Re: [infomap-nlp-devel] PERL/CGI: associate -v or -p: bad options?

[Dominic W. <wi...@ma...>]

Dear Zbynek,

Sorry for not responding sooner. I see what your problem is now. When  
we cleaned up the infomap codebase for public release, we only had a  
couple of months before the project's funding ended, and decided that  
the clustering and contrasting pairs options were bleeding edge and  
optional. So we left them out, hoping to put them into later releases.

We only released the web interface code more recently, and in a  
"strictly beta" fashion - it hasn't been through the same cleaning up  
process. It turns out that the Perl web interface code is making  
calls against options in the core C infomap engine that won't be  
there in your release.

I will think about trying to solve this (and Scott, if you have any  
time to help, that would be great). I was never 100% happy with the  
former clustering code, it wasn't a great clustering algorithm, and  
it was very wrapped in to the "associate" executable. It might be  
much easier to create and maintain a more modular architecture, where  
associate writes out the vectors to be clustered (e.g. the top 200)  
to a file using the "-f" option, and clustering libraries read these  
files. It wouldn't be as efficient, but I don't believe that this  
would make too much difference in practice (not for a single user  
running the algorithm once as part of a browser interface - other  
latencies are greater than writing and reading a file some where on  
your web server).

This way we could write or reuse many clustering algorithms quite  
easily. It's also the way that the Java word spectrum plotter works.

If you want to try wrapping in the clustering algorithm from the  
original infomap source, I could send you the files and try to help  
you. But it may actually take longer, I'm not sure.
Best wishes,
Dominic

On Oct 24, 2006, at 5:19 AM, Zbynek Studenovsky wrote:

> Dear Scott,
>
> thank you for your prompt respond. Unfortunately, I am not able to run
> associate from the command line with the -p or -v options. The only
> available options are in the attached man file (associate_man.txt)  
> and here:
>
> Usage:associate [-w | -d | -q]
>                 [-i type_of_input(d or w)] [-f vector_output_file]
>                 ( [-t] | [-m model_dir] )
>                 [-c <model_tag>]
>                 [-n num_neighbors] [-f vector_output_file]
>                 <pos_term_1> [pos_term_2 ... pos_term_n]
>                 [NOT neg_term_1 ... neg_term_n]
>
>         Task:   -w      associate words (DEFAULT)
>                 -d      associate documents
>                 -q      print query vector
>
> I have also compiled a new version of associate from CVS (1.2) and  
> it runs
> with the same results.
>
> I think the problem could be an old code in the public version of  
> associate
> in Infomap 0.8.6 and I think no one is able to run associate with - 
> v or -p
> options. It would be nice, if you or Beate Dorow could add a  
> revision of
> associate in CVS.
>
> Many thanks for your help and best regards
>
> Zbynek Studenovsky
> -----------------------------------------
> email: zb...@ma...
> homepage: http://homepage.mac.com/zbynek
>
> Am 23.10.2006 18:13 Uhr schrieb "Scott Cederberg" unter
> <ced...@gm...>:
>
>> Hi Zbynek,
>>
>>      I'm glad to hear that you've gotten the Web frontend working.
>> Are you able to run associate from the command line with the -p or -v
>> options?
>>
>>     Unfortunately I'm not that familiar with these options... I'll
>> give them a try tonight when I get home, though, to see if they work
>> in my version of the software.
>>
>>
>>                       Scott
>>
>> On 10/23/06, Zbynek Studenovsky <zb...@ma...> wrote:
>>> Dear Sirs,
>>>
>>> I use a Infomap software to build a language model (Greek New  
>>> Testament and
>>> LXX) for my doctoral thesis. For publishing I would like to make  
>>> my model
>>> available for another researches via www. For this reason I have  
>>> installed
>>> on my system (Mac OS X 10.3.9 PowerPC) an Infomap demo PERL and  
>>> CGI scripts
>>> from CVS (webif) directory. All scripts are running great and I  
>>> can search
>>> for nearest neighbors of related words and retrieve documents  
>>> without
>>> problems, also with negative keywords.
>>>
>>> Regrettably, I am unable to search for "clustered results" and  
>>> "contrasting
>>> pairs" with my version of associate (?) - my Apache server  
>>> (version 1.3)
>>> records in error_log "Bad option: -v" for "clustered results" and  
>>> "Bad
>>> option: -p" for "contrasting pairs".
>>>
>>> My question is: Is the 'problem' in air file code (lines 74-79):
>>>
>>> #71 sub associate(){
>>> #72     $command = "associate -w -c " . $input{'corpus'};
>>> #73     if( $input{'contrast'} eq 'clustered' ){
>>> #74   $command = $command . " -v clusters " . $input{'results'} .  
>>> " "
>>> #75 . $input{'clusters'};
>>> #76   }
>>> #77     if( $input{'contrast'} eq 'pairs' ){
>>> #78   $command = $command . " -p";
>>> #79   }
>>>
>>> or in my installed 'old' version of associate?
>>>
>>> Many thanks for your help and best regards from Prague
>>>
>>> Zbynek Studenovsky
>>> -----------------------------------------
>>> email: zb...@ma...
>>> homepage: http://homepage.mac.com/zbynek
>>>
>>>
>>>
>
>
> <associate_man.txt>