Jérémie Kalfon (15):
Update README.md
Update LICENSE
Refactor transformer handling with FlashTransformer
Merge branch 'main' into breaking
Add files via upload
Add files via upload
Revise README with updated links and content
Update README.md
Update Codecov badge link in README.md
Update README.md
Fix links to hugging face pages for scPRINT models
Update checkpoint paths in README commands
Delete src directory
Delete .cursorignore
Delete output.h5ad_imputed.h5ad
jkobject (269):
add performer attention
few debugs
more debugs
more debugs
debug
adding esm2 finetuning and
classic forgot
wip
debug issue
add wip gnn
Merge remote-tracking branch 'origin/dev' into gnn
actually adding a KL loss and setting up better package versions
testing models
debug
better params for get knn cells and sota denoising
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
debug knn cells
debugging cli, and slurm runs
updating defaults
debug of a key circular import and start to solve gene emb
debug embedding gene issue
debug gene encoder and making it load prev model versions
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
wip on the large task front
Merge remote-tracking branch 'origin/main' into dev
merge solve
some debug
Merge commit 'b06953e4e0b0d44d2d53b2c759f3747f60045cfe' into dev
debug
debug
new parameter and some debug
solving many issues
Merge remote-tracking branch 'cantini/main' into dev
wip
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
debug gnn mode
debugs and improvements
debugs and imrpovements
one more debug
work on notebooks
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
debugs cleanups and adding docu
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
final debug
many new run formats, masking zeros, simplify attn, hyper attn, some debugs, gnn faster,
updating the train
wip on different tests
wip embedding
print on protein emb
simplifying stuff
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
changing default params, removing useless input, improving hier classifier, adding back adv class
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
quick debug
dbug adv loss
nothing really
adding organism back
dbug
solve a loading of model issue
trying to solve issue
debug model loading
add configs
add one elem
adding splicing heads, debugging cell transformer and embs (making it work for smaller dim)
debug some issues with the model
add better params
cleaning up the notebooks
improving the tests and adding new parameters
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
adding more tests
new test function, better savings, preventing OOMs
likely solution
final debug of the test, it is now working fully
updating some stuff
debuging VAE
Merge remote-tracking branch 'cantini/main' into dev
solving gene memap and cleanup
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
testing better class compression
quick solve
nothing really
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
debug
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
dbug
debug
debug
couple things that seemed to help
debug
testing different parameters
debug
debugged embeddings
debug
more
debug
testing this
tiny debug
what a debug
working on the notebooks
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
setting ft ge to false, preventing OOM cell emb
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
that should help my life
comparing embeddings
applying prev stash
debug
key debug to apply
generating gene locs and logging more val
before base_v3
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
a debug
again
more
some different base_v3 parameters
changing activation location
ecs/cce, cell transf as params, invert TF weights
Revert "changing activation location"
adding VAE
seems needed
quick change
Merge commit '32ba88ec8910a4b93bdd5bb3d1c0baf929ff300c' into making-it-work
adding back mask zeros
debugged embeddings
reverting some from previous version - TO RUN as VAE
adding all important things from model/*
same
Merge commit '8e5706db1a27bdb56174f79c2b6de7fb7a524e18' into making-it-work-2
simple debug
Merge branch 'making-it-work-2' into dev
debug
nothing
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
wip
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'main' into dev
ES update
novel task definition for generation and solve es
debugs
adding new function to potentially improve classification results
issue with test datasets, removing
make binning work wip
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
improv
improv
make it work on non jz
solving knn-cells and adv bugs
some debug
Merge remote-tracking branch 'origin/dev' into breaking
testing out stuff
Merge remote-tracking branch 'origin/dev' into breaking
novel weight init
debug multi cell model
debug long run times
debug long run times
making nocls and binning works
Merge branch 'dev' into breaking
trying to prevent NaNs
should work better now
solution to logging issues on wandb
solve some GNN random expr stuff and masking genes
max_cont_len useless
dbug
debug pred embedding in case of no cell_emb
debug stuff
simple dbug
should be more similar to prev version
did we solve it?
quick cell emb db
dbug
dbug adv class
runnning notebooks
debug tf masking
zarr better
debug submit & large
Merge branch 'dev' into breaking
more complex loss
more complex loss
dbug
nothing really
Merge remote-tracking branch 'origin/dev' into breaking
debug was no gene fine tuning!!!
debug was no gene fine tuning (forgot commit)
removing blocking
wip on the notebooks
work in progress
more
Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
debug
easy debug
debug hyper test and binning, mask zeros,
one more debug
debug
Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
debug
real debug
debug
Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
debug
save wip
continuing notebooks
update
update
make it work
debug
WIP on latest questions
correct versions
latest notebook version
Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
wip
higher scale class. final notebook version
new gitignore
Merge branch 'breaking'
cleanup
more cleanups and better readme
Merge branch 'main' of https://github.com/cantinilab/scPRINT-2
improve readme
formating
final runs
adding the nice datamaplot
adding this
adding that
adding this
adding
cleanup
nothing
nothing
updates
moved it
update the model name everywhere
cleanups
some updates
making it all more prod ready 1/4
Merge branch 'main' of https://github.com/cantinilab/scPRINT-2
release: version 0.9.1 🚀
cleanup
release: version 0.9.2 🚀
some more results and improvements
update codecov
some more debugs
Merge branch 'main' of https://github.com/cantinilab/scPRINT-2
cleanup 3/4
release: version 0.9.6 🚀
debug the doc
cleanup
debug
release: version 0.9.8 🚀
debugs ci
Merge branch 'main' of https://github.com/cantinilab/scPRINT-2
update lamindb version
release: version 1.0.0 🚀
many debugs and cleanups
release: version 1.0.1 🚀
adding docker
update
Merge branch 'main' of https://github.com/cantinilab/scPRINT-2
wip
release: version 1.0.2 🚀
making sure no flash
release: version 1.0.2 🚀
improving readme and index
release: version 1.0.2 🚀
adding some more infos
adding logo
Merge branch 'main' of https://github.com/cantinilab/scPRINT
Revert "Merge branch 'main' of https://github.com/cantinilab/scPRINT"
update history
dbugging easy setup
debug
release: version 1.0.3 🚀
jkobject-jz (14):
adding to model.py
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
nothing
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
for jz
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
jkobject-tower (74):
linting
good version and params
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
new model packages v and some debug
some improvements and multiple debugs
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
adding one more adv_cls
dbug?
solving issue further
debug
again
again
trying to log
hope to be final dbug
again
wip on many notebooks
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
update package version, gene names as dict, gene emb task, generate denoise task, better emb saving, better expr saving
xenium, output emb, denoisin, cross species wip or finished
denoising, cross species wip or finished
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
working on files
adding gitignore
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
debug tf masker
debug tf masker
works1
works
works
xenium, output emb, denoisin, cross species wip or finished
denoising, cross species wip or finished
working on files
adding gitignore
debug tf masker
works
solve for previous versions
debug tf masker
debugs
all debugs
nothing
debug
some more debugs
debug more
testing novel parameters
esm works back
running different examples
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
running the notebooks
using gene_pos file and giving it to the model for more clarity
update ablation study too
redbug
more debugs
simplification and device-wide contrastive loss
missed some files in prev commit
improvements
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
working on notebook and better adv clss
better sq classifier loc
exprBasedFT
simple dbug
all the notebook
working on notebooks
wip
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
running notebooks
Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
adding ft v2
wip
Merge branch 'dev' into breaking
WIP
Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
nothing
nothing
Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
