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35 Open 7 Closed
35 Open 7 Closed
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Issues list

Incorrect docker container tag for nightly builds bug Something isn't working
#653 opened Jan 23, 2025 by xinyu-dev
[BUG] fix unit test: esm2/model/test_convert.py::test_nemo2_conversion_equivalent_650m bug Something isn't working
#646 opened Jan 23, 2025 by dorotat-nv
@pstjohn
MolMIM weights are not named correctly bug Something isn't working
#645 opened Jan 23, 2025 by xinyu-dev
AWS Deep Learning AMI not compatible with multi-GPU training of MolMIM bug Something isn't working
#644 opened Jan 23, 2025 by xinyu-dev
Make model weights searchable on NGC bug Something isn't working
#613 opened Jan 16, 2025 by xinyu-dev
1
Add descriptions for the params in the config YAML file of MolMIM enhancement New feature or request
#612 opened Jan 16, 2025 by xinyu-dev
Change default overlap param gather of geneformer to match esm2.
#585 opened Jan 9, 2025 by jstjohn
fine-tuning/retraining esm2
#565 opened Jan 2, 2025 by MarjanHJ
Installing SCDL raises a missing dependency
#472 opened Nov 23, 2024 by edawson
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
9
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
@skothenhill-nv
1
Refactor geneformer_mlm_loss_eval script to use a better mechanism for getting the tokenizer.
#402 opened Nov 5, 2024 by jstjohn
Write test for geneformer_mlm_loss_eval script.
#401 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 contribution label to their PR documentation Improvements or additions to documentation good first issue Good for newcomers
#309 opened Oct 14, 2024 by jstjohn
1
Enable sequence_parallel and tp_comm_overlap in ESM2
#305 opened Oct 11, 2024 by jstjohn
Support virtual pipeline parallel in global batch size calculation
#286 opened Oct 8, 2024 by jstjohn
1
Automatically determine/override config settings when loading from checkpoint
#275 opened Oct 8, 2024 by jstjohn
@skothenhill-nv
1
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
1
fix failing unit tests in bionemo1 github related to hardware changes
#195 opened Sep 25, 2024 by dorotat-nv
@dorotat-nv
Add documentation describing what modifications you need (head/loss/inputs) to support different parallelisms of transformer block
#170 opened Sep 17, 2024 by jstjohn
[docs] Emphasize that notebook examples should have saved outputs
#162 opened Sep 16, 2024 by pstjohn
ProTip! What’s not been updated in a month: updated:<2024-12-26.