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Breaking - #11

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jkobject wants to merge 508 commits into

jkobject:mainfrom

cantinilab:breaking

Closed

Breaking#11
jkobject wants to merge 508 commits into
jkobject:mainfrom
cantinilab:breaking

This pull request is big! We're only showing the most recent 250 commits

Commits on May 16, 2025
- adding more tests
  jkobject
  committed
  6e0fb04
Commits on May 19, 2025
- new test function, better savings, preventing OOMs
  jkobject
  committed
  1029217
Commits on May 20, 2025
- likely solution
  jkobject
  committed
  d03134e
Commits on May 21, 2025
- final debug of the test, it is now working fully
  jkobject
  committed
  b32e23a
Commits on May 22, 2025
- debug of some issues
  jkobject
  committed
  8aa8bdd
- better readme
  jkobject
  committed
  cad61f0
- release: version 2.3.0 🚀
  jkobject
  committed
  6d16a03
Commits on May 26, 2025
- updating some stuff
  jkobject
  committed
  dda3e3e
- debuging VAE
  jkobject
  committed
  b072a7d
- nothing
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  committed
  8ef0069
Commits on May 27, 2025
- solving last part
  jkobject
  committed
  d45f6b9
- removing pdb
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  committed
  a386771
- Merge remote-tracking branch 'cantini/main' into dev
  jkobject
  committed
  aa33ca1
Commits on May 28, 2025
- solving gene memap and cleanup
  jkobject
  committed
  c8727e1
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  2617b3c
- testing better class compression
  jkobject
  committed
  c16c73e
- quick solve
  jkobject
  committed
  725526a
- nothing really
  jkobject
  committed
  4f8066d
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  ef69c4c
- debug
  jkobject
  committed
  9cd5d12
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  7374fc1
- dbug
  jkobject
  committed
  0363cb4
- debug
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  committed
  d129703
- debug
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  committed
  eb67c61
Commits on May 29, 2025
- couple things that seemed to help
  jkobject
  committed
  17791e4
- debug
  jkobject
  committed
  4caf729
Commits on May 31, 2025
- testing different parameters
  jkobject
  committed
  59d2f96
- debug
  jkobject
  committed
  32ba88e
Commits on Jun 2, 2025
- debugged embeddings
  jkobject
  committed
  ea77f44
- debug
  jkobject
  committed
  fa2db8b
- more
  jkobject
  committed
  a6b47c6
Commits on Jun 3, 2025
- debug
  jkobject
  committed
  353925d
Commits on Jun 4, 2025
- testing this
  jkobject
  committed
  387699b
- tiny debug
  jkobject
  committed
  569a15a
Commits on Jun 5, 2025
- what a debug
  jkobject
  committed
  d874325
Commits on Jun 6, 2025
- working on the notebooks
  jkobject
  committed
  150121e
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  688a561
Commits on Jun 8, 2025
- setting ft ge to false, preventing OOM cell emb
  jkobject
  committed
  1f978ef
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  625919d
Commits on Jun 10, 2025
- that should help my life
  jkobject
  committed
  74004f4
- comparing embeddings
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  committed
  2124540
- applying prev stash
  jkobject
  committed
  975cb60
- debug
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  committed
  cb53164
Commits on Jun 11, 2025
- key debug to apply
  jkobject
  committed
  a1ae9d9
Commits on Jun 13, 2025
- generating gene locs and logging more val
  jkobject
  committed
  dbc7548
- before base_v3
  jkobject
  committed
  329bd17
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  8e5706d
- a debug
  jkobject
  committed
  d4fd345
- again
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  committed
  3737551
- more
  jkobject
  committed
  a9e5c59
Commits on Jun 16, 2025
- some different base_v3 parameters
  jkobject
  committed
  a2e1cae
- changing activation location
  jkobject
  committed
  c5e2f58
- ecs/cce, cell transf as params, invert TF weights
  jkobject
  committed
  eb5d9dd
Commits on Jun 18, 2025
- Revert "changing activation location"
  jkobject
  committed
  a4b4de7
- adding VAE
  jkobject
  committed
  fd5bb6d
- seems needed
  jkobject
  committed
  2238ac3
- quick change
  jkobject
  committed
  ccb1888
- Merge commit '32ba88ec8910a4b93bdd5bb3d1c0baf929ff300c' into making-it-work
  jkobject
  committed
  f4d6e2a
- adding back mask zeros
  jkobject
  committed
  6c65861
- debugged embeddings
  jkobject
  committed
  fbb53c0
- reverting some from previous version - TO RUN as VAE
  jkobject
  committed
  95511c9
- adding all important things from model/*
  jkobject
  committed
  b90e615
- same
  jkobject
  committed
  851e46d
Commits on Jun 19, 2025
- Merge commit '8e5706db1a27bdb56174f79c2b6de7fb7a524e18' into making-it-work-2
  jkobject
  committed
  effb5a9
Commits on Jun 23, 2025
- fix lamib-db schema deprication - README.md
  unikill066
  authored
  f7216a7
Commits on Jun 29, 2025
- Merge pull request #36 from unikill066/main
  jkobject
  authored
  b1ed92f
Commits on Jun 30, 2025
- Update Dockerfile
  jkobject
  authored
  9dfad09
- Update README.md
  jkobject
  authored
  7b9db90
- simple debug
  jkobject
  committed
  6728bac
- linting
  jkobject
  committed
  f79f1e1
- good version and params
  jkobject
  committed
  e0f0909
- Merge branch 'making-it-work-2' into dev
  jkobject
  committed
  6276ce3
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  423995b
Commits on Jul 1, 2025
- new model packages v and some debug
  jkobject
  committed
  978babc
Commits on Jul 22, 2025
- debug
  jkobject
  committed
  378e046
Commits on Jul 28, 2025
- nothing
  jkobject
  committed
  0750d1a
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  106bb62
Commits on Jul 29, 2025
- Update README.md
  jkobject
  authored
  712e95e
Commits on Jul 31, 2025
- some improvements and multiple debugs
  jkobject
  committed
  a301f2a
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  ebd6c49
- adding one more adv_cls
  jkobject
  committed
  6112b3f
Commits on Aug 3, 2025
- dbug?
  jkobject
  committed
  f5dde53
- solving issue further
  jkobject
  committed
  1bd709d
Commits on Aug 4, 2025
- debug
  jkobject
  committed
  bd54778
- again
  jkobject
  committed
  2cee53a
- again
  jkobject
  committed
  bef071a
- wip
  jkobject
  committed
  4d2b725
- trying to log
  jkobject
  committed
  5f38d18
- hope to be final dbug
  jkobject
  committed
  2879744
Commits on Aug 5, 2025
- again
  jkobject
  committed
  9dae438
- improvements and debugs
  jkobject
  committed
  bc330e1
- release: version 2.3.1 🚀
  jkobject
  committed
  29a6a60
- Update README.md
  jkobject
  authored
  0a74931
- Update README.md
  jkobject
  authored
  fa6af1d
- release: version 2.3.2 🚀
  jkobject
  committed
  0c95008
- release: version 2.3.3 🚀
  jkobject
  committed
  6a205a5
- Update README.md
  jkobject
  authored
  6585e2d
- debug
  jkobject
  committed
  2826635
- Merge branch 'main' of https://github.com/cantinilab/scPRINT
  jkobject
  committed
  d6256cb
- release: version 2.3.4 🚀
  jkobject
  committed
  6f92f13
- by default umap generation
  jkobject
  committed
  3f3e67a
- release: version 2.3.5 🚀
  jkobject
  committed
  d7b834a
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  eb4fb03
- Merge branch 'main' into dev
  jkobject
  committed
  7e8d608
Commits on Aug 6, 2025
- wip on many notebooks
  jkobject
  committed
  9c1afbc
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  1ffade8
Commits on Aug 11, 2025
- ES update
  jkobject
  committed
  d1e10bf
- novel task definition for generation and solve es
  jkobject
  committed
  288309b
Commits on Aug 12, 2025
Commits on Aug 13, 2025
- debugs
  jkobject
  committed
  29e3f60
- working on files
  jkobject
  committed
  1311c7f
- adding gitignore
  jkobject
  committed
  cf2ee04
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  918750b
Commits on Aug 18, 2025
- debug tf masker
  jkobject
  committed
  a6555e3
- debug tf masker
  jkobject
  committed
  230e4ea
- works1
  jkobject
  committed
  42eeeb7
- works
  jkobject
  committed
  03bcc57
- works
  jkobject
  committed
  4adc7cb
- xenium, output emb, denoisin, cross species wip or finished
  jkobject
  committed
  e311075
- denoising, cross species wip or finished
  jkobject
  committed
  4edcec1
- working on files
  jkobject
  committed
  002a866
- adding gitignore
  jkobject
  committed
  45d4523
- debug tf masker
  jkobject
  committed
  ab7127a
- works
  jkobject
  committed
  2ef296c
- solve for previous versions
  jkobject
  committed
  cc1a9ce
- debug tf masker
  jkobject
  committed
  0fa464c
- debugs
  jkobject
  committed
  0072795
- adding new function to potentially improve classification results
  jkobject
  committed
  4367db5
- all debugs
  jkobject
  committed
  335a25a
- nothing
  jkobject
  committed
  2392133
Commits on Aug 19, 2025
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  d161fb1
- debug
  jkobject
  committed
  f35c80a
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  72cdbc3
- for jz
  jkobject
  committed
  679d858
- some more debugs
  jkobject
  committed
  3200b1a
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  84e3222
- debug more
  jkobject
  committed
  8477594
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  7653559
- issue with test datasets, removing
  jkobject
  committed
  7b01bcc
Commits on Aug 21, 2025
- testing novel parameters
  jkobject
  committed
  f946fbe
- esm works back
  jkobject
  committed
  0cfd875
- running different examples
  jkobject
  committed
  add3011
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  b349a10
Commits on Aug 27, 2025
- running the notebooks
  jkobject
  committed
  5691aee
- using gene_pos file and giving it to the model for more clarity
  jkobject
  committed
  3df4338
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  189c17d
- update ablation study too
  jkobject
  committed
  29f1b8d
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  dda838f
- redbug
  jkobject
  committed
  64bff64
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  b97a0b1
Commits on Aug 28, 2025
- more debugs
  jkobject
  committed
  e936cf7
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  9178115
- simplification and device-wide contrastive loss
  jkobject
  committed
  bfb5e67
- missed some files in prev commit
  jkobject
  committed
  eb6366e
Commits on Aug 29, 2025
- make binning work wip
  jkobject
  committed
  c9bcb13
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  12bcb55
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  4b3c63b
- improv
  jkobject
  committed
  5bfc4e0
- improv
  jkobject
  committed
  9f8a44f
- improvements
  jkobject
  committed
  5c6cfa7
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  ad18e7c
Commits on Aug 31, 2025
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  2338ce7
Commits on Sep 1, 2025
- make it work on non jz
  jkobject
  committed
  dcd456e
- working on notebook and better adv clss
  jkobject
  committed
  18c97af
- better sq classifier loc
  jkobject
  committed
  28ab6c1
- exprBasedFT
  jkobject
  committed
  cce6a24
Commits on Sep 2, 2025
- simple dbug
  jkobject
  committed
  ec714b7
Commits on Sep 4, 2025
- solving knn-cells and adv bugs
  jkobject
  committed
  d7d341c
Commits on Sep 9, 2025
- all the notebook
  jkobject
  committed
  fcc4478
- some debug
  jkobject
  committed
  9513220
- Merge remote-tracking branch 'origin/dev' into breaking
  jkobject
  committed
  14a0e82
Commits on Sep 10, 2025
- working on notebooks
  jkobject
  committed
  8baea69
Commits on Sep 11, 2025
- testing out stuff
  jkobject
  committed
  fe5ef35
- Merge remote-tracking branch 'origin/dev' into breaking
  jkobject
  committed
  4a0df59
- novel weight init
  jkobject
  committed
  00ec72a
- debug multi cell model
  jkobject
  committed
  f3fd0fd
Commits on Sep 12, 2025
- debug long run times
  jkobject
  committed
  ee517af
- debug long run times
  jkobject
  committed
  7bd506b
Commits on Sep 15, 2025
- making nocls and binning works
  jkobject
  committed
  8d93360
- Merge branch 'dev' into breaking
  jkobject
  committed
  bf125d9
Commits on Sep 16, 2025
- trying to prevent NaNs
  jkobject
  committed
  1268d2e
Commits on Sep 17, 2025
- should work better now
  jkobject
  committed
  05badae
- solution to logging issues on wandb
  jkobject
  committed
  9c91e24
- wip
  jkobject
  committed
  34b5d44
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  e39619d
Commits on Sep 21, 2025
- solve some GNN random expr stuff and masking genes
  jkobject
  committed
  995d348
- max_cont_len useless
  jkobject
  committed
  7993de0
- Refactor transformer handling with FlashTransformer
  jkobject
  authored
  35f09c8
- dbug
  jkobject
  committed
  1b1f407
Commits on Sep 22, 2025
- debug pred embedding in case of no cell_emb
  jkobject
  committed
  6f48987
- debug stuff
  jkobject
  committed
  042d6ac
- simple dbug
  jkobject
  committed
  6e2e13f
Commits on Sep 23, 2025
- should be more similar to prev version
  jkobject
  committed
  295971f
Commits on Sep 24, 2025
- did we solve it?
  jkobject
  committed
  4e0ee05
- quick cell emb db
  jkobject
  committed
  ad4c2df
- dbug
  jkobject
  committed
  22a1e41
Commits on Sep 26, 2025
- dbug adv class
  jkobject
  committed
  6e1e287
Commits on Sep 30, 2025
- runnning notebooks
  jkobject
  committed
  52fa89d
Commits on Oct 1, 2025
- debug tf masking
  jkobject
  committed
  4281097
- running notebooks
  jkobject
  committed
  c3cbaf3
- Merge branch 'dev' of https://github.com/cantinilab/scPRINT into dev
  jkobject
  committed
  61fe5cf
Commits on Oct 3, 2025
- zarr better
  jkobject
  committed
  228195e
- debug submit & large
  jkobject
  committed
  06f2434
- Merge branch 'dev' into breaking
  jkobject
  committed
  6b138fe
Commits on Oct 5, 2025
- more complex loss
  jkobject
  committed
  837142f
- more complex loss
  jkobject
  committed
  5c8a7f0
- dbug
  jkobject
  committed
  2b6c5a9
Commits on Oct 6, 2025
- adding ft v2
  jkobject
  committed
  8ac3c1a
- nothing really
  jkobject
  committed
  3c69a89
- Merge remote-tracking branch 'origin/dev' into breaking
  jkobject
  committed
  1f170fe
Commits on Oct 8, 2025
- debug was no gene fine tuning!!!
  jkobject
  committed
  7425d9e
- debug was no gene fine tuning (forgot commit)
  jkobject
  committed
  474ae3c
Commits on Oct 10, 2025
- removing blocking
  jkobject
  committed
  a4eeee3
Commits on Oct 27, 2025
- wip on the notebooks
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  committed
  378fe36
Commits on Oct 28, 2025
- wip
  jkobject
  committed
  a94e9d6
- Merge branch 'dev' into breaking
  jkobject
  committed
  b796fb6
Commits on Oct 29, 2025
- work in progress
  jkobject
  committed
  d2cf215
- more
  jkobject
  committed
  42aa318
- Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
  jkobject
  committed
  85acb62
- debug
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  committed
  7af8845
Commits on Oct 30, 2025
- WIP
  jkobject
  committed
  191a7cf
- Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
  jkobject
  committed
  1020b69
Commits on Oct 31, 2025
- easy debug
  jkobject
  committed
  f9b333e
Commits on Nov 2, 2025
- debug hyper test and binning, mask zeros,
  jkobject
  committed
  fcb68e9
- one more debug
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  committed
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Commits on Nov 3, 2025
- nothing
  jkobject
  committed
  cee0da9
Commits on Nov 4, 2025
- debug
  jkobject
  committed
  14dbf5d
- Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
  jkobject
  committed
  da3c3a0
Commits on Nov 5, 2025
- debug
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  committed
  c913258
- real debug
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  committed
  24cefea
- nothing
  jkobject
  committed
  ea27544
- Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
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  committed
  5e5ad11
Commits on Nov 6, 2025
- debug
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  committed
  968b98b
- Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
  jkobject
  committed
  9c3a3c1
Commits on Nov 7, 2025
- debug
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  committed
  dc2553b
Commits on Nov 12, 2025
- save wip
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  committed
  060d5cd
- continuing notebooks
  jkobject
  committed
  914ecd6
Commits on Nov 13, 2025
- update
  jkobject
  committed
  c56190f
- update
  jkobject
  committed
  f0b3897
- make it work
  jkobject
  committed
  cdd5c42
Commits on Nov 14, 2025
- debug
  jkobject
  committed
  3b6ad04
Commits on Nov 16, 2025
- WIP on latest questions
  jkobject
  committed
  3dd4d38
Commits on Nov 19, 2025
- correct versions
  jkobject
  committed
  e95f075
- Merge branch 'main' into breaking
  jkobject
  authored
  9af3922
- latest notebook version
  jkobject
  committed
  00c0ebe
- Merge branch 'breaking' of https://github.com/cantinilab/scPRINT into breaking
  jkobject
  committed
  3f453b0
Commits on Nov 22, 2025
- wip
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  committed
  ddec5b6

Commits

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