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Atom type sampling powerup #99

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wants to merge 218 commits into from
Closed

Atom type sampling powerup #99

wants to merge 218 commits into from

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sblackburn86
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Single atom transition option
&
greedy sampling option
&
atom type update in corrector step

sblackburn-mila and others added 30 commits October 23, 2024 13:29
@sblackburn-mila
sample noisy version of the atom types
b4ce805
@sblackburn-mila
adding beta_t, q_t and others in the noise scheduler
1f18f10
@sblackburn-mila
broadcast function for q_t and q_bar_t
e30d7c0
@sblackburn-mila
loss as AXL and d3pm loss module
059e454
@sblackburn-mila
big chunk in the lightning base model to support atom type training
9df68c6
@sblackburn-mila
update instantiate diffusion model to AXL model
cabb9c6
@sblackburn-mila
score network base update for AXL
3f473af
@rousseab
Fix broken code.
8468bd8
@rousseab
Renamed various things related to drawing diffusion samples.
981a54b
@rousseab
Renamed various things related to drawing diffusion samples.
32e69c4
@sblackburn-mila
analytical score model and mace diffusion
65a42f0
@rousseab
Refactored away the weasel word "sampler".
b1c29e6
@rousseab
Fix executable path.
945eeb0
@rousseab
Use the name "noiser".
5c40e79
@rousseab
Fix data folder imports.
0b699d8
@rousseab
Fixing imports
8da066c
@rousseab
remove broken script
99cba10
@rousseab
Fixing imports
76c99a3
@rousseab
More consistent name.
ecab049
@rousseab
Put NoiseParameters in its own module.
3b9439a
@rousseab
Systematically use the ExplodingVariance object instead of recoding t…
1b38d87 
…he same stuff over and over.
@rousseab
No more dump.yaml after test.
e4d06d1
@rousseab
No more dump.yaml after test.
7162db2
@sblackburn-mila
egnn with AXL thing
fcdfe7c
@sblackburn-mila
various namedtupl snafu
50faeea
@sblackburn-mila
more fixes
b86ac2d
@rousseab
Merge most issues.
aff150d
@rousseab
Merged conflicts in the NoiseScheduler class.
b20bf38
@rousseab
Noisers.
f4c9420
@rousseab
Noisers
ffec518
rousseab and others added 29 commits November 13, 2024 20:35
@rousseab
Fix analytical score network to deal with atom types properly.
45e5c68
@rousseab
Account for the mask logit = -infinity in the atomic loss.
9d894cb
@rousseab
Impose that the MASK probability is zero.
944fa51
@rousseab
Update config files.
8f5b0a0
@rousseab
Instantiate for device discoverability.
f3ac952
@brunorousseau
fix broken test.
a5f2c51
@brunorousseau
a dummy file to test github connection
4623496
@brunorousseau
Removing needless file.
a4b7ade
@brunorousseau
Make sure all layers of the score network will be put on the correct …
c480707 
…device.
@brunorousseau
Fixing device bjorks.
9a82223
@brunorousseau
Fixing device bjorks.
45772b2
@brunorousseau
Update run script.
73571e5
@brunorousseau
Add the MPS device, if available.
7b58288
@brunorousseau
Skip global tests on MPS.
8432c8f
@brunorousseau
Deprecate something to fix later.
66c11af
@brunorousseau
remove needless test
d2acb90
@brunorousseau
Fixing device bjorks.
2974fa1
@sblackburn86
Merge pull request #96 from mila-iqia/dataloader_for_atom_types
4b47380 
Dataloader for atom types
@brunorousseau
Fix the loss to align with the overleaf document.
19b24a0
@brunorousseau
Squash divergent MASK value in CE calculation.
22ce7f4
@brunorousseau
Use a bette rname for the module!
87677a6
@brunorousseau
Fix name.
8e15243
@brunorousseau
Sanity test on p_a0_given_a1.
5e8c875
@brunorousseau
new configs to generate SiGe datasets
671c83b
@brunorousseau
input scripts
a7d7450
@sblackburn86
Merge pull request #97 from mila-iqia/fix_atomic_loss
6fffabb 
Fix atomic loss
@sblackburn86
Merge pull request #98 from mila-iqia/new_datasets
9f2636c 
New datasets
@sblackburn-mila
adding single transtion & greedy option for transitions in Langevin g…
2466f60 
…enerator for atom type
@sblackburn-mila
atom type update in corrector step
a66d8f4
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4 participants
@sblackburn86 @sblackburn-mila @rousseab @brunorousseau