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Numba parallel weights computation + dataloader #5

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Numba parallel weights computation + dataloader #5

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Commits on May 11, 2021

  1. Added some slurm scripts, small changes to VAE_model for file handling

    Lodevicus Van Niekerk committed May 11, 2021
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Commits on May 12, 2021

  1. defined instance variables in __init__ for clarity; extracted one_hot… 

    …_encoding function; minor linting, changed seq_name_to_sequence to a string instead of list of chars
    @loodvn
    loodvn committed May 12, 2021
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Commits on May 23, 2021

  1. change focus_seq_trimmed to a string instead of list of chars; added … 

    …minor printouts to MSA_processing
    @loodvn
    loodvn committed May 23, 2021
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Commits on Jun 16, 2021

  1. error checking in compute_evol_indices 

    passing z_dim into train_VAE script
manually passing in args for VAE checkpoint reloading
small typos in scripts
    @loodvn
    loodvn committed Jun 16, 2021
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  2. merged data_utils

    @loodvn
    loodvn committed Jun 16, 2021
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Commits on Jul 13, 2021

  1. added joint training, one-hot sequence functions

    @loodvn
    loodvn committed Jul 13, 2021
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  2. Merge remote-tracking branch 'origin/master' into master

    @loodvn
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  3. moved optimizer.zero_grad() outside of if-else

    @loodvn
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Commits on Jul 15, 2021

  1. had to comment out the alternating joint training for now, to switch … 

    …to mixed batch joint training.

Initialising the bias to mean(y_train) for much better convergence, still not great performance though.
Moved parameter reading outside of main function so that we can override the z_dim size
    @loodvn
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Commits on Aug 6, 2021

  1. joint training script improvements: 

    saving vae checkpoints,
checkpoint loading vs train from scratch,
added sigmoid+bce loss,
added 3 very long functions for mixed/alternating/frozen training modes to switch from command line,
added linear model loss weight
    @loodvn
    loodvn committed Aug 6, 2021
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Commits on Sep 9, 2021

  1. Joint training: parameterize lm_loss_weight 

    linting
    @loodvn
    loodvn committed Sep 9, 2021
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Commits on Mar 16, 2022

  1. adding EVcouplings versions, some data checks, and need to check that… 

    … outputs are equal
    @loodvn
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  2. temp hehe

    @loodvn
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Commits on Mar 18, 2022

  1. committing all ideas for parallelising the weights calculation for re… 

    …cord, will delete the bad ones
    @loodvn
    loodvn committed Mar 18, 2022
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  2. checking on O2 now

    @loodvn
    loodvn committed Mar 18, 2022
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  3. adding mapping files

    @loodvn
    loodvn committed Mar 18, 2022
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  4. running as array

    @loodvn
    loodvn committed Mar 18, 2022
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  5. changed logging dir

    @loodvn
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  6. removed old training flags

    @loodvn
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  7. some slurm script changes

    @loodvn
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  8. updating conda bin and log output dir

    @loodvn
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  9. print equality

    @loodvn
    loodvn committed Mar 18, 2022
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  10. added directory exists checking

    @loodvn
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  11. running all proteins now

    @loodvn
    loodvn committed Mar 18, 2022
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  12. 74 MSAs

    @loodvn
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  13. oops was still debugging

    @loodvn
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  14. using new MSAs

    @loodvn
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  15. wrong MSA location

    @loodvn
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  16. explicitly setting number of CPUs to use

    @loodvn
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  17. also testing only 1 cpu

    @loodvn
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  18. trying to add method as a parameter - flags are pretentious

    @loodvn
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  19. changed reading in calc_weights option

    @loodvn
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  20. bugfixes

    @loodvn
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  21. bugfixes

    @loodvn
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  22. another bug

    @loodvn
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  23. using specific python from conda env because other jobs were lagging

    @loodvn
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  24. skipping existing files because we'll get runtimes from logs anyway

    @loodvn
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Commits on Mar 21, 2022

  1. using multiprocessing + numba now, is roughly as fast as parallel num… 

    …ba, but both aren't scaling as well as expected..
    @loodvn
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  2. going to try run all the weights and check

    @loodvn
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  3. typo

    @loodvn
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  4. moved all the tmp EVE vs EVCouplings checks out into calc_weights.py,… 

    … where it'll be deleted soon

also got rid of confusing calc_method flags, will just call specific methods from calc_weights.py
    @loodvn
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  5. going big, 40 cpus

    @loodvn
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Commits on Mar 22, 2022

  1. moved all the tmp EVE vs EVCouplings checks out into calc_weights.py,… 

    … where it'll be deleted soon
    @loodvn
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  2. going to calc all weights with 2h timeout for 8cpus (and later 4cpus)

    @loodvn
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  3. moved all the weights calc into a different utils file

    @loodvn
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  4. added flag option to train_VAE.py to fail if weights not found (usefu… 

    …l to make sure that weights are precomoputed on CPU)
    @loodvn
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  5. separated the slurm calc_weights from local calc_weights.sh

    @loodvn
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  6. modifying some other changes I made early on

    @loodvn
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  7. Merge branch 'OATML:master' into lood/speedup_weights

    @loodvn
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  8. cleaned up one_hot_3D

    @loodvn
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  9. Merge branch 'OATML:master' into master

    @loodvn
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  10. check - editing readme

    @loodvn
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  11. Merge branch 'master' of https://github.com/loodvn/EVE

    @loodvn
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  12. Committing all together, other branch corrupt

    @loodvn
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  13. temporarily removing data/* because git tree corrupt

    @loodvn
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  14. removed circular dependency in utils/weights 

    refactored another one_hot_encoding
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  15. removing ADRB2, and old masters-project-specific files

    @loodvn
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Commits on Mar 23, 2022

  1. Merge branch 'master' into lood/speedup_weights2

    @loodvn
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  2. changed EVcouplings code to > insteead of >= theta

    @loodvn
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  3. Merge remote-tracking branch 'origin/lood/speedup_weights2' into lood… 

    …/speedup_weights2
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  4. moved calc_weights to top level instead of nested in gen_alignment; 

    also moved preprocess_MSA into its own function because it bugged me
    @loodvn
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  5. removed all the timing and speed comparison stuff from calc_weights.py

    @loodvn
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Commits on Jul 28, 2022

  1. changed initial num_neighbors to 1 because num_neighbors = 0 didn't m… 

    …ake sense
    @loodvn
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  2. merged with Marks-OATML master

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  3. Merge remote-tracking branch 'marks/master' 

    # Conflicts:
#	train_VAE.py
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  4. don't need weights for scoring

    @loodvn
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  5. Merge branch 'lood/speedup_weights' 

    # Conflicts:
#	EVE/VAE_model.py
#	train_VAE.py
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  6. grabbed some nice files from deepseq_reproduce branch

    @loodvn
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Commits on Aug 2, 2022

  1. move constants out, 

    added threshold_focus_cols_frac_gaps command line argument
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  2. adding disorder mapping file and script

    @loodvn
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  3. Merge branch 'lood/speedup_weights'

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  4. got mapping from deepseq_reproduce branch

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  5. adding disorder mapping file and script

    @loodvn
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  6. added threshold_focus_cols_frac_gaps to calc_weights too, also rerunn… 

    …ing script
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  7. added overwrite_weights for my specific use case, just to be sure

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  8. Merge remote-tracking branch 'origin/master' 

    # Conflicts:
#	scripts/2022_08_01_disorder_O2.sh
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  9. added weight shape check, using threshold_focus_cols_frac_gaps = 1 si… 

    …nce then it includes all sequences
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Commits on Aug 3, 2022

  1. rerunning with longer time limit

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Commits on Aug 8, 2022

  1. imported compute_evol_indices from deepseq_reproduce

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  2. kicking off scoring, had to recheckout compute_evol_indices from deep… 

    …seq_reproduce
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Commits on Aug 9, 2022

  1. turned DMS filename assertion into just a warning for now, need to fi… 

    …gure out properly later
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  2. using updated MSA and DMS files (v7?), rerunning training/scoring acc… 

    …ordingly
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Commits on Aug 10, 2022

  1. added new disordered MSA using notebook in disorder_human project

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Commits on Aug 11, 2022

  1. using new DMS and MSA mapping and new suffix

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Commits on Sep 23, 2022

  1. adpred scripts

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Commits on Oct 18, 2022

  1. allowed to pass in a MSA file directly to calc_weights instead of a m… 

    …apping file

also added "identity" weights for completion
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  2. Merge branch 'lood/speedup_weights2' 

    # Conflicts:
#	EVE/VAE_model.py
#	calc_weights.py
#	compute_evol_indices.py
#	data/mappings/example_mapping.csv
#	examples/Step0_optional_calc_weights.sh
#	examples/Step0_optional_calc_weights_slurm.sh
#	train_VAE.py
#	utils/data_utils.py
#	utils/weights.py
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  3. reformatted whitespace PEP8

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  4. some more minor whitespace formatting

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  5. syntax errors: added overwrite_weights to signature and fixed :: synt… 

    …ax error
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  6. added overwrite_weights option to calc_weights.py

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  7. added overwrite_weights option to calc_weights.py

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Commits on Sep 13, 2023

  1. Weights calc: 

    Added progress bar, weights-only calc mode
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  2. Training: Added some checks to input/output files

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  3. Tweaked progress bar; removed debugging statements

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Commits on Sep 14, 2023

  1. Streaming one-hot-encodings is working well 

    Fallback to normal mode also works well
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Commits on Sep 19, 2023

  1. Using a --experimental_stream_data flag, a bit cleaner

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Commits on Feb 28, 2024

  1. Skipping synonymous mutants in the filtering, fixed tqdm bug

    @loodvn
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  2. Using protein_name in compute_evol_indices, added some logging

    @loodvn
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  3. Removed weights calculation comparison tests, cleaned up dataloader

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Commits on Mar 6, 2024

  1. Computing one-hot encodings on the fly for evol_indices using dataloa… 

    …der, merged in changes from ProteinGym.

Removed the aggregation methods for evol indices.
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Commits on Mar 15, 2024

  1. Using dataloaders for train and validation, use multi-cpu weights by … 

    …default, tested with DLG4

(cherry picked from commit fcb7894)
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    loodvn committed Mar 15, 2024
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Commits on Mar 16, 2024

  1. Added files back from upstream repo to match master before PR

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    loodvn committed Mar 16, 2024
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  2. deleted internal scripts

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    loodvn committed Mar 16, 2024
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