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Merge refactor to main #88

Merged
merged 140 commits into from
Feb 13, 2023
Merged

Merge refactor to main #88

merged 140 commits into from
Feb 13, 2023

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KPHippe
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@KPHippe KPHippe commented Feb 13, 2023

Updates

  • Made scalable inference generation script
    • Added infrastructure around embedding generation to gather/work with embeddings
  • Removed legacy inference/dataset code
  • Added fasta utilities (faster reading/writing than standard BioPython)

braceal and others added 30 commits January 27, 2023 11:45
@braceal
output callback can do multiple options
716523c
@braceal
inference dataset for improved efficiency
70f4385
@braceal
remove inference logic from train script
bda0435
@braceal
typing
81216ee
@braceal
scalable inference output script
2891e47
@braceal
scalable inference output script
7bb5b83
@braceal
scalable inference output script
a996b80
@braceal
scalable inference output script
f984039
@braceal
scalable inference output script
7bd9bdf
@braceal
scalable inference output script
b1d5736
@braceal
scalable inference output script
f789558
@braceal
scalable inference output script
8140c6d
@braceal
scalable inference output script
2a8aa2f
@braceal
scalable inference output script
38d7483
@braceal
ragged
4f63151
@KPHippe
Testing h5 distributed inference
20bfafa
@KPHippe
Testing h5 distributed inference
ce681a6
@KPHippe
Testing h5 distributed inference
05e44f1
@KPHippe
Testing h5 distributed inference
21efa90
@KPHippe
Testing h5 distributed inference
eb9f57a
@KPHippe
Testing h5 distributed inference
4931a17
@KPHippe
Testing h5 distributed inference
9060e62
@KPHippe
Testing h5 distributed inference
d28d006
@KPHippe
Testing h5 distributed inference
c05fe57
@KPHippe
Testing h5 distributed inference
591ee8d
@KPHippe
Testing h5 distributed inference
14b83b3
@KPHippe
Testing h5 distributed inference
8fd8e82
@KPHippe
Testing h5 distributed inference
9bd1723
@KPHippe
Testing h5 distributed inference
1d875a9
@KPHippe
Testing h5 distributed inference
ad9ba86
@KPHippe
Testing bulk inference
ca8f9a3
@KPHippe
Testing bulk inference
55f5752
@KPHippe
Testing bulk inference
7e6a1c8
@KPHippe
Need to see env vars
a46ee50
@KPHippe
Need to see env vars
46c686a
@KPHippe
Need to see env vars
30dca76
@KPHippe
Note that this script does not work as intended (at all)
857776b
@KPHippe
Adding logic for gathering logits
bfda2f4
@KPHippe
Update logit glob pattern
e4b79b5
@KPHippe
Update logit outfile name
94711e9
@KPHippe
Exposing verbosity
95cb055
@KPHippe
moving h5 to after predict start
964d393
@KPHippe
silence logging
bc770c9
@KPHippe
silence logging
c90c482
@KPHippe
Testing failures
43a3ae6
@KPHippe
FIXING SEQ LEN
5386d55
@KPHippe
Squeeze the life out of me
d7852ac
@KPHippe
Double checking sequence lengths
8085ccc
@KPHippe
Verifying that the dataset (tokenizer) is and forever shall be correct
89ecf4e
@KPHippe
Refactor/cleanup for inference at scale
f39aa6a
@KPHippe
Merge branch 'patch/output-callback' of github.com:ramanathanlab/gene…
14fc66b 
…_transformer into patch/output-callback
@KPHippe
Remove bogus utils :)
5019990
@KPHippe
Linting and documentation
ef98ba2
@KPHippe
Remove mean reduction references
f6cfffb
@KPHippe
Merge pull request #85 from ramanathanlab/patch/output-callback
dbcbac1 
Patch/output callback
@KPHippe
Increase version corresponding to recent refactor
670d53b
KPHippe
KPHippe commented Feb 13, 2023
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Same as patch/output-callback

@KPHippe KPHippe requested a review from braceal February 13, 2023 18:46
@braceal braceal merged commit b2c3a7a into main Feb 13, 2023
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@braceal braceal braceal approved these changes

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@KPHippe @braceal