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SystemsGenetics / KINC

Knowledge Independent Network Construction
MIT License
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KINC extract slow compute time #146

Open JohnHadish opened 4 years ago

JohnHadish commented 4 years ago

Extracting 63G .csm that results in 46G network takes 34 hours.

Look into extract may be beneficial to determine if optimization is possible.

bentsherman commented 4 years ago

@JohnHadish Did you use the latest KINC commits? When I released v3.4.1 I included a small change to extract which cut the runtime nearly in half.

JohnHadish commented 4 years ago

Yes, I was using 3.4.1

spficklin commented 4 years ago

I think we need to make this a parallel analytic to help speed it up.