Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

O2vae integration #1

Open
wants to merge 220 commits into
base: main
Choose a base branch
from
Open

O2vae integration #1

wants to merge 220 commits into from

Commits on Jan 15, 2024

  1. Removing umap feature compression

    @ctr26
    ctr26 committed Jan 15, 2024
    Configuration menu
    Copy the full SHA
    7b43109 View commit details
    Browse the repository at this point in the history

Commits on Jan 17, 2024

  1. Merge pull request uhlmanngroup#19 from ctr26/decoder_fix 

    Decoder fix
    @ctr26
    ctr26 authored Jan 17, 2024
    Configuration menu
    Copy the full SHA
    e58fbac View commit details
    Browse the repository at this point in the history

  2. Merge pull request uhlmanngroup#21 from ctr26/no_umap 

    Removing umap feature compression
    @ctr26
    ctr26 authored Jan 17, 2024
    Configuration menu
    Copy the full SHA
    38cf94d View commit details
    Browse the repository at this point in the history

  3. Indexation augmentation (forgot this wasnt in here)

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    b17827a View commit details
    Browse the repository at this point in the history

  4. Fixed the import issue

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    5cf77fc View commit details
    Browse the repository at this point in the history

  5. missing import

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    9273f8c View commit details
    Browse the repository at this point in the history

  6. Merge pull request uhlmanngroup#17 from ctr26/indexation_aug 

    Indexation augmentation (forgot this wasnt in here)
    @ctr26
    ctr26 authored Jan 17, 2024
    Configuration menu
    Copy the full SHA
    1abc9d6 View commit details
    Browse the repository at this point in the history

  7. Fixing tests

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    5f46b74 View commit details
    Browse the repository at this point in the history

  8. First attempt at setting up the testing cicd

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    0fc9066 View commit details
    Browse the repository at this point in the history

  9. adding windows back in?

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    8a2d14d View commit details
    Browse the repository at this point in the history

  10. commented instead I think this makes more sense

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    74f2d13 View commit details
    Browse the repository at this point in the history

  11. removing snakemake from env

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    c190e04 View commit details
    Browse the repository at this point in the history

  12. Forgot to remove sourceing

    @ctr26
    ctr26 committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    1e657fd View commit details
    Browse the repository at this point in the history

  13. Merge pull request uhlmanngroup#22 from ctr26/cicd 

    First attempt at setting up the testing cicd
    @ctr26
    ctr26 authored Jan 17, 2024
    Configuration menu
    Copy the full SHA
    9a61af2 View commit details
    Browse the repository at this point in the history

Commits on Jan 18, 2024

  1. Generalised the logging a bit

    @ctr26
    ctr26 committed Jan 18, 2024
    Configuration menu
    Copy the full SHA
    510aa04 View commit details
    Browse the repository at this point in the history

  2. First attempt as arg hashing for checkpoints

    @ctr26
    ctr26 committed Jan 18, 2024
    Configuration menu
    Copy the full SHA
    3b37ca9 View commit details
    Browse the repository at this point in the history

  3. Early stopping on val loss to stop overfitting

    @ctr26
    ctr26 committed Jan 18, 2024
    Configuration menu
    Copy the full SHA
    8e18943 View commit details
    Browse the repository at this point in the history

  4. Attempt at cli

    @ctr26
    ctr26 committed Jan 18, 2024
    Configuration menu
    Copy the full SHA
    397abe8 View commit details
    Browse the repository at this point in the history

Commits on Jan 19, 2024

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

    …ether
    @afoix
    afoix committed Jan 19, 2024
    Configuration menu
    Copy the full SHA
    8534143 View commit details
    Browse the repository at this point in the history

  2. Merge pull request uhlmanngroup#34 from ctr26/logger_improve 

    Generalised the logging a bit
    @ctr26
    ctr26 authored Jan 19, 2024
    Configuration menu
    Copy the full SHA
    e4e26a9 View commit details
    Browse the repository at this point in the history

  3. Merge pull request uhlmanngroup#35 from ctr26/hashing_model_args 

    First attempt as arg hashing for checkpoints
    @ctr26
    ctr26 authored Jan 19, 2024
    Configuration menu
    Copy the full SHA
    820b816 View commit details
    Browse the repository at this point in the history

  4. Early stopping on val loss to stop overfitting

    @ctr26
    ctr26 committed Jan 19, 2024
    Configuration menu
    Copy the full SHA
    4bf27f9 View commit details
    Browse the repository at this point in the history

Commits on Jan 20, 2024

  1. adding branch prose back

    @ctr26
    ctr26 committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    4ca9dd0 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'master' into all_together

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    0068fa0 View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    26bf58c View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    1d5c49c View commit details
    Browse the repository at this point in the history

  5. local changes to run

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    a34ee72 View commit details
    Browse the repository at this point in the history

  6. command line arguments

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    9135043 View commit details
    Browse the repository at this point in the history

  7. enable testing + uncomment dataset

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    43c6ed0 View commit details
    Browse the repository at this point in the history

  8. added a slurm python script

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    e4e0aae View commit details
    Browse the repository at this point in the history

  9. fix cli type

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    e78afd6 View commit details
    Browse the repository at this point in the history

  10. add correct name for the jobs

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    ee021c6 View commit details
    Browse the repository at this point in the history

  11. Log f1 score mean and std in wandb

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    30c34cc View commit details
    Browse the repository at this point in the history

  12. choose memory allocation base on latent space size

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    b77c4fc View commit details
    Browse the repository at this point in the history

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

    …ion as well
    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    8f7d9d8 View commit details
    Browse the repository at this point in the history

  14. fix gpu allocation typo

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    41dec50 View commit details
    Browse the repository at this point in the history

  15. comment out all the mean and std login for f1

    @afoix
    afoix committed Jan 20, 2024
    Configuration menu
    Copy the full SHA
    775548a View commit details
    Browse the repository at this point in the history

Commits on Jan 23, 2024

  1. added a --clear-checkpoints clarg

    @afoix
    afoix committed Jan 23, 2024
    Configuration menu
    Copy the full SHA
    1cf6646 View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Jan 23, 2024
    Configuration menu
    Copy the full SHA
    704c88f View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Jan 23, 2024
    Configuration menu
    Copy the full SHA
    15343f6 View commit details
    Browse the repository at this point in the history

Commits on Feb 21, 2024

  1. Updating pythae

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    4981381 View commit details
    Browse the repository at this point in the history

  2. Adding standard scalar to df scoring fun

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    9da2a22 View commit details
    Browse the repository at this point in the history

  3. Refactoring and adding back umap

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    873ef92 View commit details
    Browse the repository at this point in the history

  4. Seed "everything"

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    7527363 View commit details
    Browse the repository at this point in the history

  5. Reduce k folds (should be a hparam)

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    afb0368 View commit details
    Browse the repository at this point in the history

  6. Update args to match what we now think is good

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    941dc80 View commit details
    Browse the repository at this point in the history

  7. Dynamic best weights finding

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    2ccf8b4 View commit details
    Browse the repository at this point in the history

  8. Fixed umap

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    d7761b6 View commit details
    Browse the repository at this point in the history

  9. Made the class column categorical

    @ctr26
    ctr26 committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    22832d6 View commit details
    Browse the repository at this point in the history

Commits on Feb 22, 2024

  1. modification for slurm

    @afoix
    afoix committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    e567748 View commit details
    Browse the repository at this point in the history

  2. changes in the shape embed script

    @afoix
    afoix committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    161b0a0 View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    ae215ae View commit details
    Browse the repository at this point in the history

  4. Merge pull request uhlmanngroup#40 from ctr26/shape_embed

    @ctr26
    ctr26 authored Feb 22, 2024
    Configuration menu
    Copy the full SHA
    faf72e4 View commit details
    Browse the repository at this point in the history

  5. fix merge commit + add command line args for dataset (name and path) … 

    …and wandb project
    @afoix
    afoix committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    a6cb292 View commit details
    Browse the repository at this point in the history

  6. duplicated slurm script + specify dataset

    @afoix
    afoix committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    1999076 View commit details
    Browse the repository at this point in the history

  7. Fix wandb logger

    @afoix
    afoix committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    d3525a8 View commit details
    Browse the repository at this point in the history

  8. Add helakyoto dataset to the slurm script

    @afoix
    afoix committed Feb 22, 2024
    Configuration menu
    Copy the full SHA
    7a60b2a View commit details
    Browse the repository at this point in the history

Commits on Feb 29, 2024

  1. better imports

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    e43e839 View commit details
    Browse the repository at this point in the history

  2. Adding dataset path to args for better checkpointing

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    ffbd8ea View commit details
    Browse the repository at this point in the history

  3. Imrproved dataset logic so that dist depends on coords

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    a3e82a9 View commit details
    Browse the repository at this point in the history

  4. Improved data rejection for datatsets

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    5b720d4 View commit details
    Browse the repository at this point in the history

  5. Removing redundant code and adding logging

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    dea41f6 View commit details
    Browse the repository at this point in the history

  6. [bug] Removing hard coded idx mapper

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    85f1211 View commit details
    Browse the repository at this point in the history

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

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    e411a9d View commit details
    Browse the repository at this point in the history

  8. More logging

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    66df0b9 View commit details
    Browse the repository at this point in the history

  9. Adding a disk cleanup step

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    b5db367 View commit details
    Browse the repository at this point in the history

  10. Reverting to other path structure

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    f580f97 View commit details
    Browse the repository at this point in the history

  11. Adding average cross val to logs

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    ae9f8d1 View commit details
    Browse the repository at this point in the history

  12. Adding opencv to env file

    @ctr26
    ctr26 committed Feb 29, 2024
    Configuration menu
    Copy the full SHA
    dcdfa63 View commit details
    Browse the repository at this point in the history

Commits on Mar 1, 2024

  1. Added allen dataset

    @afoix
    afoix committed Mar 1, 2024
    Configuration menu
    Copy the full SHA
    e8ca2cb View commit details
    Browse the repository at this point in the history

  2. Limit time per job increased to 24h

    @afoix
    afoix committed Mar 1, 2024
    Configuration menu
    Copy the full SHA
    775442c View commit details
    Browse the repository at this point in the history

  3. Merge branch 'shape_embed' into slurm

    @afoix
    afoix committed Mar 1, 2024
    Configuration menu
    Copy the full SHA
    5e21453 View commit details
    Browse the repository at this point in the history

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

    @ctr26
    ctr26 committed Mar 1, 2024
    Configuration menu
    Copy the full SHA
    2fce547 View commit details
    Browse the repository at this point in the history

Commits on Mar 3, 2024

  1. Merge branch 'bad_data_fix' into slurm

    @afoix
    afoix committed Mar 3, 2024
    Configuration menu
    Copy the full SHA
    f88da4f View commit details
    Browse the repository at this point in the history

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

    …name and latent space size
    @afoix
    afoix committed Mar 3, 2024
    Configuration menu
    Copy the full SHA
    6e14ffd View commit details
    Browse the repository at this point in the history

  3. added back dataset subseting

    @afoix
    afoix committed Mar 3, 2024
    Configuration menu
    Copy the full SHA
    f31b9a0 View commit details
    Browse the repository at this point in the history

  4. Added a tiny dataset for quick debugging (commented out in the slurm … 

    …script)
    @afoix
    afoix committed Mar 3, 2024
    Configuration menu
    Copy the full SHA
    d052800 View commit details
    Browse the repository at this point in the history

Commits on Mar 4, 2024

  1. use specific gpu resource

    @afoix
    afoix committed Mar 4, 2024
    Configuration menu
    Copy the full SHA
    df41415 View commit details
    Browse the repository at this point in the history

Commits on Mar 5, 2024

  1. Adding roc_auc and using balanced accuracy

    @ctr26
    ctr26 committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    f1e5a3c View commit details
    Browse the repository at this point in the history

  2. Probably should stratify

    @ctr26
    ctr26 committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    d31ca96 View commit details
    Browse the repository at this point in the history

  3. Adding coordinate debug (unchecked)

    @ctr26
    ctr26 committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    abe2664 View commit details
    Browse the repository at this point in the history

Commits on Mar 6, 2024

  1. put back frobenius norm false

    @afoix
    afoix committed Mar 6, 2024
    Configuration menu
    Copy the full SHA
    ab48c09 View commit details
    Browse the repository at this point in the history

  2. merge of Craig's branch

    @afoix
    afoix committed Mar 6, 2024
    Configuration menu
    Copy the full SHA
    67e3708 View commit details
    Browse the repository at this point in the history

  3. Forgot an import

    @ctr26
    ctr26 committed Mar 6, 2024
    Configuration menu
    Copy the full SHA
    46eb3d1 View commit details
    Browse the repository at this point in the history

Commits on Mar 7, 2024

  1. add the hardcode entity and add model dir

    @afoix
    afoix committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    db88d34 View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Mar 7, 2024
    Configuration menu
    Copy the full SHA
    162ae51 View commit details
    Browse the repository at this point in the history

Commits on Mar 11, 2024

  1. reduce epochs

    @afoix
    afoix committed Mar 11, 2024
    Configuration menu
    Copy the full SHA
    2505a2d View commit details
    Browse the repository at this point in the history

Commits on Mar 27, 2024

  1. all changes

    @afoix
    afoix committed Mar 27, 2024
    Configuration menu
    Copy the full SHA
    f588a2d View commit details
    Browse the repository at this point in the history

  2. first structure

    @afoix
    afoix committed Mar 27, 2024
    Configuration menu
    Copy the full SHA
    6151a6f View commit details
    Browse the repository at this point in the history

Commits on Apr 1, 2024

  1. Properly overwrite default params from clargs

    @afoix
    afoix committed Apr 1, 2024
    Configuration menu
    Copy the full SHA
    8208238 View commit details
    Browse the repository at this point in the history

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

    …nels copy for models to be happy
    @afoix
    afoix committed Apr 1, 2024
    Configuration menu
    Copy the full SHA
    aacac25 View commit details
    Browse the repository at this point in the history

  3. Disable checkpoints in training by default (maybe re-enable at some f… 

    …uture point)
    @afoix
    afoix committed Apr 1, 2024
    Configuration menu
    Copy the full SHA
    579ab0b View commit details
    Browse the repository at this point in the history

  4. Enable gpu accelleration by default

    @afoix
    afoix committed Apr 1, 2024
    Configuration menu
    Copy the full SHA
    f0fee88 View commit details
    Browse the repository at this point in the history

  5. more informative verbose print

    @afoix
    afoix committed Apr 1, 2024
    Configuration menu
    Copy the full SHA
    5e97713 View commit details
    Browse the repository at this point in the history

  6. bring argparse to the masks2distmatrices script

    @afoix
    afoix committed Apr 1, 2024
    Configuration menu
    Copy the full SHA
    bb425df View commit details
    Browse the repository at this point in the history

Commits on Apr 2, 2024

  1. training and test model

    @afoix
    afoix committed Apr 2, 2024
    Configuration menu
    Copy the full SHA
    ac3b85a View commit details
    Browse the repository at this point in the history

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

    … space
    @afoix
    afoix committed Apr 2, 2024
    Configuration menu
    Copy the full SHA
    7e7c7a2 View commit details
    Browse the repository at this point in the history

  3. Added wandb logging

    @afoix
    afoix committed Apr 2, 2024
    Configuration menu
    Copy the full SHA
    da4acf8 View commit details
    Browse the repository at this point in the history

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

    …utput dir
    @afoix
    afoix committed Apr 2, 2024
    Configuration menu
    Copy the full SHA
    fd7d122 View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Apr 2, 2024
    Configuration menu
    Copy the full SHA
    ee7cd7f View commit details
    Browse the repository at this point in the history

Commits on Apr 9, 2024

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

    …tours from dm
    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    20db342 View commit details
    Browse the repository at this point in the history

  2. masks2distmat: turn find_contour into find_longest_contour

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    7844798 View commit details
    Browse the repository at this point in the history

  3. masks2distmat: enable periodic splprep for closed contours

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    177df9e View commit details
    Browse the repository at this point in the history

  4. masks2distmat: updated default sparsity to 4

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    4bd1487 View commit details
    Browse the repository at this point in the history

  5. distmat2contour: removed spurious return statement in vprint

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    6d951e4 View commit details
    Browse the repository at this point in the history

  6. drawContourFromDM: removed spurious return statement in vprint

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    1481b51 View commit details
    Browse the repository at this point in the history

  7. set correct aspect ratio for distmat2contour scripts

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    01c499a View commit details
    Browse the repository at this point in the history

  8. add different normalisations in dataset initial transformations

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    879c5f4 View commit details
    Browse the repository at this point in the history

  9. Add notion of class label to ditmat2emb script output

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    fc58ad3 View commit details
    Browse the repository at this point in the history

  10. Updated default model path in distmat2emb script

    @afoix
    afoix committed Apr 9, 2024
    Configuration menu
    Copy the full SHA
    2a4d955 View commit details
    Browse the repository at this point in the history

Commits on Apr 15, 2024

  1. Added umap and kmeans + original filenames list

    @afoix
    afoix committed Apr 15, 2024
    Configuration menu
    Copy the full SHA
    0c166ec View commit details
    Browse the repository at this point in the history

Commits on Apr 17, 2024

  1. dist2emb: random seed for np and pl

    @afoix
    afoix committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    4826ba3 View commit details
    Browse the repository at this point in the history

  2. dist2emb: test different initial transformations

    @afoix
    afoix committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    3e56247 View commit details
    Browse the repository at this point in the history

  3. dist2emb: remove "TODO" from prints

    @afoix
    afoix committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    a29c57d View commit details
    Browse the repository at this point in the history

  4. cosmetics

    @afoix
    afoix committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    bf5ce7f View commit details
    Browse the repository at this point in the history

  5. LitAutoEncoderTorch: return both loss and recon_loss

    @afoix
    afoix committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    41890e5 View commit details
    Browse the repository at this point in the history

  6. MaskEmbed: turn off normalisation in DistanceMatrixLoss

    @afoix
    afoix committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    beb5714 View commit details
    Browse the repository at this point in the history

  7. MaskEmbed: log losses in loss_function method

    @afoix
    afoix committed Apr 17, 2024
    Configuration menu
    Copy the full SHA
    da092b5 View commit details
    Browse the repository at this point in the history

Commits on Apr 24, 2024

  1. renamed varitional_loss to vq_loss + comment out kdl_vae_loss

    @afoix
    afoix committed Apr 24, 2024
    Configuration menu
    Copy the full SHA
    78d067d View commit details
    Browse the repository at this point in the history

  2. removed new line

    @afoix
    afoix committed Apr 24, 2024
    Configuration menu
    Copy the full SHA
    d0c4ffb View commit details
    Browse the repository at this point in the history

  3. Normalise contour coord in mask2distmat script

    @afoix
    afoix committed Apr 24, 2024
    Configuration menu
    Copy the full SHA
    253b3f4 View commit details
    Browse the repository at this point in the history

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

    @afoix
    afoix committed Apr 24, 2024
    Configuration menu
    Copy the full SHA
    5066e3d View commit details
    Browse the repository at this point in the history

Commits on Apr 25, 2024

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

    … gen UMAPs script
    @afoix
    afoix committed Apr 25, 2024
    Configuration menu
    Copy the full SHA
    977620e View commit details
    Browse the repository at this point in the history

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)
    @afoix
    afoix committed Apr 26, 2024
    Configuration menu
    Copy the full SHA
    ccdc090 View commit details
    Browse the repository at this point in the history

Commits on Apr 29, 2024

  1. minor config + comments

    @afoix
    afoix committed Apr 29, 2024
    Configuration menu
    Copy the full SHA
    3601e3b View commit details
    Browse the repository at this point in the history

Commits on May 8, 2024

  1. added a beta vae model

    @afoix
    afoix committed May 8, 2024
    Configuration menu
    Copy the full SHA
    3f98d06 View commit details
    Browse the repository at this point in the history

  2. added extra parameters in the wandb jobname

    @afoix
    afoix committed May 8, 2024
    Configuration menu
    Copy the full SHA
    f6ee1ac View commit details
    Browse the repository at this point in the history

Commits on May 10, 2024

  1. finer grained clargs around latent space related parameters

    @afoix
    afoix committed May 10, 2024
    Configuration menu
    Copy the full SHA
    01b746f View commit details
    Browse the repository at this point in the history

  2. log different losses for vq or beta models

    @afoix
    afoix committed May 10, 2024
    Configuration menu
    Copy the full SHA
    d493ea5 View commit details
    Browse the repository at this point in the history

Commits on May 13, 2024

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

    @afoix
    afoix committed May 13, 2024
    Configuration menu
    Copy the full SHA
    b15dff4 View commit details
    Browse the repository at this point in the history

Commits on Jun 5, 2024

  1. new latent space size

    @afoix
    afoix committed Jun 5, 2024
    Configuration menu
    Copy the full SHA
    1a2bcf1 View commit details
    Browse the repository at this point in the history

  2. Added imports that will be needed for next commits

    @afoix
    afoix committed Jun 5, 2024
    Configuration menu
    Copy the full SHA
    b6f12c2 View commit details
    Browse the repository at this point in the history

  3. Added checkpoint mechanism

    @afoix
    afoix committed Jun 5, 2024
    Configuration menu
    Copy the full SHA
    79e75ce View commit details
    Browse the repository at this point in the history

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

    …o synthetic shapes dataset needs to be generalised)
    @afoix
    afoix committed Jun 5, 2024
    Configuration menu
    Copy the full SHA
    a8406ea View commit details
    Browse the repository at this point in the history

Commits on Jun 16, 2024

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

    @afoix
    afoix committed Jun 16, 2024
    Configuration menu
    Copy the full SHA
    03a4cf7 View commit details
    Browse the repository at this point in the history

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

    … cross validation
    @afoix
    afoix committed Jun 16, 2024
    Configuration menu
    Copy the full SHA
    5467f9f View commit details
    Browse the repository at this point in the history

  3. hardcoded commited setup now points to quick test setup

    @afoix
    afoix committed Jun 16, 2024
    Configuration menu
    Copy the full SHA
    344c8ab View commit details
    Browse the repository at this point in the history

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

    …ng metrics
    @afoix
    afoix committed Jun 16, 2024
    Configuration menu
    Copy the full SHA
    9a6456e View commit details
    Browse the repository at this point in the history

Commits on Jun 17, 2024

  1. Added predictions + kmeans of input data

    @afoix
    afoix committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    751394e View commit details
    Browse the repository at this point in the history

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

    …oring
    @afoix
    afoix committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    949254d View commit details
    Browse the repository at this point in the history

Commits on Jun 18, 2024

  1. cleaner logging + score shapeembed itself

    @afoix
    afoix committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    43a3969 View commit details
    Browse the repository at this point in the history

  2. reshaped shapeembed reported dataframe

    @afoix
    afoix committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    9030e48 View commit details
    Browse the repository at this point in the history

  3. renamed label to class

    @afoix
    afoix committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    6a5c7d0 View commit details
    Browse the repository at this point in the history

  4. updated scoring function + collate and save results

    @afoix
    afoix committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    d216cc7 View commit details
    Browse the repository at this point in the history

  5. Added clargs to control matrix normalization and roll

    @afoix
    afoix committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    7e2bdbd View commit details
    Browse the repository at this point in the history

  6. Added umap_plot

    @afoix
    afoix committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    86ede7b View commit details
    Browse the repository at this point in the history

Commits on Jun 24, 2024

  1. fix dataset clarg

    @afoix
    afoix committed Jun 24, 2024
    Configuration menu
    Copy the full SHA
    19edf47 View commit details
    Browse the repository at this point in the history

  2. fix model name clarg

    @afoix
    afoix committed Jun 24, 2024
    Configuration menu
    Copy the full SHA
    976edc2 View commit details
    Browse the repository at this point in the history

  3. fix model_name clarg again

    @afoix
    afoix committed Jun 24, 2024
    Configuration menu
    Copy the full SHA
    d1c5d3c View commit details
    Browse the repository at this point in the history

Commits on Jun 25, 2024

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

    @afoix
    afoix committed Jun 25, 2024
    Configuration menu
    Copy the full SHA
    4851241 View commit details
    Browse the repository at this point in the history

Commits on Jun 26, 2024

  1. added confusion matrices to scoring function

    @afoix
    afoix committed Jun 26, 2024
    Configuration menu
    Copy the full SHA
    b95272e View commit details
    Browse the repository at this point in the history

  2. use integer division for compression factor clarg

    @afoix
    afoix committed Jun 26, 2024
    Configuration menu
    Copy the full SHA
    222f698 View commit details
    Browse the repository at this point in the history

  3. explicitly binarise image when running regionprops

    @afoix
    afoix committed Jun 26, 2024
    Configuration menu
    Copy the full SHA
    793b720 View commit details
    Browse the repository at this point in the history

  4. keep 'class' as a column rather than index + keeps column names as st… 

    …rings
    @afoix
    afoix committed Jun 26, 2024
    Configuration menu
    Copy the full SHA
    43673ee View commit details
    Browse the repository at this point in the history

  5. change len for shape[0]

    @afoix
    afoix committed Jun 26, 2024
    Configuration menu
    Copy the full SHA
    11a6e69 View commit details
    Browse the repository at this point in the history

  6. drop not needed return value from run_predictions

    @afoix
    afoix committed Jun 26, 2024
    Configuration menu
    Copy the full SHA
    91dd1c5 View commit details
    Browse the repository at this point in the history

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

    … kmeans
    @afoix
    afoix committed Jun 26, 2024
    Configuration menu
    Copy the full SHA
    963d590 View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2024

  1. save combined score

    @afoix
    afoix committed Jun 27, 2024
    Configuration menu
    Copy the full SHA
    df09ad5 View commit details
    Browse the repository at this point in the history

  2. save confusion matrices

    @afoix
    afoix committed Jun 27, 2024
    Configuration menu
    Copy the full SHA
    ff6fbd4 View commit details
    Browse the repository at this point in the history

Commits on Jul 5, 2024

  1. First attempt at a result gathering script

    @afoix
    afoix committed Jul 5, 2024
    Configuration menu
    Copy the full SHA
    ebadaff View commit details
    Browse the repository at this point in the history

  2. added barplots

    @afoix
    afoix committed Jul 5, 2024
    Configuration menu
    Copy the full SHA
    59fab42 View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2024

  1. Added a separate regionprops script

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    bfab20d View commit details
    Browse the repository at this point in the history

  2. added a separate efd script

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    c4a3a23 View commit details
    Browse the repository at this point in the history

  3. refactor efd and regionprops out of evaluation helpers

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    b799803 View commit details
    Browse the repository at this point in the history

  4. less debug info by default + create outdir if not there

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    6bc1947 View commit details
    Browse the repository at this point in the history

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

    …sation
    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    db47da9 View commit details
    Browse the repository at this point in the history

  6. unify file names across efd/regionprops/shapeembed

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    5a8b274 View commit details
    Browse the repository at this point in the history

  7. Added a readme

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    9d3a053 View commit details
    Browse the repository at this point in the history

  8. track params in reporting

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    8326afc View commit details
    Browse the repository at this point in the history

  9. also add model specific params as tag columns

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    aaa55db View commit details
    Browse the repository at this point in the history

  10. added a slurm script to sweap shapeembed parameters

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    ba67d36 View commit details
    Browse the repository at this point in the history

  11. added resnet50_beta_vae to the factory

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    7c422b1 View commit details
    Browse the repository at this point in the history

  12. added resnet50_beta_vae to the shapeembed script

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    1307579 View commit details
    Browse the repository at this point in the history

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

    …sweap
    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    1f82d9f View commit details
    Browse the repository at this point in the history

  14. better slurm jobname

    @afoix
    afoix committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    2c49fc9 View commit details
    Browse the repository at this point in the history

Commits on Jul 19, 2024

  1. removed compression factor 20

    @afoix
    afoix committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    a291c03 View commit details
    Browse the repository at this point in the history

  2. bumped up memory allocation to 250G

    @afoix
    afoix committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    a29b6bd View commit details
    Browse the repository at this point in the history

  3. added --no-early-stop flag

    @afoix
    afoix committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    dde96fc View commit details
    Browse the repository at this point in the history

Commits on Jul 20, 2024

  1. added an oom_retry function

    @afoix
    afoix committed Jul 20, 2024
    Configuration menu
    Copy the full SHA
    8dbf551 View commit details
    Browse the repository at this point in the history

  2. refined min / max epochs clargs

    @afoix
    afoix committed Jul 20, 2024
    Configuration menu
    Copy the full SHA
    38a9ff6 View commit details
    Browse the repository at this point in the history

  3. slurm script refactor args + force 150 epochs

    @afoix
    afoix committed Jul 20, 2024
    Configuration menu
    Copy the full SHA
    10c8b50 View commit details
    Browse the repository at this point in the history

  4. bring triangular + compression computation in named function (to shar… 

    …e use)
    @afoix
    afoix committed Jul 20, 2024
    Configuration menu
    Copy the full SHA
    c0cd3b4 View commit details
    Browse the repository at this point in the history

  5. fix in model_str function test of model_args

    @afoix
    afoix committed Jul 20, 2024
    Configuration menu
    Copy the full SHA
    3b1fdda View commit details
    Browse the repository at this point in the history

  6. refactor slurm script to detect already completed jobs

    @afoix
    afoix committed Jul 20, 2024
    Configuration menu
    Copy the full SHA
    65842f6 View commit details
    Browse the repository at this point in the history

  7. factored out some common helpers

    @afoix
    afoix committed Jul 20, 2024
    Configuration menu
    Copy the full SHA
    f97657e View commit details
    Browse the repository at this point in the history

Commits on Jul 21, 2024

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

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    b74be39 View commit details
    Browse the repository at this point in the history

  2. added a function to find currently submitted slurm jobs

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    9b8e934 View commit details
    Browse the repository at this point in the history

  3. added clargs for job filtering enabling/disabling (enabled by default)

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    2cead3d View commit details
    Browse the repository at this point in the history

  4. typo fix: sweap -> sweep

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    650fcc1 View commit details
    Browse the repository at this point in the history

  5. parse dataset as a SimpleNamespace from job string

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    62704af View commit details
    Browse the repository at this point in the history

  6. updated data gathering script to newer changes (still TODO for figures)

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    6e9ffcf View commit details
    Browse the repository at this point in the history

  7. removed stale script string

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    ffce0d3 View commit details
    Browse the repository at this point in the history

  8. Split model name in two columns if there are model args

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    d802f9a View commit details
    Browse the repository at this point in the history

  9. remove stale import

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    663cc52 View commit details
    Browse the repository at this point in the history

  10. experiment with plots

    @afoix
    afoix committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    7d328d9 View commit details
    Browse the repository at this point in the history

Commits on Jul 22, 2024

  1. keep exploring potential plots

    @afoix
    afoix committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    e3796ba View commit details
    Browse the repository at this point in the history

  2. more graphs

    @afoix
    afoix committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    cecde4e View commit details
    Browse the repository at this point in the history

  3. fix model name in shapeembed output csv

    @afoix
    afoix committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    344cff1 View commit details
    Browse the repository at this point in the history

  4. Added loss / mse to shapeembed's generated csv

    @afoix
    afoix committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    6846ce1 View commit details
    Browse the repository at this point in the history

Commits on Jul 25, 2024

  1. updated slurm script with regex filtering of squeue output

    @afoix
    afoix committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    7a8972f View commit details
    Browse the repository at this point in the history

  2. added a simple latex table to the gather_run_results script

    @afoix
    afoix committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    d9c87a3 View commit details
    Browse the repository at this point in the history

Commits on Jul 27, 2024

  1. minor refactor in efd

    @afoix
    afoix committed Jul 27, 2024
    Configuration menu
    Copy the full SHA
    cced4e9 View commit details
    Browse the repository at this point in the history

  2. minor refactor in regionprops

    @afoix
    afoix committed Jul 27, 2024
    Configuration menu
    Copy the full SHA
    3e6e4c9 View commit details
    Browse the repository at this point in the history

  3. generated plots and more tables in gather_run_results

    @afoix
    afoix committed Jul 27, 2024
    Configuration menu
    Copy the full SHA
    2908c15 View commit details
    Browse the repository at this point in the history

  4. added regionprops and efd to gather results script

    @afoix
    afoix committed Jul 27, 2024
    Configuration menu
    Copy the full SHA
    41d4603 View commit details
    Browse the repository at this point in the history

Commits on Jul 29, 2024

  1. Updated graphs titles

    @afoix
    afoix committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    251d85f View commit details
    Browse the repository at this point in the history

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

    …f1 Vs Mse comparison
    @afoix
    afoix committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    932b13a View commit details
    Browse the repository at this point in the history

  3. updated datasets + only find jobs and scores if corresponding filter … 

    …active
    @afoix
    afoix committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    61f8e17 View commit details
    Browse the repository at this point in the history

  4. bugfix overwriting loop dataframe

    @afoix
    afoix committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    583e835 View commit details
    Browse the repository at this point in the history

Commits on Jul 30, 2024

  1. dded a clarg to control region prop properties

    @afoix
    afoix committed Jul 30, 2024
    Configuration menu
    Copy the full SHA
    07bb89c View commit details
    Browse the repository at this point in the history

Commits on Aug 8, 2024

  1. Added random order to efd and regionprops

    @afoix
    afoix committed Aug 8, 2024
    Configuration menu
    Copy the full SHA
    a35490c View commit details
    Browse the repository at this point in the history

Commits on Sep 7, 2024

  1. force different markers for scatter plot F1vMSE

    @afoix
    afoix committed Sep 7, 2024
    Configuration menu
    Copy the full SHA
    83a7679 View commit details
    Browse the repository at this point in the history

Commits on Sep 9, 2024

  1. updated scatterplot

    @afoix
    afoix committed Sep 9, 2024
    Configuration menu
    Copy the full SHA
    b9c64d5 View commit details
    Browse the repository at this point in the history

Commits on Sep 27, 2024

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

    @afoix
    afoix committed Sep 27, 2024
    Configuration menu
    Copy the full SHA
    d51a120 View commit details
    Browse the repository at this point in the history

  2. modification slurm script

    @afoix
    afoix committed Sep 27, 2024
    Configuration menu
    Copy the full SHA
    c0232c7 View commit details
    Browse the repository at this point in the history

Commits on Sep 29, 2024

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

    … present in bioimage_embed/modles/o2vae
    @afoix
    afoix committed Sep 29, 2024
    Configuration menu
    Copy the full SHA
    870aa42 View commit details
    Browse the repository at this point in the history

  2. off-by-one in square recrop

    @afoix
    afoix committed Sep 29, 2024
    Configuration menu
    Copy the full SHA
    6fa5cc9 View commit details
    Browse the repository at this point in the history

Commits on Sep 30, 2024

  1. added drop_last for uneven dataset sizes

    @afoix
    afoix committed Sep 30, 2024
    Configuration menu
    Copy the full SHA
    85ce853 View commit details
    Browse the repository at this point in the history

  2. specialized slurm script

    @afoix
    afoix committed Sep 30, 2024
    Configuration menu
    Copy the full SHA
    db3a4fb View commit details
    Browse the repository at this point in the history

  3. added o2vae repo patch

    @afoix
    afoix committed Sep 30, 2024
    Configuration menu
    Copy the full SHA
    c45b884 View commit details
    Browse the repository at this point in the history