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Permutation in analytical score #113

Merged
merged 24 commits into from
Jan 8, 2025
Merged

Permutation in analytical score #113

merged 24 commits into from
Jan 8, 2025

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rousseab
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In this PR,

  • Data Module creation is made more flexible: we can now create an "on-the-fly" Gaussian dataset for testing ideas
  • the analytical score is revamped to be callable like any Score Network
  • the EGNN score network now works in 1D, 2D and 3D.
  • a score visualization class and a corresponding callback are created to let us look at the score along specified direction.
    This is great for seeing what is going on in a simple 2 atoms test case:
Screenshot 2024-12-26 at 7 43 20 PM

@rousseab
Compute log wrapped gaussians.
439d7d8
@rousseab
Permutation over atomic indices.
12d7871
@rousseab
Code a trivial factorial function to avoid importing something else.
83e99b8
@rousseab
Improved analytical score network.
58c3734
@rousseab
Refactor name of datamodule module.
ecfe3ce
@rousseab
Rename lammps preprocessor code.
b1f7255
@rousseab
Better name.
51a612c
@rousseab
Align test name.
7f10189
@rousseab
Better naming and clean data module instantiation.
d6fc645
@rousseab
A new data module for on-the-fly Gaussian datasets.
14825ca
@rousseab
The ability to instantiate a Gaussian data module.
8d54ef4
@rousseab
Make it easier to instantiate the analytical score network from a con…
bfb8506 
…fig file.
@rousseab
Add analytical score network to possible models to instantiate.
99bbaf4
@rousseab
Fix exp details.
778b4d9
@rousseab
Cleaner data module instantiation.
27c566a
@rousseab
More comments for debug server.
714b583
@rousseab
Make it possible to turn off the optimizer.
bb7e1f3 
This way, we can pass the analytical score network through the main code.
@rousseab
Class to plot the scores along a direction.
89fb2ad
@rousseab
Fancier score viewer.
9da231e
@rousseab
Bring scores back to cpu.
d0d0b23
@rousseab
New callback to show scores along a path.
f335322
@rousseab
Fix assert error comment.
4071d3a
@rousseab
Ensure that the EGNN score network works in 1D, 2D and 3D.
98afd87
@rousseab
an example using the on-the-fly data module
fd25a21
@sblackburn86 sblackburn86 merged commit 0fe4f6d into main Jan 8, 2025
1 check passed
@sblackburn86 sblackburn86 deleted the permutation_in_analytical_score branch January 8, 2025 15:58
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@sblackburn86 sblackburn86 sblackburn86 approved these changes

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@rousseab @sblackburn86