dev
>> >
>> > Does it work for you? If not, what's the error message?
>> >
>> > --
>> > Tamas
>> >
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gnu.org/pipermail/igraph-help/attachments/20100115/b190d924/attachment.html
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Fri, 15 Jan 2010 07:32:01 -0500
>> From: Neal Becker <address@hidden>
>> Subject: [igraph] segfault in self-test
>> To: address@hidden
>> Message-ID: <address@hidden>
>> Content-Type: Text/Plain; charset="us-ascii"
>>
>> I maintain igraph (and python-igraph) on Fedora. python-igraph is now
>> failing
>> on (bleeding edge) rawhide builds. The report is here:
>>
>> https://bugzilla.redhat.com/attachment.cgi?id=383932
>>
>> failure is:
>> testAuthorityScore (igraph.test.structural.CentralityTests) ...
>> /var/tmp/rpm-
>> tmp.tE6lTM: line 30: 22398 Segmentation fault (core dumped)
>> PYTHONPATH=$RPM_BUILD_ROOT/usr/lib64/python2.6/site-packages
>> /usr/bin/python -
>> c 'import igraph.test; igraph.test.test();'
>>
>> The build target was x86_64. igraph is 0.5.2.
>>
>> I have no idea what might have changed in the enviroment that is causing
>> this,
>> perhaps a newer gcc?
>>
>> I have no direct access to a system configured in this way, these builds
>> are
>> done remotely on systems I have no direct access to.
>>
>> I wonder if anyone has seen a problem like this?
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Fri, 15 Jan 2010 12:42:45 +0000
>> From: Tamas Nepusz <address@hidden>
>> Subject: Re: [igraph] question about installing C packages
>> To: Help for igraph users <address@hidden>
>> Message-ID: <address@hidden>
>> Content-Type: text/plain; charset=us-ascii
>>
>> Can you please post the contents of your /etc/apt/sources.list file?
>> It definitely works for me, so there's something wrong on your
>> side.
>>
>> --
>> Tamas
>>
>> On Fri, Jan 15, 2010 at 02:23:13PM +0200, gunce orman wrote:
>> > it is not working
>> >
>> > here the message:
>> >
>> > Reading package lists... Done
>> > Building dependency tree
>> > Reading state information... Done
>> > E: Couldn't find package libigraph
>> >
>> >
>> > On Fri, Jan 15, 2010 at 2:15 PM, Tamas Nepusz <address@hidden> wrote:
>> >
>> > > > yes
>> > > In that case, I don't know what's wrong with Synaptic, but you can
>> > > open
>> > > up a terminal and type:
>> > >
>> > > apt-get install libigraph libigraph-dev
>> > >
>> > > Does it work for you? If not, what's the error message?
>> > >
>> > > --
>> > > Tamas
>> > >
>> > >
>> > > _______________________________________________
>> > > igraph-help mailing list
>> > > address@hidden
>> > > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> > >
>>
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 10
>> Date: Fri, 15 Jan 2010 14:46:15 +0200
>> From: gunce orman <address@hidden>
>> Subject: Re: [igraph] question about installing C packages
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="utf-8"
>>
>> I've found the new repository for amd64 bits from your main page :
>> http://ppa.launchpad.net/igraph/ppa/ubuntu/pool/main/i/igraph/... I've
>> downloaded packages and now it's working... The problem was due to use old
>> repository... there wasn't suitable packages for my system... Now I
>> installed it... thank you very much
>>
>> On Fri, Jan 15, 2010 at 2:42 PM, Tamas Nepusz <address@hidden> wrote:
>>
>> > Can you please post the contents of your /etc/apt/sources.list file?
>> > It definitely works for me, so there's something wrong on your
>> > side.
>> >
>> > --
>> > Tamas
>> >
>> > On Fri, Jan 15, 2010 at 02:23:13PM +0200, gunce orman wrote:
>> > > it is not working
>> > >
>> > > here the message:
>> > >
>> > > Reading package lists... Done
>> > > Building dependency tree
>> > > Reading state information... Done
>> > > E: Couldn't find package libigraph
>> > >
>> > >
>> > > On Fri, Jan 15, 2010 at 2:15 PM, Tamas Nepusz <address@hidden>
>> > > wrote:
>> > >
>> > > > > yes
>> > > > In that case, I don't know what's wrong with Synaptic, but you can
>> > > > open
>> > > > up a terminal and type:
>> > > >
>> > > > apt-get install libigraph libigraph-dev
>> > > >
>> > > > Does it work for you? If not, what's the error message?
>> > > >
>> > > > --
>> > > > Tamas
>> > > >
>> > > >
>> > > > _______________________________________________
>> > > > igraph-help mailing list
>> > > > address@hidden
>> > > > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> > > >
>> >
>> > > _______________________________________________
>> > > igraph-help mailing list
>> > > address@hidden
>> > > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> >
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gnu.org/pipermail/igraph-help/attachments/20100115/19164036/attachment.html
>>
>> ------------------------------
>>
>> Message: 11
>> Date: Fri, 15 Jan 2010 09:36:52 -0500
>> From: zhengjun chen <address@hidden>
>> Subject: Re: [igraph] Question about vector
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi
>>
>> Got it. Thanks.
>>
>> On Fri, Jan 15, 2010 at 5:30 AM, Tamas Nepusz <address@hidden> wrote:
>>
>> > Hi,
>> >
>> > Please send a full code that reproduces the error. It might have
>> > happened that your membership vector is not initialized properly for
>> > instance. By the way, there is an easier way to treat a C array as an
>> > igraph_vector_t, see:
>> >
>> > http://igraph.sourceforge.net/doc-0.5/html/ch06s02s05.html
>> >
>> > Make sure that you neither modify nor destroy vectors created this way.
>> > Modifying the underlying array is fine.
>> >
>> > --
>> > Tamas
>> >
>> >
>> > > vector. The code is in the following:
>> > >
>> > > int member[12000] ;
>> > > ..........
>> > > for(j=0; j<nodes; j++) // nodes is the number of nodes in the
>> > > graph
>> > > {
>> > > igraph_vector_set( &membership, j, (double) member [j] ); //
>> > member
>> > > array stores the membership of vertices
>> > > printf( "%f\n", (double)VECTOR(membership)[j] );
>> > > }
>> > > igraph_modularity( &graph, &membership, &modu, NULL );
>> > >
>> > > The vector membership is initialized correctly. But when running
>> > > igraph_modularity() function, it reports the following errors:
>> > >
>> > > *** glibc detected *** ./modularity: malloc(): memory corruption
>> > > (fast):
>> > > 0x08084318 ***
>> > > ======= Backtrace: =========
>> > > /lib/i686/nosegneg/libc.so.6[0x45dbfc6e]
>> > > /lib/i686/nosegneg/libc.so.6(__libc_calloc+0x94)[0x45dc0874]
>> > > /usr/local/lib/libigraph.so.0(igraph_vector_init+0x33)[0xeb1143]
>> > > /usr/local/lib/libigraph.so.0(igraph_modularity+0x5f)[0xf0600f]
>> > > ./modularity[0x8048980]
>> > > /lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x45d6ddec]
>> > > ./modularity[0x8048691]
>> > >
>> > > So, I am a bit confused. Where is wrong?
>> > > --
>> > > Thanks
>> > > zhengjun
>> > >
>> > > Graduate research assistant
>> > > Dept of Computer Science and Engineering
>> > > Lehigh University
>> >
>> > > _______________________________________________
>> > > igraph-help mailing list
>> > > address@hidden
>> > > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> >
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>>
>>
>>
>> --
>> Thanks
>> zhengjun
>>
>> Graduate research assistant
>> Dept of Computer Science and Engineering
>> Lehigh University
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gnu.org/pipermail/igraph-help/attachments/20100115/2c110c7a/attachment.html
>>
>> ------------------------------
>>
>> Message: 12
>> Date: Fri, 15 Jan 2010 09:49:42 -0500
>> From: zhengjun chen <address@hidden>
>> Subject: [igraph] edge_betweenness community detection
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>> I run igraph_community_edge_betweenness () on my dataset. The dataset
>> consists of 12,000 nodes and 222,156 edges.
>> The program has been running the whole night. It still does not finish.
>> In contrast, fastgreedy community detection can finish in much less time.
>> So, could anyone can tell me a rough time that the edge_betweenness()
>> needs
>> to detect community?
>> --
>> Thanks
>> zhengjun
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gnu.org/pipermail/igraph-help/attachments/20100115/26cf3026/attachment.html
>>
>> ------------------------------
>>
>> Message: 13
>> Date: Fri, 15 Jan 2010 15:55:05 +0100
>> From: G?bor Cs?rdi <address@hidden>
>> Subject: Re: [igraph] edge_betweenness community detection
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi,
>>
>> how should we know that? It depends on your computer and on your graph.
>>
>> But you can try to estimate it yourself. Try running a simple edge
>> betweenness calculation and measure the running time (T). The running
>> time for the community detection will be 1/2 n * T, where n is the
>> number of vertices in the graph. This is just a rough estimate.
>>
>> To get a better estimate, run the community detection on smaller
>> graphs with similar density and degree distribution, for graph with
>> (say) 50, 100, 200, 500, 1000 vertices and extrapolate from that.
>>
>> Best,
>> Gabor
>>
>> On Fri, Jan 15, 2010 at 3:49 PM, zhengjun chen <address@hidden>
>> wrote:
>> > Hi,
>> > I run igraph_community_edge_betweenness () on my dataset. The dataset
>> > consists of 12,000 nodes and 222,156 edges.
>> > The program has been running the whole night. It still does not finish.
>> > In contrast, fastgreedy community detection can finish in much less
>> > time.
>> > So, could anyone can tell me a rough time that the edge_betweenness()
>> > needs
>> > to detect community?
>> > --
>> > Thanks
>> > zhengjun
>> >
>> >
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> >
>>
>>
>>
>> --
>> Gabor Csardi <address@hidden> UNIL DGM
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 14
>> Date: Fri, 15 Jan 2010 14:56:33 +0000
>> From: Tamas Nepusz <address@hidden>
>> Subject: Re: [igraph] edge_betweenness community detection
>> To: Help for igraph users <address@hidden>
>> Message-ID: <address@hidden>
>> Content-Type: text/plain; charset=us-ascii
>>
>> > I run igraph_community_edge_betweenness () on my dataset. The dataset
>> > consists of 12,000 nodes and 222,156 edges.
>> > The program has been running the whole night. It still does not finish.
>> > In contrast, fastgreedy community detection can finish in much less
>> > time.
>> > So, could anyone can tell me a rough time that the edge_betweenness()
>> > needs
>> > to detect community?
>> A rough estimate is something like "a LOT". :)
>>
>> The edge betweenness method calculates the betweennesses of ALL the
>> edges in EVERY step of the algorithm. The algorithm will take 222.156
>> steps since it removes edges one by one. So, a quick estimate can be
>> given by doing the following:
>>
>> 1. Measure the time it takes to calculate all the edge betweennesses
>> (222.156 edges) in the network.
>>
>> 2. Multiply it by, say, half the number of edges. This gives you a rough
>> estimate.
>>
>> --
>> Tamas
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 15
>> Date: Fri, 15 Jan 2010 16:02:15 +0100
>> From: G?bor Cs?rdi <address@hidden>
>> Subject: Re: [igraph] edge_betweenness community detection
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> On Fri, Jan 15, 2010 at 3:55 PM, Gábor Csárdi <address@hidden> wrote:
>> > Hi,
>> >
>> > how should we know that? It depends on your computer and on your graph.
>> >
>> > But you can try to estimate it yourself. Try running a simple edge
>> > betweenness calculation and measure the running time (T). The running
>> > time for the community detection will be 1/2 n * T, where n is the
>> > number of vertices in the graph. This is just a rough estimate.
>>
>> Ooops, Tamas is right of course, n is the number of edges in this
>> formula....
>>
>> G.
>>
>> > To get a better estimate, run the community detection on smaller
>> > graphs with similar density and degree distribution, for graph with
>> > (say) 50, 100, 200, 500, 1000 vertices and extrapolate from that.
>> >
>> > Best,
>> > Gabor
>> >
>> > On Fri, Jan 15, 2010 at 3:49 PM, zhengjun chen <address@hidden>
>> > wrote:
>> >> Hi,
>> >> I run igraph_community_edge_betweenness () on my dataset. The dataset
>> >> consists of 12,000 nodes and 222,156 edges.
>> >> The program has been running the whole night. It still does not finish.
>> >> In contrast, fastgreedy community detection can finish in much less
>> >> time.
>> >> So, could anyone can tell me a rough time that the edge_betweenness()
>> >> needs
>> >> to detect community?
>> >> --
>> >> Thanks
>> >> zhengjun
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> igraph-help mailing list
>> >> address@hidden
>> >> http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >>
>> >>
>> >
>> >
>> >
>> > --
>> > Gabor Csardi <address@hidden> UNIL DGM
>> >
>>
>>
>>
>> --
>> Gabor Csardi <address@hidden> UNIL DGM
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 16
>> Date: Fri, 15 Jan 2010 21:28:15 +0530
>> From: Vijaykumar Muley <address@hidden>
>> Subject: [igraph] Query regarding modularity calculations
>> To: address@hidden
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Dear all,
>>
>> I tried to run modularity calculations for a graph which has 4000 nodes
>> and
>> 60,000 interactions. I performed these calculations using modularity
>> function of the igraph packages the R code is as follow
>>
>> x is a graph
>>
>> b <- edge.betweenness.community( x )
>> comm <- community.to.membership( x, b$merges, steps=10)
>> modularity=modularity(x, comm$membership)
>>
>> but I am getting negative values for modularity moreover it took around 5
>> days.
>> am I doing anything wrong ? can you suggests me where I am going wrong and
>> the estimated time to perform these calculations ?
>> is there alternate ways to calculate modularity ?
>> Please, do help me to overcome this problem.
>>
>>
>> Thanks and Regards
>>
>>
>> --
>> Vijaykumar Yogesh Muley
>>
>> Senior Research Fellow,
>> Dr. Akash Ranjan's Group,
>> Computational and Functional Genomics Laboratory (CFG),
>> Centre for DNA Fingerprinting and Diagnostics (CDFD),
>> Bldg.7, Gruhakalpa
>> 5-4-399/B, Nampally
>> Hyderabad- 500001
>> India
>>
>> Ph.No: +91 9441189013
>> E-mail : address@hidden
>>
>> Life : A journey from Cell to Cell
>> ----------------------------------------------
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 17
>> Date: Fri, 15 Jan 2010 17:04:06 +0100
>> From: G?bor Cs?rdi <address@hidden>
>> Subject: Re: [igraph] Query regarding modularity calculations
>> To: Help for igraph users <address@hidden>
>> Message-ID:
>> <address@hidden>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Dear Vijaykumar Yogesh Muley,
>>
>> On Fri, Jan 15, 2010 at 4:58 PM, Vijaykumar Muley <address@hidden>
>> wrote:
>> > Dear all,
>> >
>> > I tried to run modularity calculations for a graph which has 4000 nodes
>> > and
>> > 60,000 interactions. I performed these calculations using modularity
>> > function of the igraph packages the R code is as follow
>> >
>> > x is a graph
>> >
>> > b <- edge.betweenness.community( x )
>> > comm <- community.to.membership( x, b$merges, steps=10)
>> > modularity=modularity(x, comm$membership)
>> >
>> > but I am getting negative values for modularity moreover it took around
>> > 5
>> > days.
>>
>> as I already wrote you, it is not the modularity calculation that
>> takes a long time, but the edge-betweenness based community structure
>> detection. The modularity calculation should be fast.
>>
>> Moreover, the negative value is normal, modularity is not necessarily
>> positive. If you just take 10 merges in such a big graph, as you did,
>> then you will have very poor communities and the modularity score will
>> be negative.
>>
>> Best Regards,
>> Gabor
>>
>> > am I doing anything wrong ? can you suggests me where I am going wrong
>> > and
>> > the estimated time to perform these calculations ?
>> > is there alternate ways to calculate modularity ?
>> > Please, do help me to overcome this problem.
>> >
>> >
>> > Thanks and Regards
>> >
>> >
>> > --
>> > Vijaykumar Yogesh Muley
>> >
>> > Senior Research Fellow,
>> > Dr. Akash Ranjan's Group,
>> > Computational and Functional Genomics Laboratory (CFG),
>> > Centre for DNA Fingerprinting and Diagnostics (CDFD),
>> > Bldg.7, Gruhakalpa
>> > 5-4-399/B, Nampally
>> > Hyderabad- 500001
>> > India
>> >
>> > Ph.No: +91 9441189013
>> > E-mail : address@hidden
>> >
>> > Life : A journey from Cell to Cell
>> > ----------------------------------------------
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> >
>>
>>
>>
>> --
>> Gabor Csardi <address@hidden> UNIL DGM
>>
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>>
>> End of igraph-help Digest, Vol 42, Issue 11
>> *******************************************
>
>
>
> --
> Vijaykumar Yogesh Muley
>
> Senior Research Fellow,
> Dr. Akash Ranjan's Group,
> Computational and Functional Genomics Laboratory (CFG),
> Centre for DNA Fingerprinting and Diagnostics (CDFD),
> Bldg.7, Gruhakalpa
> 5-4-399/B, Nampally
> Hyderabad- 500001
> India
>
> Ph.No: +91 9441189013
> E-mail : address@hidden
>
> Life : A journey from Cell to Cell
> ----------------------------------------------
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
--
Gabor Csardi <address@hidden> UNIL DGM