boomer selects suboptimal solution in simple 3-node problem about boomer HOT 6 OPEN

I can confirm it's not avoiding any collapses, as if I reduce the ptable to omit 1

ie

A:1	B:1	0.0	0.0	0.95	0.05
B:1	C:1	0.0	0.0	0.95	0.05
A:1	C:1	0.99	0.0	0.01	0.0

then it correctly finds

B:1 EquivalentTo C:1    (most probable) 0.95
A:1 EquivalentTo B:1    (most probable) 0.95

from boomer.

I think the issue here is the high number of "windows" requested (100). Input rows are sorted according to their best probability, then the list of rows is chunked into the given number of windows. Across each independent run, shuffling occurs within each window, but the windows stay in the same total order. So it will always first add A ProperSubClassOf C. If you use a window value of 1, the rows are completely randomized and it is able to find the best solution.

from boomer.

See the logging at the beginning of a run (with 100 windows requested):

2021.02.05 14:32:54:070 [zio-def...] [INFO ] org.monarchinitiative.boomer.Boom.evaluate:30 - Bin size: 1; Most probable: 0.99
2021.02.05 14:32:54:091 [zio-def...] [INFO ] org.monarchinitiative.boomer.Boom.evaluate:30 - Bin size: 2; Most probable: 0.95
2021.02.05 14:32:54:095 [zio-def...] [INFO ] org.monarchinitiative.boomer.Boom.evaluate:33 - Max possible joint probability: -0.11263692462860261

The axioms in the first bin will always be added before proceeding to the next bin. Different runs will just shuffle the order of the two items in the second bin.

from boomer.

my ticket is in error... more later

from boomer.

I think we cleared this up. "windows" may not be as obvious as they ought to be but I think the UI will continue to evolve.

from boomer.

still an issue

A:1	B:1	0.0	0.0	0.95	0.05
B:1	C:1	0.0	0.0	0.95	0.05
A:1	C:1	0.99	0.0	0.01	0.0

running
boomer -t triangle.ptable.tsv -a triangle.owl -p prefixes.yaml -r 500 -w 1 -e 200 --output-internal-axioms true

yields

## SINGLETONS
Method: singletons
Score: -0.05129329438755058
Estimated probability: 1.0
Confidence: 1.0
Subsequent scores (max 10):

- [B:1](http://purl.obolibrary.org/obo/B_1) EquivalentTo [C:1](http://purl.obolibrary.org/obo/C_1)      (most probable) 0.95

and an incoherent output.ofn

from boomer.