[OTDev] New applications
surajit ray mr.surajit.ray at gmail.comWed Oct 26 23:21:07 CEST 2011
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Yeah, I am. Infact part 2 is something I tried already, but gave up because the SVM I was using was from a JNI wrapper and it did not have clean memory management, and the application would hang with an out of memory error. I never got the time to try a pure Java SVM, but I feel it is possible to optimize parameters in a "timebound-predictable" manner, especially with case of SVM. It is something I am going to explore when I make a faster SMSD version of Maxtox. >From what i observed of the process a) Extensive parameter variation is easy to conceive, but difficult to outline in reality b) When a parameter or parameters are varied, the logic usually has a close connection to the algorithm itself - meaning a generic mechanism may not work. c) Intelligent choice of direction of parameter optimization, itself plays a big role in obtaining an acceptable model in reasonable time d) Serious computational resources are required especially when such requirements often spiral exponentially. One way out was to run in a cloud like EC2 on Amazon, and start and stop extra server instances from within the code - to cater to exponential demands. e) Lastly and I feel most importantly, if we are to assume consumer indiscretion (in raw terms - more dumb than bright) , then there has to be a component of AI in the workflow for parameter optimization. A blunt "try everything" approach will simply not cut it (or for that matter satisfy our target audience) Cheers Suro On 26 October 2011 14:37, Barry Hardy <barry.hardy at douglasconnect.com>wrote: > Two application needs based on OpenTox components that have surfaced: > > a. an application allowing user choice on algorithm and parameters for > creating a validated model > > b. an application/workflow supporting automated extensive > parameter/algorithm variation to produce an optimed model based on > user-supplied criteria > > Let us know if you are interested! > > Barry > > Am 26.10.2011 10:58, schrieb Christoph Helma: > >> Starting a new thread from a semi-private conversation. >> >> On Wed, 26 Oct 2011 10:01:51 +0200, Barry Hardy<barry.hardy@** >> douglasconnect.com <barry.hardy at douglasconnect.com>> wrote: >> >>> I don't this is a good argument for ToxCreate. It might be for say >>> "Christoph's lazar application" or a controlled "ToxReachModeller". >>> >>> From the point of view of the ToxCreate Use Case, and OpenTox and a >>> component-based design, in my opinion, the application should allow the >>> user to select the algorithm. >>> >> ToxCreate should be a simple tool for novice users (without an >> understanding of algorithms and parameters). How can we expect that a >> novice user makes an informed decision if even we (i.e. the experts) >> cannot provide better alternatives? >> >> Christoph >> >> PS We have been discussing a medium-level GUI with selection of >> algorithms and parameters from the beginning, but I have always clearly >> stated that we will not have the resources to implement that in >> ToxCreate. Anyone who is interested can take our opento-ruby library and >> wrap a GUI around it. >> >> >> > ______________________________**_________________ > Development mailing list > Development at opentox.org > http://www.opentox.org/**mailman/listinfo/development<http://www.opentox.org/mailman/listinfo/development> > -- Surajit Ray Partner www.rareindianart.com
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