Add reconstruction decoder (ReconDecoder) + recon_emb pipeline#16
Open
xiaotong743 wants to merge 2 commits into
Open
Add reconstruction decoder (ReconDecoder) + recon_emb pipeline#16xiaotong743 wants to merge 2 commits into
xiaotong743 wants to merge 2 commits into
Conversation
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
| """ | ||
| import os | ||
|
|
||
| os.environ.setdefault("TF_GPU_ALLOCATOR", "cuda_malloc_async") |
Collaborator
There was a problem hiding this comment.
why was this needed? can you maybe add a comment to explain?
| from scaleflow.model._recon import Autoencoder, Decoder, ReconDecoder | ||
|
|
||
| # anndata moved write_elem across versions; import defensively. | ||
| try: |
Collaborator
There was a problem hiding this comment.
just lower bound anndata to newer versions, that should be better
| # ── pure-reconstruction metrics on train / val / test ── | ||
| metrics = {} | ||
| for s in SPLITS: | ||
| pred = batched_apply(module, state.params, inp[idx[s]]) |
Collaborator
There was a problem hiding this comment.
why did you need this? out of gpu memory error? If so can you write in comments. It would be good to know. How big is the model? how big is the batches and how big is the whole thing?
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Added a decoder module in src. other codes just for the exp