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New kernel implementations, nominal model implementation, and training CLI #12

Merged
merged 117 commits into from
Oct 9, 2024
Merged

New kernel implementations, nominal model implementation, and training CLI #12

merged 117 commits into from
Oct 9, 2024

Commits on Aug 15, 2024

  1. notebook: functional notebook for refactorization 

    Signed-off-by: Lee, Kin Long Kelvin <[email protected]>
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    laserkelvin committed Aug 15, 2024
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Commits on Aug 19, 2024

  1. feat: added utility function to calculate number of parallel blocks

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    laserkelvin committed Aug 19, 2024
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  2. feat: added unravel index function

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    laserkelvin committed Aug 19, 2024
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Commits on Aug 21, 2024

  1. refactor: modifying num block calculation with matching arithmetic

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    laserkelvin committed Aug 21, 2024
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  2. feat: added direct second order implementation

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    laserkelvin committed Aug 21, 2024
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  3. feat: adding automatically formatted kernels

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    laserkelvin committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. style: ran ruff on modules 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Aug 22, 2024
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  2. notebook: updated implementations to substitute powers

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    laserkelvin committed Aug 22, 2024
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  3. Merge branch 'individual-l-embeds' of github.com:laserkelvin/EquiTrit… 

    …on into individual-l-embeds
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  4. refactor: constraining export to wrapper class for second order

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    laserkelvin committed Aug 22, 2024
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  5. feat: implemented fifth order

    @laserkelvin
    laserkelvin committed Aug 22, 2024
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  6. feat: exposing direct wrapper functions

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    laserkelvin committed Aug 22, 2024
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  7. refactor & feat: added standardized utility functions for running sph… 

    …erical harmonics
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  8. test: refactored unit test to be generalized

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    laserkelvin committed Aug 22, 2024
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  9. fix: correcting programmatic library importing mechanism

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    laserkelvin committed Aug 22, 2024
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  10. feat: implemented tenth order terms

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    laserkelvin committed Aug 22, 2024
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  11. feat: exposing tenth order to direct namespace

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  12. feat & test: functioning tenth order done

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  13. chore: exposing utility function to direct namespace

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  14. feat: implemented fused second order kernel

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    laserkelvin committed Aug 22, 2024
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  15. docs: added short write up for direct

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Commits on Aug 24, 2024

  1. feat: implemented third order terms

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  2. fix: correcting output allocation shape for third order

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  3. tests: updating unit test for third order

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  4. feat: implemented fourth order terms

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    laserkelvin committed Aug 24, 2024
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  5. test: added parametrized test for fourth order

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  6. feat: added sixth order terms

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  7. test: added parameters for sixth order test

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  8. feat: added seventh order terms

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  9. test: parameterized seventh order

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  10. feat: added eighth order terms

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  11. tests: parameterized eighth order

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  12. feat: added ninth order terms

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  13. fix: correcting eighth order backward stride

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  14. test: parameterized ninth order tests

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Commits on Aug 26, 2024

  1. feat: added utility function for calculating irreps shapes

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  2. fix: making assert check actually positive instead

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    laserkelvin committed Aug 26, 2024
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  3. feat: added first order terms

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    laserkelvin committed Aug 26, 2024
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  4. feat: added hacky zeroth order and udpate tests

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    laserkelvin committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. deps: added training dependencies

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  2. git: ignoring aux files

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    laserkelvin committed Aug 27, 2024
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  3. notebook: added self-contained notebook for testing baseline architec… 

    …ture
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  4. notebook: updating latest direct evaluation notebook

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  5. baseline notebook: equivariance test?

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    migalkin committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. notebook: added e3nn equivariance checks

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  2. feat: transcribed block implementations from notebook

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  3. feat: defining __all__ for blocks

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    laserkelvin committed Aug 28, 2024
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  4. feat: defining model namespace

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  5. chore: adding explicit dependencies

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  6. notebook: updating notebook with fix to subsequent layers needing irr… 

    …eps not scalar features
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  7. chore: bumping version to 0.2.0

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  8. chore: adding jsonargparse as dependency

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  9. feat: added CLI script to train QM9

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  10. fix: resolving e3nn nn import 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  11. fix: correcting data loader import to pyg 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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Commits on Aug 29, 2024

  1. fix: addressing config overwrite and data loader spawning 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  2. config: added config files for QM9 experiments 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  3. git: ignoring logging and dataset folders 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  4. chore: added requirements file for experiments 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  5. refactor: moving lightning components to equitriton module 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Aug 29, 2024
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  6. refactor: using imported lightning modules in train script 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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Commits on Aug 30, 2024

  1. script: adding SMILES output to phate analysis 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  2. feat: adding embedding function to model 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  3. feat: updating __all__ definition for utils

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  4. feat: added utility function for number of projections

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    laserkelvin committed Aug 30, 2024
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  5. feat: adding utility functions for grabbing triton implementations

    @laserkelvin
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Commits on Sep 2, 2024

  1. refactor: changing spherical harmonic interface with preallocation

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  2. refactor: making first and third order accept offset values

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  3. refactor: second order fwd with col offset

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  4. refactor: second order backward with col offset

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  5. refactor: updating autograd.Function for second order

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  6. refactor: making third order autograd Function accept output stride

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  7. refactor: making second order autograd.Function consistent with third… 

    … order
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  8. refactor: making fourth order kernels accept stride and col offset

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  9. refactor: updating fourth order interface for consistency

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  10. refactor: making fifth order accept col offset and stride

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  11. refactor: updating fifth order autograd.Function interface

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  12. refactor: allowing sixth order to accept col offset and output stride

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  13. refactor: updating sixth order to accept col offset

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  14. refactor: updating seventh order to accept col offset and output stride

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  15. refactor: updating seventh order autograd.Function interface

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  16. refactor: eighth order with col offset and output stride

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  17. refactor: updating eighth order Function interface

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  18. refactor: ninth order with col offset and output stride

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  19. refactor: updating ninth order Function with new interface

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  20. refactor: tenth order with col offset and output stride

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  21. refactor: updating tenth order Function interface

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  22. refactor: making zeroth order consistent

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  23. refactor: adding coord ptr back to zeroth order for consistency

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  24. refactor: updating zeroth order Function interface for consistency

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  25. refactor: correcting zeroth order bwd for consistency

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  26. fix: making second order add to gradients instead of overwrite

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  27. refactor: making third order add to gradients

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  28. refactor: making fourth order add to gradients

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  29. refactor: making fifth order add to gradients

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  30. refactor: making sixth order add to gradients

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  31. refactor: making seventh order add to gradients

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  32. refactor: making eighth order add gradients

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  33. refactor: ninth order adds grads

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  34. refactor: tenth order adds grads

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  35. refactor: changing direct module namespace

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  36. refactor: using preallocated interface for production

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  37. refactor: supporting triton_spherical_harmonics_function for backward… 

    …s compatibility
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Commits on Sep 3, 2024

  1. feat: added model property to count irrep shapes 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  2. feat: added embedding separation utility 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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  3. refactor: adding splitting utility into __all__ 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Sep 3, 2024
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  4. refactor: letting embedding split function take numpy arrays 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Sep 3, 2024
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Commits on Oct 8, 2024

  1. configs: updating configs used in experiments 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Oct 8, 2024
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  2. git: ignoring artifact download from wandb 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Oct 8, 2024
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  3. script: committing phate script used for experiments 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Oct 8, 2024
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  4. docs: added docstrings for phate embedding script 

    Signed-off-by: Kin Long Kelvin Lee <[email protected]>
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    laserkelvin committed Oct 8, 2024
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  5. style: ran sort on generate phate imports

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    laserkelvin committed Oct 8, 2024
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  6. docs: updated citation

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    laserkelvin committed Oct 8, 2024
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  7. docs: added note on new interface

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  8. notebook: cleaned up notebook for pedagogy 

    Signed-off-by: Kelvin Lee <[email protected]>
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    laserkelvin committed Oct 8, 2024
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  9. notebook: cleaned up notebook for pedagogy 

    Signed-off-by: Kelvin Lee <[email protected]>
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    laserkelvin committed Oct 8, 2024
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  10. docs: linking new kernels to notebook

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    laserkelvin committed Oct 8, 2024
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