Contrastive_dataloader #99
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ziw-liu
added a commit
that referenced
this pull request
Aug 2, 2024
* first draft of contrastive learning model * fixed stem and projection head, drafted lightning module * Contrastive_dataloader (#99) * initial dataloader.py * Update dataloader_test.py * Update dataloader_test.py * Update dataloader_test.py * Update dataloader_test.py * rename training script * move contrastive network to viscy.representation module * Update hcs.py * refactored class names * correct imports * cleaner names for model arch and module * new imports * Fixed epoch loss logging and WandB integration in ContrastiveModule * updated training_script.py * Update hcs.py * contrastive.py * engine.py * script to test data i/o speed from different filesystems * moved applications folder to viscy.applications so that pip install -e . works. * add resnet50 to ContrastiveEncoder * rename training_script.py to training_script_resnet.py * test dataloader on lustre and vast * move training_script_resnet to viscy.applications so that `pip install -e .` works * refined the tests for contrastive dataloader * sbatch script for dataloader * delete redundant module * nits: updated the model construction of contrastive resnet encoder. * Updated training script, HCS data handling, engine, and contrastive representation * Fix normalization, visualization issues, logging and multi-channel prediction * updated training and prediction * update training and prediction script * formatting * combine the application directories * lint * replace notebook with script * format script * rename scripts conflicting with pytest * lint application scripts * do not filter all warnings * log instead of print * split data modules by task * clean up imports * update typing * use pathlib * remove redundant file * updated predict.py * better typing * wip: triplet dataset * avoid forward ref this might increase code analysis time a tiny bit but should not have any effect at runtime * check that z range is valid and fix indexing * clean up and explain random sampling * sample dict instead of tuple and include track index * take out generic HCS methods for reuse * implement TripletDataModule * use new batch type in engine * better typing * read normalization metadata * docstring for data module * drop normalization metadata after transformation * remove unused import * fix initial crop size * Infection state (#118) * updated prediction code * updated predict code * updated code * fixed the stem and forward pass (#115) * fixed the stem and forward pass * update forward calls to encoder * self.encoder -> self.model * nits * l2 normalize projections * black compliance * black compliance * WIP: Save progress before merging * updated contrastive.py * stem update * updated predict code * Delete viscy/applications/contrastive_phenotyping/PCA.ipynb * pushing dataloader test updated * pca deleted * training and dataloader test * updated structure * deleted files * updated training merged files * removed commented code * removed uneeded code * removed uneeded code * removed comments * snake_case * fixed CI issues * removed num_fovs --------- Co-authored-by: Shalin Mehta <[email protected]> --------- Co-authored-by: Shalin Mehta <[email protected]> Co-authored-by: Alishba Imran <[email protected]> Co-authored-by: Alishba Imran <[email protected]> Co-authored-by: Alishba Imran <[email protected]> Co-authored-by: Duo Peng <[email protected]>
edyoshikun
pushed a commit
that referenced
this pull request
Aug 7, 2024
* first draft of contrastive learning model * fixed stem and projection head, drafted lightning module * Contrastive_dataloader (#99) * initial dataloader.py * Update dataloader_test.py * Update dataloader_test.py * Update dataloader_test.py * Update dataloader_test.py * rename training script * move contrastive network to viscy.representation module * Update hcs.py * refactored class names * correct imports * cleaner names for model arch and module * new imports * Fixed epoch loss logging and WandB integration in ContrastiveModule * updated training_script.py * Update hcs.py * contrastive.py * engine.py * script to test data i/o speed from different filesystems * moved applications folder to viscy.applications so that pip install -e . works. * add resnet50 to ContrastiveEncoder * rename training_script.py to training_script_resnet.py * test dataloader on lustre and vast * move training_script_resnet to viscy.applications so that `pip install -e .` works * refined the tests for contrastive dataloader * sbatch script for dataloader * delete redundant module * nits: updated the model construction of contrastive resnet encoder. * Updated training script, HCS data handling, engine, and contrastive representation * Fix normalization, visualization issues, logging and multi-channel prediction * updated training and prediction * update training and prediction script * formatting * combine the application directories * lint * replace notebook with script * format script * rename scripts conflicting with pytest * lint application scripts * do not filter all warnings * log instead of print * split data modules by task * clean up imports * update typing * use pathlib * remove redundant file * updated predict.py * better typing * wip: triplet dataset * avoid forward ref this might increase code analysis time a tiny bit but should not have any effect at runtime * check that z range is valid and fix indexing * clean up and explain random sampling * sample dict instead of tuple and include track index * take out generic HCS methods for reuse * implement TripletDataModule * use new batch type in engine * better typing * read normalization metadata * docstring for data module * drop normalization metadata after transformation * remove unused import * fix initial crop size * Infection state (#118) * updated prediction code * updated predict code * updated code * fixed the stem and forward pass (#115) * fixed the stem and forward pass * update forward calls to encoder * self.encoder -> self.model * nits * l2 normalize projections * black compliance * black compliance * WIP: Save progress before merging * updated contrastive.py * stem update * updated predict code * Delete viscy/applications/contrastive_phenotyping/PCA.ipynb * pushing dataloader test updated * pca deleted * training and dataloader test * updated structure * deleted files * updated training merged files * removed commented code * removed uneeded code * removed uneeded code * removed comments * snake_case * fixed CI issues * removed num_fovs --------- Co-authored-by: Shalin Mehta <[email protected]> --------- Co-authored-by: Shalin Mehta <[email protected]> Co-authored-by: Alishba Imran <[email protected]> Co-authored-by: Alishba Imran <[email protected]> Co-authored-by: Alishba Imran <[email protected]> Co-authored-by: Duo Peng <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.