Ecosyste.ms: Timeline
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pgarrison closed an issue on AllenCell/benchmarking_representations
Cite the paper from the README
* ~Make the title Benchmarking Representations~ * Reference the paper in the README, with citation * ~Make the following it's own step in the instructions, and make the connection to the followin...
pgarrison closed an issue on AllenCell/benchmarking_representations
Cite the paper from the README
* ~Make the title Benchmarking Representations~ * Reference the paper in the README, with citation * ~Make the following it's own step in the instructions, and make the connection to the followin...
pgarrison closed a pull request on AllenCell/benchmarking_representations
Reference paper in README
See formatted version here: https://github.com/AllenCell/benchmarking_representations/blob/reference-to-paper/README.md. I copied this citation format from bioRxiv, feel free to pick another for...
pgarrison opened a pull request on AllenCell/benchmarking_representations
Reference paper in README
See formatted version here: https://github.com/AllenCell/benchmarking_representations/blob/reference-to-paper/README.md. I copied this citation format from bioRxiv, feel free to pick another for...
pgarrison pushed 1 commit to reference-to-paper AllenCell/benchmarking_representations
- Link to bioRxiv e9ba372
pgarrison created a branch on AllenCell/benchmarking_representations
reference-to-paper - Benchmarking different methods for extracting unsupervised representations from images
pgarrison created a review on a pull request on AllenCell/benchmarking_representations
Great! I did not run it myself, but the code looks appropriate. I can confirm that the command in the PR description is identical to the one in the README (run_features.
pgarrison created a comment on a pull request on AllenCell/benchmarking_representations
I added these `.gitkeep` files to support [these instructions](https://github.com/AllenCell/benchmarking_representations/blob/main/docs/USAGE.md#option-2-download-individual-checkpoints) > By de...
pgarrison created a review comment on a pull request on AllenCell/benchmarking_representations
Didn't know this was here! Glad to see it removed
pgarrison closed an issue on AllenCell/benchmarking_representations
Instructions for using checkpoints
Model checkpoint instructions should be more explicit than the current "To skip model training, download pre-trained models." Where do the checkpoints go? What to do about the fact that the `.yaml`...
pgarrison pushed 15 commits to main AllenCell/benchmarking_representations
- gitignore for pdm ae31ffc
- Clean up source trees facd66b
- Section headers for training, inference, and analysis 738c226
- Make table of where to download .ckpt files 3d209e6
- pre-commit 7be4df2
- Remove unused image f4ac18b
- Copy examples for run_embeddings and friends f1f17ea
- Merge remote-tracking branch 'origin/main' into ckpt-docs 375f9a2
- Table of embedding commands 7dc536e
- Clarify multiple s per folder 23f615e
- Clean up source tree c3eb680
- Clean up source tree 3c0bed5
- pre-commit 0b1be12
- Download .ckpt files into morphology_appropriate_representation_learning/model_checkpoints f416574
- Merge pull request #61 from AllenCell/ckpt-docs Ckpt docs 36e07a7
pgarrison closed a pull request on AllenCell/benchmarking_representations
Ckpt docs
# Issue We need to explain how to download and use the checkpoints. Closes #6 # Changes * Write a table describing how to copy checkpoints to folders like `configs/experiment/cellpack/ckpt...
pgarrison pushed 2 commits to main AllenCell/benchmarking_representations
pgarrison closed a pull request on AllenCell/benchmarking_representations
Preprocessing config: Dummy values for fields the user must edit.
# Issue There's ambiguity in many of our config files, and this one in particular, about what variables the user is supposed to set, and which can be left blank. Ritvik said the `samples_per_st...
pgarrison created a comment on a pull request on AllenCell/benchmarking_representations
Updated with instructions to download to `morphology_appropriate_representation_learning/model_checkpoints`
pgarrison created a review comment on a pull request on AllenCell/benchmarking_representations
Removed the table entirely: [f416574](https://github.com/AllenCell/benchmarking_representations/pull/61/commits/f416574e47f28ec38bfa09206abcdc04a6d426ca)
pgarrison pushed 1 commit to ckpt-docs AllenCell/benchmarking_representations
- Download .ckpt files into morphology_appropriate_representation_learning/model_checkpoints f416574
pgarrison created a branch on AllenCell/benchmarking_representations
downgrade-codecarbon - Benchmarking different methods for extracting unsupervised representations from images
pgarrison created a branch on AllenCell/benchmarking_representations
preprocessing-config-placeholders - Benchmarking different methods for extracting unsupervised representations from images
pgarrison closed an issue on AllenCell/benchmarking_representations
Remove ML Flow dependency
We should not expect external users to run mlflow. * Use CSV logger by default in all experiments * Instructions should not have steps that require mlflow
pgarrison pushed 1 commit to ckpt-docs AllenCell/benchmarking_representations
- Clean up source tree c3eb680
pgarrison pushed 1 commit to ckpt-docs AllenCell/benchmarking_representations
- Clarify multiple s per folder 23f615e
pgarrison pushed 43 commits to ckpt-docs AllenCell/benchmarking_representations
- delete hidden snakemake folder d5e1942
- change pcna result order beb3110
- add setup function to prereq to handle SDF/pc differences 9458d4a
- add classes and labels to results config 8069271
- move to run_embeddings and run_features acf4055
- remove hidden snakemake files be3fd45
- use cytodl config path for dataloading 1689542
- debug runs c734d7f
- test runs for embeddings and features pass for PCNA dataset cf470b3
- remove pdb 1292b7f
- move gpu stuff to utils 34447f6
- move fig notebooks into single analysis script 512ccd2
- working analysis script for punctate structures 178a826
- add sdf analysis utils and merge script 4faae2b
- fix nonetype error 5e9e07b
- working sdf analysis runs eceefa4
- Update data paths in the results config for other_polymorphic.yaml cfd4eb7
- Update data paths in the results config for npm1_perturb.yaml 18945d2
- Update data paths in the results config for other_punctate.yaml a8b4bb8
- Update other_punctate.yaml Reverted this change! 06228bb
- and 23 more ...
pgarrison created a branch on AllenCell/benchmarking_representations
ckpt-docs - Benchmarking different methods for extracting unsupervised representations from images