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O2vae integration #74

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O2vae integration #74

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Commits on Jan 15, 2024

  1. Removing umap feature compression

    @ctr26
    ctr26 committed Jan 15, 2024
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Commits on Jan 17, 2024

  1. Merge pull request #19 from ctr26/decoder_fix 

    Decoder fix
    @ctr26
    ctr26 authored Jan 17, 2024
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  2. Merge pull request #21 from ctr26/no_umap 

    Removing umap feature compression
    @ctr26
    ctr26 authored Jan 17, 2024
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  3. Indexation augmentation (forgot this wasnt in here)

    @ctr26
    ctr26 committed Jan 17, 2024
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  4. Fixed the import issue

    @ctr26
    ctr26 committed Jan 17, 2024
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  5. missing import

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  6. Merge pull request #17 from ctr26/indexation_aug 

    Indexation augmentation (forgot this wasnt in here)
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    ctr26 authored Jan 17, 2024
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  7. Fixing tests

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  8. First attempt at setting up the testing cicd

    @ctr26
    ctr26 committed Jan 17, 2024
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  9. adding windows back in?

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  10. commented instead I think this makes more sense

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  11. removing snakemake from env

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    ctr26 committed Jan 17, 2024
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  12. Forgot to remove sourceing

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  13. Merge pull request #22 from ctr26/cicd 

    First attempt at setting up the testing cicd
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Commits on Jan 18, 2024

  1. Generalised the logging a bit

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  2. First attempt as arg hashing for checkpoints

    @ctr26
    ctr26 committed Jan 18, 2024
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  3. Early stopping on val loss to stop overfitting

    @ctr26
    ctr26 committed Jan 18, 2024
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  4. Attempt at cli

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Commits on Jan 19, 2024

  1. Merge remote-tracking branch 'origin/hashing_model_args' into all_tog… 

    …ether
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  2. Merge pull request #34 from ctr26/logger_improve 

    Generalised the logging a bit
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  3. Merge pull request #35 from ctr26/hashing_model_args 

    First attempt as arg hashing for checkpoints
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  4. Early stopping on val loss to stop overfitting

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    ctr26 committed Jan 19, 2024
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Commits on Jan 20, 2024

  1. adding branch prose back

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  2. Merge branch 'master' into all_together

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  3. Merge remote-tracking branch 'origin/early_stopping' into all_together

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  4. Merge remote-tracking branch 'origin/readme_edits' into all_together

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  5. local changes to run

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    afoix committed Jan 20, 2024
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  6. command line arguments

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    afoix committed Jan 20, 2024
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  7. enable testing + uncomment dataset

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    afoix committed Jan 20, 2024
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  8. added a slurm python script

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    afoix committed Jan 20, 2024
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  9. fix cli type

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    afoix committed Jan 20, 2024
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  10. add correct name for the jobs

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    afoix committed Jan 20, 2024
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  11. Log f1 score mean and std in wandb

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  12. choose memory allocation base on latent space size

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  13. dynamically chose n gpus based on latent space size + fix mem allocat… 

    …ion as well
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  14. fix gpu allocation typo

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    afoix committed Jan 20, 2024
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  15. comment out all the mean and std login for f1

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Commits on Jan 23, 2024

  1. added a --clear-checkpoints clarg

    @afoix
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  2. use wandblogger to log info (mean, std dev...)

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  3. run individual jobs in own folder to work around checkpoints

    @afoix
    afoix committed Jan 23, 2024
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Commits on Feb 21, 2024

  1. Updating pythae

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  2. Adding standard scalar to df scoring fun

    @ctr26
    ctr26 committed Feb 21, 2024
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  3. Refactoring and adding back umap

    @ctr26
    ctr26 committed Feb 21, 2024
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  4. Seed "everything"

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    ctr26 committed Feb 21, 2024
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  5. Reduce k folds (should be a hparam)

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    ctr26 committed Feb 21, 2024
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  6. Update args to match what we now think is good

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    ctr26 committed Feb 21, 2024
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  7. Dynamic best weights finding

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  8. Fixed umap

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    ctr26 committed Feb 21, 2024
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  9. Made the class column categorical

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    ctr26 committed Feb 21, 2024
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Commits on Feb 22, 2024

  1. modification for slurm

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    afoix committed Feb 22, 2024
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  2. changes in the shape embed script

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    afoix committed Feb 22, 2024
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  3. Merge remote-tracking branch 'origin/shape_embed' into slurm

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    afoix committed Feb 22, 2024
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  4. Merge pull request #40 from ctr26/shape_embed

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    ctr26 authored Feb 22, 2024
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  5. fix merge commit + add command line args for dataset (name and path) … 

    …and wandb project
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  6. duplicated slurm script + specify dataset

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    afoix committed Feb 22, 2024
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  7. Fix wandb logger

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    afoix committed Feb 22, 2024
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  8. Add helakyoto dataset to the slurm script

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    afoix committed Feb 22, 2024
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Commits on Feb 29, 2024

  1. better imports

    @ctr26
    ctr26 committed Feb 29, 2024
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  2. Adding dataset path to args for better checkpointing

    @ctr26
    ctr26 committed Feb 29, 2024
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  3. Imrproved dataset logic so that dist depends on coords

    @ctr26
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  4. Improved data rejection for datatsets

    @ctr26
    ctr26 committed Feb 29, 2024
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  5. Removing redundant code and adding logging

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  6. [bug] Removing hard coded idx mapper

    @ctr26
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  7. Adding logging and and tqdm so it doesnt look like the code is hanging

    @ctr26
    ctr26 committed Feb 29, 2024
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  8. More logging

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  9. Adding a disk cleanup step

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  10. Reverting to other path structure

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  11. Adding average cross val to logs

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  12. Adding opencv to env file

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Commits on Mar 1, 2024

  1. Added allen dataset

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  2. Limit time per job increased to 24h

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    afoix committed Mar 1, 2024
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  3. Merge branch 'shape_embed' into slurm

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  4. Fixing case where multiple contours are found, chose the longest

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Commits on Mar 3, 2024

  1. Merge branch 'bad_data_fix' into slurm

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  2. change back to use dataset name from clarg + change default wandb job… 

    …name and latent space size
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  3. added back dataset subseting

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    afoix committed Mar 3, 2024
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  4. Added a tiny dataset for quick debugging (commented out in the slurm … 

    …script)
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Commits on Mar 4, 2024

  1. use specific gpu resource

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Commits on Mar 5, 2024

  1. Adding roc_auc and using balanced accuracy

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  2. Probably should stratify

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  3. Adding coordinate debug (unchecked)

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Commits on Mar 6, 2024

  1. put back frobenius norm false

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  2. merge of Craig's branch

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  3. Forgot an import

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Commits on Mar 7, 2024

  1. add the hardcode entity and add model dir

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  2. Merge remote-tracking branch 'origin/shape_embed' into slurm

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    afoix committed Mar 7, 2024
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Commits on Mar 11, 2024

  1. reduce epochs

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Commits on Mar 27, 2024

  1. all changes

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  2. first structure

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Commits on Apr 1, 2024

  1. Properly overwrite default params from clargs

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  2. Use DatasetFolder to load .npy and turn the dist matrix into a 3 chan… 

    …nels copy for models to be happy
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  3. Disable checkpoints in training by default (maybe re-enable at some f… 

    …uture point)
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  4. Enable gpu accelleration by default

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  5. more informative verbose print

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  6. bring argparse to the masks2distmatrices script

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Commits on Apr 2, 2024

  1. training and test model

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  2. Roll indices + normalisation + sanity_check + dataset name for latent… 

    … space
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  3. Added wandb logging

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  4. Added the extraction of original/reconstructed matrices + clarg for o… 

    …utput dir
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  5. created a script that renders dist matrices .npy as .png images

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Commits on Apr 9, 2024

  1. new changes: sparisity, periodicity and also add a script to draw con… 

    …tours from dm
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  2. masks2distmat: turn find_contour into find_longest_contour

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  3. masks2distmat: enable periodic splprep for closed contours

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  4. masks2distmat: updated default sparsity to 4

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  5. distmat2contour: removed spurious return statement in vprint

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  6. drawContourFromDM: removed spurious return statement in vprint

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  7. set correct aspect ratio for distmat2contour scripts

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    afoix committed Apr 9, 2024
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  8. add different normalisations in dataset initial transformations

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    afoix committed Apr 9, 2024
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  9. Add notion of class label to ditmat2emb script output

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    afoix committed Apr 9, 2024
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  10. Updated default model path in distmat2emb script

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    afoix committed Apr 9, 2024
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Commits on Apr 15, 2024

  1. Added umap and kmeans + original filenames list

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Commits on Apr 17, 2024

  1. dist2emb: random seed for np and pl

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  2. dist2emb: test different initial transformations

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  3. dist2emb: remove "TODO" from prints

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  4. cosmetics

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  5. LitAutoEncoderTorch: return both loss and recon_loss

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  6. MaskEmbed: turn off normalisation in DistanceMatrixLoss

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  7. MaskEmbed: log losses in loss_function method

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Commits on Apr 24, 2024

  1. renamed varitional_loss to vq_loss + comment out kdl_vae_loss

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  2. removed new line

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  3. Normalise contour coord in mask2distmat script

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  4. Use bokeh for interactive umap plot (save as html file)

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Commits on Apr 25, 2024

  1. save latent_space with extra info as pickle again and have a separate… 

    … gen UMAPs script
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Commits on Apr 26, 2024

  1. updated the render umap script with a _hardcoded_ trick to extract in… 

    …dex from filename for the tree dataset (should use a user specified regex instead)
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Commits on Apr 29, 2024

  1. minor config + comments

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Commits on May 8, 2024

  1. added a beta vae model

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  2. added extra parameters in the wandb jobname

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Commits on May 10, 2024

  1. finer grained clargs around latent space related parameters

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  2. log different losses for vq or beta models

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Commits on May 13, 2024

  1. code to do classification using the features of the latent space

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Commits on Jun 5, 2024

  1. new latent space size

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  2. Added imports that will be needed for next commits

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  3. Added checkpoint mechanism

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  4. Added regionprops + fourrier decomposition trials (! hardcoded path t… 

    …o synthetic shapes dataset needs to be generalised)
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Commits on Jun 16, 2024

  1. Adding a n compression parameter for the latent space size

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  2. improve scoring function and use StratifiedKFold instead of KFold for… 

    … cross validation
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  3. hardcoded commited setup now points to quick test setup

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  4. initial refactor commit, script with split up functionnalities, missi… 

    …ng metrics
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Commits on Jun 17, 2024

  1. Added predictions + kmeans of input data

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  2. factored out evaluation functionality + added regionprops, efd and sc… 

    …oring
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Commits on Jun 18, 2024

  1. cleaner logging + score shapeembed itself

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  2. reshaped shapeembed reported dataframe

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    afoix committed Jun 18, 2024
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  3. renamed label to class

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  4. updated scoring function + collate and save results

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  5. Added clargs to control matrix normalization and roll

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  6. Added umap_plot

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    afoix committed Jun 18, 2024
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Commits on Jun 24, 2024

  1. fix dataset clarg

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    afoix committed Jun 24, 2024
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  2. fix model name clarg

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    afoix committed Jun 24, 2024
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  3. fix model_name clarg again

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Commits on Jun 25, 2024

  1. Added early stop clarg (default no early stop)

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Commits on Jun 26, 2024

  1. added confusion matrices to scoring function

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  2. use integer division for compression factor clarg

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    afoix committed Jun 26, 2024
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  3. explicitly binarise image when running regionprops

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    afoix committed Jun 26, 2024
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  4. keep 'class' as a column rather than index + keeps column names as st… 

    …rings
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  5. change len for shape[0]

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    afoix committed Jun 26, 2024
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  6. drop not needed return value from run_predictions

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  7. added combined shapeembed + efd + regionprops scoring and comment out… 

    … kmeans
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Commits on Jun 27, 2024

  1. save combined score

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  2. save confusion matrices

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    afoix committed Jun 27, 2024
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Commits on Jul 5, 2024

  1. First attempt at a result gathering script

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  2. added barplots

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Commits on Jul 18, 2024

  1. Added a separate regionprops script

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  2. added a separate efd script

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    afoix committed Jul 18, 2024
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  3. refactor efd and regionprops out of evaluation helpers

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    afoix committed Jul 18, 2024
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  4. less debug info by default + create outdir if not there

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  5. removed regionprops/efd from main shapeembed script + filename saniti… 

    …sation
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  6. unify file names across efd/regionprops/shapeembed

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    afoix committed Jul 18, 2024
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  7. Added a readme

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    afoix committed Jul 18, 2024
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  8. track params in reporting

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    afoix committed Jul 18, 2024
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  9. also add model specific params as tag columns

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  10. added a slurm script to sweap shapeembed parameters

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  11. added resnet50_beta_vae to the factory

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  12. added resnet50_beta_vae to the shapeembed script

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  13. handle per model params in slurm script + chose some param values to … 

    …sweap
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  14. better slurm jobname

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    afoix committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. removed compression factor 20

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  2. bumped up memory allocation to 250G

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    afoix committed Jul 19, 2024
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  3. added --no-early-stop flag

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    afoix committed Jul 19, 2024
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Commits on Jul 20, 2024

  1. added an oom_retry function

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    afoix committed Jul 20, 2024
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  2. refined min / max epochs clargs

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    afoix committed Jul 20, 2024
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  3. slurm script refactor args + force 150 epochs

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    afoix committed Jul 20, 2024
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  4. bring triangular + compression computation in named function (to shar… 

    …e use)
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    afoix committed Jul 20, 2024
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  5. fix in model_str function test of model_args

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    afoix committed Jul 20, 2024
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  6. refactor slurm script to detect already completed jobs

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    afoix committed Jul 20, 2024
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  7. factored out some common helpers

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    afoix committed Jul 20, 2024
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Commits on Jul 21, 2024

  1. Add a comment/uncomment block for quick ad-hoc single config run

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  2. added a function to find currently submitted slurm jobs

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    afoix committed Jul 21, 2024
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  3. added clargs for job filtering enabling/disabling (enabled by default)

    @afoix
    afoix committed Jul 21, 2024
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  4. typo fix: sweap -> sweep

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    afoix committed Jul 21, 2024
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  5. parse dataset as a SimpleNamespace from job string

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    afoix committed Jul 21, 2024
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  6. updated data gathering script to newer changes (still TODO for figures)

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    afoix committed Jul 21, 2024
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  7. removed stale script string

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    afoix committed Jul 21, 2024
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  8. Split model name in two columns if there are model args

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    afoix committed Jul 21, 2024
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  9. remove stale import

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    afoix committed Jul 21, 2024
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  10. experiment with plots

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    afoix committed Jul 21, 2024
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Commits on Jul 22, 2024

  1. keep exploring potential plots

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    afoix committed Jul 22, 2024
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  2. more graphs

    @afoix
    afoix committed Jul 22, 2024
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  3. fix model name in shapeembed output csv

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    afoix committed Jul 22, 2024
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  4. Added loss / mse to shapeembed's generated csv

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    afoix committed Jul 22, 2024
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Commits on Jul 25, 2024

  1. updated slurm script with regex filtering of squeue output

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  2. added a simple latex table to the gather_run_results script

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    afoix committed Jul 25, 2024
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Commits on Jul 27, 2024

  1. minor refactor in efd

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  2. minor refactor in regionprops

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    afoix committed Jul 27, 2024
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  3. generated plots and more tables in gather_run_results

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  4. added regionprops and efd to gather results script

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    afoix committed Jul 27, 2024
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Commits on Jul 29, 2024

  1. Updated graphs titles

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  2. fake beta column if necessary and filter out regionprops and efd for … 

    …f1 Vs Mse comparison
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  3. updated datasets + only find jobs and scores if corresponding filter … 

    …active
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    afoix committed Jul 29, 2024
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  4. bugfix overwriting loop dataframe

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    afoix committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. dded a clarg to control region prop properties

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Commits on Aug 8, 2024

  1. Added random order to efd and regionprops

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Commits on Sep 7, 2024

  1. force different markers for scatter plot F1vMSE

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    afoix committed Sep 7, 2024
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Commits on Sep 9, 2024

  1. updated scatterplot

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    afoix committed Sep 9, 2024
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Commits on Sep 27, 2024

  1. add standard deviation to the report for regions props and efd

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    afoix committed Sep 27, 2024
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  2. modification slurm script

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Commits on Sep 29, 2024

  1. changes to test o2vae integration XXX relies on an adapted o2vae repo… 

    … present in bioimage_embed/modles/o2vae
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  2. off-by-one in square recrop

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    afoix committed Sep 29, 2024
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Commits on Sep 30, 2024

  1. added drop_last for uneven dataset sizes

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    afoix committed Sep 30, 2024
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  2. specialized slurm script

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    afoix committed Sep 30, 2024
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  3. added o2vae repo patch

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    afoix committed Sep 30, 2024
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