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Merge updates in main into release #115

Merged
merged 57 commits into from
Oct 23, 2024
Merged

Merge updates in main into release #115

merged 57 commits into from
Oct 23, 2024

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mattwoodx
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mattwoodx and others added 30 commits September 26, 2024 16:20
@mattwoodx
Add regression head
0b61d82
@mattwoodx
Add fine-tuning functionality to HyenaDNA
170368f
@mattwoodx
Add dataset for HyenaDNA for batching
5e28fa0
@mattwoodx
Add batch processing for HyenaDNA get_embeddings
4fa2473
@mattwoodx
Update docstrings
3e8e7bb
@mattwoodx
Update tests for Hyena-DNA
ed648b5
@mattwoodx
Add notebook for DNA fine-tuning
8f22bfb
@mattwoodx
Add detailed notebook and update inference notebook for HyenaDNA
40cdb59
@mattwoodx
Add testing for fine-tuning HyenaDNA
8599f8a
@mattwoodx
Remove softmax
fbbbecb
@mattwoodx
Remove softmax from forward
6e8ce90
@mattwoodx
More detailed testing for fine-tuning HyenaDNA
1b3f313
@mattwoodx
Add subset percentages for notebook testing to avoid timing out
7ccdf48
@mattwoodx
Remove identical head
2caa693
@mattwoodx
Merge branch 'main' into feature/dna-fine-tune
5cf58a2
@mattwoodx
Remove unused imports
7da0a5d
@mattwoodx
Add regression head back
a3fcf5e
@mattwoodx
Add option for regression head in base
15c6e12
@mattwoodx
Replace accuracy with validation loss
063545f
@mattwoodx
Update docstrings
05e7fa6
@mattwoodx
Update docstrings
a403f40
downloading files again for UCE , for the Geneformer all the files ar…
90f2eaa 
…e now loaded in the init function.
n_proc to 1
bc9e2ce
fixed UCE download
b16597c
removed nproc from notebook
8fe8c99
@maxiallard
Merge pull request #110 from helicalAI/init_load_files
4feb9c5 
Adding downloads where initial files might not be available anymore.
Change dependency strictness
aed7272
@maxiallard
Merge pull request #111 from helicalAI/dependency-change
035b7f4 
Change dependency strictness
Merge branch 'main' into feature/dna-fine-tune
4aeacf9
@mattwoodx
Remove duplicate merge code
fb763bf
mattwoodx and others added 20 commits October 4, 2024 14:54
@mattwoodx
Update testing
d6d32a1
@mattwoodx
Change default batch size
76435cb
@mattwoodx
Remove dict from geneformer process data in notebook
151e7b8
@mattwoodx
Custom attr dict no longer in process data
9b00d7a
@mattwoodx
Merge pull request #101 from helicalAI/feature/dna-fine-tune
889c784 
HyenaDNA Fine-Tuning Capabilities and Regression Head
@mattwoodx
Refactor Geneformer fine-tuning to instatiate the a standalone model …
4abf365 
…with configs
@mattwoodx
Refactor Geneformer fine-tuning to instatiate the a standalone model …
74499ac 
…with configs
@mattwoodx
Refactor HyenaDNA fine-tuning to be standalone
73857ea
@mattwoodx
Update docs
47a15d2
@mattwoodx
Refactor scGPT fine-tuning to be standalone
044f10f
@mattwoodx
Refactor UCE fine-tuning to be standalone
ab53dbe
@mattwoodx
Update examples for UCE
1532b0d
@mattwoodx
Update Notebook
13b3f70
@mattwoodx
Update workflow
1295383
@bputzeys
Remove unused import
0fa73c7
@bputzeys
Raise error if download fails and include log message
a973760
@bputzeys
Merge pull request #112 from helicalAI/refactor-fine-tuning
fe843a2 
Refactor fine-tuning
@maxiallard
Merge pull request #113 from helicalAI/raise-error-if-download-fails
6c5e7d1 
Raise error if download fails and include log message
@bputzeys
Open the file only after a successful response has been received. Oth…
e5bcdd7 
…erwise file will be opened even if the request fails, resulting in an empty file.
@bputzeys
Merge pull request #114 from helicalAI/raise-error-if-download-fails
efadd9b 
Raise error if download fails
@mattwoodx mattwoodx requested review from bputzeys and maxiallard and removed request for bputzeys October 18, 2024 13:07
@maxiallard maxiallard merged commit 5adfb80 into release Oct 23, 2024
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@bputzeys bputzeys bputzeys approved these changes

@maxiallard maxiallard Awaiting requested review from maxiallard

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3 participants
@mattwoodx @bputzeys @maxiallard