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O2vae integration#1

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ctr26 wants to merge 220 commits intomainuhlmanngroup/shape_embed:mainfrom o2vae-integrationuhlmanngroup/shape_embed:o2vae-integrationCopy head branch name to clipboard

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Commits on Jan 15, 2024

• Removing umap feature compression

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Commits on Jan 17, 2024

• Merge pull request uhlmanngroup#19 from ctr26/decoder_fix

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• Merge pull request uhlmanngroup#21 from ctr26/no_umap

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• Indexation augmentation (forgot this wasnt in here)

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• Fixed the import issue

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• missing import

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• Merge pull request uhlmanngroup#17 from ctr26/indexation_aug

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• Fixing tests

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• First attempt at setting up the testing cicd

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• adding windows back in?

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• commented instead I think this makes more sense

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• removing snakemake from env

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• Forgot to remove sourceing

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• Merge pull request uhlmanngroup#22 from ctr26/cicd

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Commits on Jan 18, 2024

• Generalised the logging a bit

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• First attempt as arg hashing for checkpoints

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• Early stopping on val loss to stop overfitting

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• Attempt at cli

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Commits on Jan 19, 2024

• Merge remote-tracking branch 'origin/hashing_model_args' into all_together

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• Merge pull request uhlmanngroup#34 from ctr26/logger_improve

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• Merge pull request uhlmanngroup#35 from ctr26/hashing_model_args

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• Early stopping on val loss to stop overfitting

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Commits on Jan 20, 2024

• adding branch prose back

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• Merge branch 'master' into all_together

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• Merge remote-tracking branch 'origin/early_stopping' into all_together

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• Merge remote-tracking branch 'origin/readme_edits' into all_together

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• local changes to run

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• command line arguments

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• enable testing + uncomment dataset

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• added a slurm python script

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• fix cli type

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• add correct name for the jobs

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• Log f1 score mean and std in wandb

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• choose memory allocation base on latent space size

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• dynamically chose n gpus based on latent space size + fix mem allocation as well

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• fix gpu allocation typo

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• comment out all the mean and std login for f1

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Commits on Jan 23, 2024

• added a --clear-checkpoints clarg

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

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• run individual jobs in own folder to work around checkpoints

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Commits on Feb 21, 2024

• Updating pythae

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• Adding standard scalar to df scoring fun

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• Refactoring and adding back umap

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• Seed "everything"

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• Reduce k folds (should be a hparam)

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• Update args to match what we now think is good

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• Dynamic best weights finding

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• Fixed umap

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• Made the class column categorical

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Commits on Feb 22, 2024

• modification for slurm

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• changes in the shape embed script

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• Merge remote-tracking branch 'origin/shape_embed' into slurm

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• Merge pull request uhlmanngroup#40 from ctr26/shape_embed

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• fix merge commit + add command line args for dataset (name and path) and wandb project

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• duplicated slurm script + specify dataset

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• Fix wandb logger

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• Add helakyoto dataset to the slurm script

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Commits on Feb 29, 2024

• better imports

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• Adding dataset path to args for better checkpointing

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• Imrproved dataset logic so that dist depends on coords

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• Improved data rejection for datatsets

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• Removing redundant code and adding logging

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• [bug] Removing hard coded idx mapper

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

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• More logging

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• Adding a disk cleanup step

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• Reverting to other path structure

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• Adding average cross val to logs

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• Adding opencv to env file

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Commits on Mar 1, 2024

• Added allen dataset

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• Limit time per job increased to 24h

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• Merge branch 'shape_embed' into slurm

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• Fixing case where multiple contours are found, chose the longest

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Commits on Mar 3, 2024

• Merge branch 'bad_data_fix' into slurm

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• change back to use dataset name from clarg + change default wandb jobname and latent space size

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• added back dataset subseting

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• Added a tiny dataset for quick debugging (commented out in the slurm script)

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Commits on Mar 4, 2024

• use specific gpu resource

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Commits on Mar 5, 2024

• Adding roc_auc and using balanced accuracy

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• Probably should stratify

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• Adding coordinate debug (unchecked)

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Commits on Mar 6, 2024

• put back frobenius norm false

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• merge of Craig's branch

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• Forgot an import

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Commits on Mar 7, 2024

• add the hardcode entity and add model dir

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• Merge remote-tracking branch 'origin/shape_embed' into slurm

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Commits on Mar 11, 2024

• reduce epochs

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Commits on Mar 27, 2024

• all changes

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• first structure

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Commits on Apr 1, 2024

• Properly overwrite default params from clargs

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• Use DatasetFolder to load .npy and turn the dist matrix into a 3 channels copy for models to be happy

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• Disable checkpoints in training by default (maybe re-enable at some future point)

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• Enable gpu accelleration by default

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• more informative verbose print

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• bring argparse to the masks2distmatrices script

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Commits on Apr 2, 2024

• training and test model

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• Roll indices + normalisation + sanity_check + dataset name for latent space

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• Added wandb logging

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• Added the extraction of original/reconstructed matrices + clarg for output dir

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

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Commits on Apr 9, 2024

• new changes: sparisity, periodicity and also add a script to draw contours from dm

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• masks2distmat: turn find_contour into find_longest_contour

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• masks2distmat: enable periodic splprep for closed contours

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• masks2distmat: updated default sparsity to 4

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• distmat2contour: removed spurious return statement in vprint

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• drawContourFromDM: removed spurious return statement in vprint

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• set correct aspect ratio for distmat2contour scripts

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• add different normalisations in dataset initial transformations

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• Add notion of class label to ditmat2emb script output

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• Updated default model path in distmat2emb script

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Commits on Apr 15, 2024

• Added umap and kmeans + original filenames list

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Commits on Apr 17, 2024

• dist2emb: random seed for np and pl

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• dist2emb: test different initial transformations

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• dist2emb: remove "TODO" from prints

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• cosmetics

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• LitAutoEncoderTorch: return both loss and recon_loss

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• MaskEmbed: turn off normalisation in DistanceMatrixLoss

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• MaskEmbed: log losses in loss_function method

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Commits on Apr 24, 2024

• renamed varitional_loss to vq_loss + comment out kdl_vae_loss

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• removed new line

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• Normalise contour coord in mask2distmat script

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

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Commits on Apr 25, 2024

• 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

• updated the render umap script with a _hardcoded_ trick to extract index from filename for the tree dataset (should use a user specified regex instead)

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Commits on Apr 29, 2024

• minor config + comments

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Commits on May 8, 2024

• added a beta vae model

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• added extra parameters in the wandb jobname

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Commits on May 10, 2024

• finer grained clargs around latent space related parameters

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• log different losses for vq or beta models

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Commits on May 13, 2024

• code to do classification using the features of the latent space

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Commits on Jun 5, 2024

• new latent space size

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• Added imports that will be needed for next commits

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• Added checkpoint mechanism

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• Added regionprops + fourrier decomposition trials (! hardcoded path to synthetic shapes dataset needs to be generalised)

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Commits on Jun 16, 2024

• Adding a n compression parameter for the latent space size

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• improve scoring function and use StratifiedKFold instead of KFold for cross validation

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• hardcoded commited setup now points to quick test setup

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• initial refactor commit, script with split up functionnalities, missing metrics

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Commits on Jun 17, 2024

• Added predictions + kmeans of input data

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• factored out evaluation functionality + added regionprops, efd and scoring

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Commits on Jun 18, 2024

• cleaner logging + score shapeembed itself

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• reshaped shapeembed reported dataframe

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• renamed label to class

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• updated scoring function + collate and save results

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• Added clargs to control matrix normalization and roll

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• Added umap_plot

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Commits on Jun 24, 2024

• fix dataset clarg

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• fix model name clarg

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• fix model_name clarg again

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Commits on Jun 25, 2024

• Added early stop clarg (default no early stop)

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Commits on Jun 26, 2024

• added confusion matrices to scoring function

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• use integer division for compression factor clarg

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• explicitly binarise image when running regionprops

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• keep 'class' as a column rather than index + keeps column names as strings

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• change len for shape[0]

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• drop not needed return value from run_predictions

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• added combined shapeembed + efd + regionprops scoring and comment out kmeans

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Commits on Jun 27, 2024

• save combined score

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• save confusion matrices

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Commits on Jul 5, 2024

• First attempt at a result gathering script

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• added barplots

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Commits on Jul 18, 2024

• Added a separate regionprops script

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• added a separate efd script

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• refactor efd and regionprops out of evaluation helpers

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• less debug info by default + create outdir if not there

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  6bc1947

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• removed regionprops/efd from main shapeembed script + filename sanitisation

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• unify file names across efd/regionprops/shapeembed

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• Added a readme

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• track params in reporting

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• also add model specific params as tag columns

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• added a slurm script to sweap shapeembed parameters

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• added resnet50_beta_vae to the factory

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• added resnet50_beta_vae to the shapeembed script

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• handle per model params in slurm script + chose some param values to sweap

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• better slurm jobname

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Commits on Jul 19, 2024

• removed compression factor 20

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• bumped up memory allocation to 250G

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• added --no-early-stop flag

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Commits on Jul 20, 2024

• added an oom_retry function

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• refined min / max epochs clargs

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• slurm script refactor args + force 150 epochs

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• bring triangular + compression computation in named function (to share use)

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• fix in model_str function test of model_args

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• refactor slurm script to detect already completed jobs

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• factored out some common helpers

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Commits on Jul 21, 2024

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

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• added a function to find currently submitted slurm jobs

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

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• typo fix: sweap -> sweep

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• parse dataset as a SimpleNamespace from job string

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

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• removed stale script string

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• Split model name in two columns if there are model args

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• remove stale import

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• experiment with plots

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Commits on Jul 22, 2024

• keep exploring potential plots

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• more graphs

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• fix model name in shapeembed output csv

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• Added loss / mse to shapeembed's generated csv

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Commits on Jul 25, 2024

• updated slurm script with regex filtering of squeue output

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• added a simple latex table to the gather_run_results script

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Commits on Jul 27, 2024

• minor refactor in efd

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• minor refactor in regionprops

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• generated plots and more tables in gather_run_results

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• added regionprops and efd to gather results script

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Commits on Jul 29, 2024

• Updated graphs titles

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• fake beta column if necessary and filter out regionprops and efd for f1 Vs Mse comparison

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• updated datasets + only find jobs and scores if corresponding filter active

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• bugfix overwriting loop dataframe

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Commits on Jul 30, 2024

• dded a clarg to control region prop properties

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Commits on Aug 8, 2024

• Added random order to efd and regionprops

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Commits on Sep 7, 2024

• force different markers for scatter plot F1vMSE

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Commits on Sep 9, 2024

• updated scatterplot

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Commits on Sep 27, 2024

• add standard deviation to the report for regions props and efd

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• modification slurm script

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Commits on Sep 29, 2024

• changes to test o2vae integration XXX relies on an adapted o2vae repo present in bioimage_embed/modles/o2vae

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• off-by-one in square recrop

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Commits on Sep 30, 2024

• added drop_last for uneven dataset sizes

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• specialized slurm script

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• added o2vae repo patch

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