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Compatibility of model weights trained in newer containers to run in older BioNeMo containers
#454
opened Nov 19, 2024 by
xinyu-dev
Enable extraction of gene embeddings from geneformer (averaging of gene embeddings across all cells)
#452
opened Nov 19, 2024 by
jstjohn
MolMIM checkpoint files ckpt to nemo conversion
bug
Something isn't working
#427
opened Nov 13, 2024 by
xinyu-dev
Geneformer + ESM2 train script and pydantic config equivalence check
#403
opened Nov 6, 2024 by
jstjohn
Refactor
geneformer_mlm_loss_eval
script to use a better mechanism for getting the tokenizer.
#402
opened Nov 5, 2024 by
jstjohn
Convert
geneformer_mlm_loss_eval
script to use pooch
for downloads.
#400
opened Nov 5, 2024 by
jstjohn
Add request that contributors from outside NVIDIA add Improvements or additions to documentation
good first issue
Good for newcomers
contribution
label to their PR
documentation
#309
opened Oct 14, 2024 by
jstjohn
Support virtual pipeline parallel in global batch size calculation
#286
opened Oct 8, 2024 by
jstjohn
Automatically determine/override config settings when loading from checkpoint
#275
opened Oct 8, 2024 by
jstjohn
Add ability for the
from_checkpoint
style functions to accept a tag
or path
object.
#242
opened Oct 3, 2024 by
jstjohn
Fix issue where nemo1 to nemo2 conversion tests (esm2 and geneformer) only work when run by themselves.
#226
opened Oct 1, 2024 by
jstjohn
fix failing unit tests in bionemo1 github related to hardware changes
#195
opened Sep 25, 2024 by
dorotat-nv
[docs] Emphasize that notebook examples should have saved outputs
#162
opened Sep 16, 2024 by
pstjohn
Fix bug checkpoint IO bug once https://github.com/NVIDIA/NeMo/pull/1024 lands
bug
Something isn't working
#134
opened Sep 4, 2024 by
jstjohn
Refactor checkpoint loading for fine-tuning for new NeMo2 workflow
#132
opened Sep 4, 2024 by
jstjohn
Refactor dataset so that when we upsample we get different masks for different queries of the same data.
#126
opened Aug 28, 2024 by
jstjohn
Copy over bionemo1 3p license file into global LICENCE folder.
bug
Something isn't working
#72
opened Aug 2, 2024 by
jstjohn
Adding DCO contributor signoff to CONTRIBUTING.md files
bug
Something isn't working
#65
opened Aug 1, 2024 by
jstjohn
Fix ruff documentation violations in existing BioNeMo v2 code
#59
opened Jul 31, 2024 by
pstjohn
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