Too much time for optimization!! about ipo HOT 6 OPEN

Hi @arpita-007! I want to acknowledge your issue, even though I can't help. The package itself is currently unsupported. I am only providing emergency updates.

I suggest engaging with the community to see if you can get help there.

from ipo.

Hi @arpita-007, you managed to solve it? I'm experiencing the same issue. Thanks!

from ipo.

Hi @song-sbio
No, we could not solve it. I think it's the issue with the file numbers. More the files, longer the time it takes. Because we recently used the IPO again with a lesser no. of files and it worked.

from ipo.

Hi @arpita-007 . Thank you for the explanation.

from ipo.

It took me about 2 days to complete the iteration for eight files.

Here is the range of each variables I set:

min_peakwidth <- c(5, 15)
max_peakwidth <- c(50,90)
ppm <- c(3, 12)
mzdiff <- c(-0.002, 0.002)
snthresh <- c(1, 10)
noise <- c(100, 1000)
prefilter <- c(1,4)
value_of_prefilter <- c(100, 1000)

The outcome is this:

ppm = 12
peakwidth = c(12, 82)
snthresh = 10
integrate = 1
noise = 361
prefilter = c(3,1090)
mzdiff = 0

I consulted my friend who is specialized in DOE. Here is his response:

From reading paper it seems that it uses a box behnken design, which is strange choice. Not very modern and they are quite big when you have as many as 8 factors. It also seems that in each iteration of the optimisation cycle, they start a new design. And it sounds like the data from the previous iteration is discarded. This is also strange and seems very wasteful.
I might be wrong, of course. Maybe I read it wrong.
I like the overall idea of the approach. But I think the DOE execution aspect could be improved.

Then he suggested this:

My approach would be to use a definitive screening design to find out the factors that have an important effect and then work sequentially from there.

from ipo.

Hi @linlennypinawa.

I do agree that the DoE approach implemented in IPO has the potential to be improved. I personally am only maintaining the package to the degree to keep it functional. But I do hope that my former employer Joanneum Research will find time and resources to take on active maintenance along with further development.

from ipo.