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Axl atom type loss review#91

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rousseab wants to merge 75 commits intomainmila-iqia/diffusion_for_multi_scale_molecular_dynamics:mainfrom AXL_atom_type_loss_reviewmila-iqia/diffusion_for_multi_scale_molecular_dynamics:AXL_atom_type_loss_reviewCopy head branch name to clipboard

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Commits on Oct 23, 2024

• sample noisy version of the atom types

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Commits on Oct 24, 2024

• adding beta_t, q_t and others in the noise scheduler

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• broadcast function for q_t and q_bar_t

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Commits on Oct 25, 2024

• loss as AXL and d3pm loss module

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• big chunk in the lightning base model to support atom type training

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• update instantiate diffusion model to AXL model

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• score network base update for AXL

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• Fix broken code.

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• Renamed various things related to drawing diffusion samples.

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• Renamed various things related to drawing diffusion samples.

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• analytical score model and mace diffusion

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• Refactored away the weasel word "sampler".

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• Fix executable path.

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• Use the name "noiser".

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• Fix data folder imports.

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  0b699d8

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• Fixing imports

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• remove broken script

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• Fixing imports

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• More consistent name.

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• Put NoiseParameters in its own module.

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• Systematically use the ExplodingVariance object instead of recoding the same stuff over and over.

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• No more dump.yaml after test.

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• No more dump.yaml after test.

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Commits on Oct 26, 2024

• egnn with AXL thing

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• various namedtupl snafu

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• more fixes

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• Merge most issues.

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• Merged conflicts in the NoiseScheduler class.

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• Noisers.

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• Noisers

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• Fix the instantiate diffusion model.

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• Update the imports in the main PL model.

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Commits on Oct 27, 2024

• Merge pull request #88 from mila-iqia/bruno_refactor

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• mace score network axl-ization

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• mlp score network axl-ization

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• axl & diffusion mace axl fixes

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• variance sampler unit tests

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• fixing test_exploding_variance

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  d91bd41

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• axl diffusion model unit test and related fixes

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• minimal fixes for generators

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• fixing generators unit tests

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• main entry point unit test fix and related fixes - partial

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• sample_diffusion unit tests fix

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Commits on Oct 28, 2024

• fixing most test_score_network except DiffusionMace

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• force field augmented unit test

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• test egnn and rm fokker planck

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• fixing most of diffusion mace

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• bug fix in diffusion mace score network

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• analytical score

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• dataloader renaming to namespace for atom types

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• fixing data preprocessing tests

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• Merge remote-tracking branch 'origin/main' into refactor_for_atom_type_diffusion

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Commits on Oct 29, 2024

• adding unit tests for d3pm loss

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• variance samplers unit tests

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• atom type noiser tests

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• d3pm utils tests

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• tensor utils unit tests

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• test egnn upgrades

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• testscorenetwork upgrade

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Commits on Oct 30, 2024

• fixing score network unit tests

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• A different seed, and no more nans.

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Commits on Oct 31, 2024

• fixing cartesion positions in mace - solving the unit test issue...

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Commits on Nov 2, 2024

• code review part 1

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• code review part 2

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• code review part 3

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• first pass complete on code review

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• saturday morning breakfast cereal comments

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Commits on Nov 3, 2024

• fixing variance_sampler and various unit tests

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Commits on Nov 4, 2024

• Merge pull request #90 from mila-iqia/refactor_for_atom_type_diffusion

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• Sorting imports, passing linting tests.

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• More granularity in the loss modules. Also, more isort.

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• Linting.

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• More granular loss testing.

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• More granular loss testing.

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• Revamped atomic type loss function.

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