[Bioclusters] Re: [Biodevelopers] Altivec enhanced codes?

[David Huen]

On Thursday 06 Nov 2003 2:48 am, Joseph Landman wrote:
> The issue which originally concerned me was the somewhat broad read I
> got out of it.  It seems to wish to cover SIMD applied in a general
> sense to a homology search.
>
> It is as far as I can tell, only at the application stage, so a cease
> and desist is really not enforcable.  It has been suggested that there
> may be applicable prior art.
>
> On Wed, 2003-11-05 at 21:33, Chris Dwan (CCGB) wrote:
> > > If this goes through, any thoughts on whether it is going to put the
> > > kabash on the AGBLAST and Altivec-ized HMM?
> >
> > If (as it says on the link) it truly covers all Smith-Watermans on
> > SIMD, we could be in a lot more trouble than that.  Time to turn off
> > those optimizing compilers folks...
> >

Insofar as it covers SW, it could be said that AGBLAST is safe as BLAST is 
algorithmically distinct from SW and not based on an LP-type optimisation.  
OTOH, AGBLAST is not fast because of it being SIMD but rather because it 
has a (much) better search algorithm than the standard NCBI one.

With Altivec-ized HMM the issue is more muddy.  SW is in effect 
mathematically equivalent to a limit case of a pair HMM.  Whether a legally 
valid claim from the particular to the general can be made, I don't know.  
But then it that is possible, then it should be noted that Intel's own 
application notes at the introduction of SSE show the application of SSE to 
Viterbi decoding of an HMM and if such generalisation were possible, it 
should invalidate the Sencel patent.

For example, Intel application note AP-811 from Jan 1999 specifically shows 
an implementation of the Viterbi decoding using SSE and refers to an 
earlier note AP-569 using MMX to do likewise.  I would say that would 
constitute prior art (certainly predates their papers and patents) insofar 
as general HMMs are concerned (so HMMer should be safe). See:-

http://www.intel.com/cd/ids/developer/asmo-na/eng/microprocessors/ia32/pentium4/resources/appnotes/sse/19048.htm

Whether a patent on the limit case can be claimed when there is prior art 
for the general case, hmmm.....  Where do you write to in the EPO to oppose 
the granting of a patent on basis of prior art? :-)

Regards,
David Huen