[Campaign-news] Smoke Test

[whsu at sfsu.edu]

Hi Kai,

> Sorry for my late reply.  I have not been well myself the last few days.

Sorry to hear that...

> First, I wanted to ask you if you are fine with me putting your names
> on a poster that I would like to present at BCatS tomorrow.  The title
> is "Using graphics processors for the clustring of biological data
> sets', and it will present the general idea of our clustering library
> and my first speed measurements.

That's fine with me.

> I talked to Tianyun about the FEATURE data set.  The way it looks we
> can merely use that data for speed comparisons, as the actual
> biophysical meaning of the derived clusters is still unclear, i.e. we
> won't be able to tell what is a 'good cluster'.

Right... it's fine for speed comparisons. It's probably not easy to  
evaluate the quality of clusters; let's keep talking about this, but  
not worry about it too much for now.

> Maybe we could best discuss this when we meet next week.  Will it be at
> Stanford this time?  For me, Tuesday or Friday are generally the best
> days, but I could fit in a meeting on other days as well.

My schedule is relatively flexible. It's fine with me to meet at  
Stanford. Marc?

Bill

> - Kai
>
>
>
>
>
> ----- Original Message ----- From: <whsu at sfsu.edu>
> To: "Kai Kohlhoff" <kohlhoff at stanford.edu>
> Cc: <campaign-news at simtk.org>
> Sent: Thursday, November 05, 2009 11:17 AM
> Subject: Re: [Campaign-news] Smoke Test
>
>
> Hi Kai,
>
> Sure, let's meet next week to firm up our current conversations about
> setting up the repository, and test data sets. Marc is not feeling
> well this week, and we've been busy battling some problems on another
> GPU-related project of ours, so things haven't been moving on that
> front.
>
> I can't do Monday the 9th, but the rest of the week looks ok.
>
> Bill
>
> Quoting Kai Kohlhoff <kohlhoff at stanford.edu>:
>
>> Hi Bill and Marc,
>>
>> I have a small FEATURE data set that we can use for testing, bit will
>> also look for something bigger. For k-centers I just completed a
>> protein rmsd kernel.
>>
>> K-centers is currently deterministic for a given seed, but this comes
>> at a performance cost. This can be easily overcome, though, because
>> clusters are always the same. Only their sequence changes.
>>
>> I will be back in the office on Wednesday and will get back to you then.
>>
>> Would it make sense to have another meeting the week after next?
>>
>> - Kai
>>
>> Sent from my kaiPhone.  Apologies for brevity or unusual tone.
>>
>> On Oct 30, 2009, at 14:39, whsu at sfsu.edu wrote:
>>
>>> I assume Kai probably has a small test data set that he uses?     
>>> k-centers can probably be deterministic if we fix the initial seed  
>>>    cluster, and have a tie-breaking mechanism for data points that  
>>>  are  equi-distant from two clusters (there might be something in   
>>> Kai's   code already). I need to spend a bit more time with the   
>>> k-means   code...
>>>
>>> Bill
>>>
>>> Quoting Marc Sosnick <marcsosnick at mac.com>:
>>>
>>>> Kai, Bill:
>>>>
>>>> Before I post to the software repository, I want to have the initial
>>>> reorganization of the system completed.  To do this I will be rewriting
>>>> all the scripts in PERL and normalizing the deployment process.
>>>>
>>>> To be in compliance with standard SE practices, we should have some
>>>> sort of smoke test against which we can test so that we don't post
>>>> non-working code to the library.  I was wondering if either of you had
>>>> a good idea as to what that smoke test could entail?  Perhaps a known
>>>> dataset and algorithm against which we could test?  Of course, it would
>>>> mean that whatever we choose, the result must be deterministic.
>>>>
>>>> I look forward to your ideas...
>>>>
>>>> Thanks!
>>>>
>>>> Marc_______________________________________________
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>>>
>>>
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>
>
>
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