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Update benchmark dataset #11

Merged
merged 56 commits into from
Dec 10, 2024
Merged

Update benchmark dataset #11

merged 56 commits into from
Dec 10, 2024

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doncamilom
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@doncamilom doncamilom commented Dec 6, 2024 •
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Improve benchmark GOSyBench.

  • Add missing nodes (molecules) to graph in benchmark.
  • Add missing SMILES for all molecules in graphs.
  • (future) Add more papers.
  • (future) Add explicit reaction nodes.

@doncamilom
first commit
a2c2492
@doncamilom
split - working
94c258d
@doncamilom
add task class
d2a3056
@doncamilom
add evaluator, and logger. update task
ca2e86a
@doncamilom
add basetype and update task to load from graph
9d53610
@doncamilom
format
637f7b1
@doncamilom
update tree metrics calc
439eeca
@doncamilom
add basetypes: every model for this task should output like this
fd60893
@doncamilom
formatting
3ea8d68
@doncamilom
update docs test
ea2a3aa
@doncamilom
move files around
4cb6c3f
@doncamilom
add metrics class
e6725da
@doncamilom
add class for metrics and doccstrs
de2cdde
@doncamilom
update actions
2ba75ef
@doncamilom
done updateing classes. some things to fix
68e7c8a
@doncamilom
adding tests
0a01309
@doncamilom
fixing metrics to pass tests
13cade0
@doncamilom
make testing bit faster
18e802d
@doncamilom
fix iso test
6c09190
@doncamilom
fix prune function test
937ab0a
@doncamilom
fix another test <> metric
f2375c7
@doncamilom
fix test - exact match
be311a8
@doncamilom
fixed one more test
ed74372
@doncamilom
finished tests
6934e39
@doncamilom
clean up
32382ca
@doncamilom
code to evaluate pre-run methods
6ec8674
@doncamilom
add preprocessing to compare graphs based on names. maybe will have t…
2e41f77 
…o fix tests
@doncamilom
add preprocessing step into Task - ensures graphs can be compared
6a52876
@doncamilom
add wandb reporting into GOSyBench calss
47e9376
@doncamilom
update results notebook
6a99c06
doncamilom and others added 26 commits December 4, 2024 16:47
@doncamilom
remove stuff from api
67ef05e
@doncamilom
rm graph preprocess from task
749c9bd
@doncamilom
linting
06ff0b6
@doncamilom
rm unnecesary
c3b8a66
@doncamilom
clean out the stuff from jasyntho in api.py
39d11b1
@doncamilom
add optimized solver to find long path with smiles (+ tests)
459301c
@doncamilom
api jasyntho TODO
8d6a5b7
@doncamilom
format
a3d8342
@doncamilom
rm extra function
b65f9e6
@doncamilom
scrip to calculate stats of dataset. simple call to packages api
fbff8d9
@doncamilom
fix calc max smiles path
4ade52b
@doncamilom
WIP adding the ground truth graphs
44c6da4
@doncamilom
Merge branch 'main' of https://github.com/schwallergroup/syn2act into…
fdc70bc 
… update_benchmark
@doncamilom
update smiles for one paper
68b945a
@doncamilom
update smiles
38ef800
@doncamilom
update package -> transition to gosybench
3eebd1b
@doncamilom
test
b7b28dd
@doncamilom
update workflows to install pkg
d7b8911
@doncamilom
update workflow
80d7225
@doncamilom
update workflows
2df8dfe
@doncamilom
hm
ad8d70f
@doncamilom
s
a0025dd
@doncamilom
Update README.md
996a8f1
@doncamilom
update names
e3acb29
@doncamilom
update txo
5eb3f95
@doncamilom
update version
e3da370
@doncamilom doncamilom merged commit a54397a into main Dec 10, 2024
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@doncamilom