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Pull requests: NVIDIA/bionemo-framework

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Pull requests list

Temporary workaround for the Arc Opengenome2 dataset inconsistency to enable training with streaming datasets to work
#1340 opened Nov 21, 2025 by savitha-eng Loading…
5 of 14 tasks
1
Context Parallel Squashed MR for recipes dir
#1338 opened Nov 20, 2025 by jomitchellnv Loading…
9 tasks
1
Context Parallel Squashed MR for models dir
#1337 opened Nov 20, 2025 by jomitchellnv Loading…
1 of 9 tasks
17
Remove ESM2, Amplify from 5D. This is now in bionemo-recipes
#1336 opened Nov 20, 2025 by trvachov Loading…
9 tasks
3
Dev/ba/fix evo2 lora test
#1335 opened Nov 20, 2025 by balvisio Loading…
9 tasks
1
starting work for swqa
#1334 opened Nov 19, 2025 by pstjohn Loading…
Update HF model card
#1333 opened Nov 19, 2025 by ohadmo Loading…
9 tasks
@ohadmo
2
Bump transformers from 4.51.3 to 4.53.0 in /bionemo-recipes/models/geneformer dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1332 opened Nov 19, 2025 by dependabot bot Loading…
1
Adding update that solves one logger issue for Evo2 training
#1331 opened Nov 18, 2025 by jstjohn Loading…
2 of 9 tasks
1
Add bionemo-recipes to documentation ciflow:skip Skip all CI tests for this PR documentation Improvements or additions to documentation
#1328 opened Nov 18, 2025 by jwilber Loading…
@jwilber
2
Add ddp/fsdp2 train scripts, tests, configs and utilities to llama3_native_te recipe
#1327 opened Nov 17, 2025 by savitha-eng Loading…
4 of 9 tasks
2
add hf token to framework CI
#1326 opened Nov 17, 2025 by pstjohn Loading…
2
Evo2 Layer Ablation Study
#1324 opened Nov 15, 2025 by jstjohn • Draft
9 tasks
1
FSDP support in Evo2
#1321 opened Nov 14, 2025 by jstjohn • Draft
9 tasks
1
Adds THD + CP for ESM2
#1320 opened Nov 13, 2025 by jomitchellnv Loading…
2 of 9 tasks
40
Training scripts, tests, and config for llama3; very similar to ESM2 …
#1319 opened Nov 12, 2025 by savitha-eng • Draft
9 tasks
8
Add nucleotide tokenizer for llama3 model to recipes
#1314 opened Nov 7, 2025 by savitha-eng Loading…
5 of 9 tasks
7
Use the FusedAdam optimizer from TE
#1313 opened Nov 5, 2025 by pstjohn • Draft
1
begin drafting yaml for fp8 thd jobs ciflow:skip Skip all CI tests for this PR
#1297 opened Oct 29, 2025 by jwilber Loading…
@jwilber
1
bump nemo ciflow:all Run all tests (unit tests, slow tests, and notebooks) for bionemo2 or enforce running all tests
#1296 opened Oct 29, 2025 by farhadrgh Loading…
9 tasks
7
Bump starlette from 0.48.0 to 0.49.1 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1294 opened Oct 28, 2025 by dependabot bot Loading…
1
feat: benchmark annbatch in scspeedtest
#1290 opened Oct 28, 2025 by ilan-gold Loading…
1 of 9 tasks
7
Bump cryptography from 42.0.8 to 44.0.1 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1287 opened Oct 28, 2025 by dependabot bot Loading…
1
Bump urllib3 from 1.26.20 to 2.5.0 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1286 opened Oct 28, 2025 by dependabot bot Loading…
1
Bump jupyterlab from 4.4.5 to 4.4.8 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1280 opened Oct 27, 2025 by dependabot bot Loading…
1
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