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Pull requests: NVIDIA-BioNeMo/bionemo-framework

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Pull requests list

fix(geneformer): add nvidia-resiliency-ext>=0.6.0 dependency
#1600 opened Jun 4, 2026 by svc-bionemo Collaborator Loading…
1
Bump qs from 6.14.1 to 6.15.2 in /bionemo-recipes/interpretability/sparse_autoencoders/recipes/codonfm/codon_dashboard dependencies Pull requests that update a dependency file javascript Pull requests that update javascript code
#1599 opened Jun 3, 2026 by dependabot Bot Loading…
1
fix(geneformer): resolve protobuf conflict with nvidia-resiliency-ext>=0.6.0
#1598 opened Jun 3, 2026 by svc-bionemo Collaborator Loading…
3
[Evo2] Switch from static to faster/more modern dynamic inference engine ciflow:notebooks Run Jupyter notebooks execution tests for docs and bionemo2
#1597 opened Jun 3, 2026 by jstjohn Collaborator Loading…
1 of 9 tasks
4
Bump qs from 6.14.1 to 6.15.2 in /bionemo-recipes/interpretability/sparse_autoencoders/recipes/esm2/protein_dashboard dependencies Pull requests that update a dependency file javascript Pull requests that update javascript code
#1593 opened Jun 2, 2026 by dependabot Bot Loading…
1
Bump idna from 3.11 to 3.15 in /bionemo-recipes/interpretability/sparse_autoencoders dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1592 opened Jun 2, 2026 by dependabot Bot Loading…
1
Bump urllib3 from 2.6.3 to 2.7.0 in /bionemo-recipes/interpretability/sparse_autoencoders dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1591 opened Jun 2, 2026 by dependabot Bot Loading…
1
Bump gitpython from 3.1.46 to 3.1.50 in /bionemo-recipes/interpretability/sparse_autoencoders dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1590 opened Jun 2, 2026 by dependabot Bot Loading…
1
Bump gitpython from 3.1.45 to 3.1.50 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1589 opened Jun 2, 2026 by dependabot Bot Loading…
1
Bump mistune from 3.1.3 to 3.2.1 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1588 opened Jun 2, 2026 by dependabot Bot Loading…
1
Bump urllib3 from 1.26.20 to 2.7.0 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1587 opened Jun 2, 2026 by dependabot Bot Loading…
1
Bump idna from 3.10 to 3.15 in /bionemo-recipes/recipes/codonfm_ptl_te dependencies Pull requests that update a dependency file python Pull requests that update Python code
#1586 opened Jun 2, 2026 by dependabot Bot Loading…
1
evo2 SAE recipe: streaming extract.py + env-overridable sweep runner
#1583 opened May 29, 2026 by polinabinder1 Collaborator • Draft
5 tasks
2
[DRAFT] Evo 2 SAE feature explorer — visualization mockup
#1582 opened May 26, 2026 by polinabinder1 Collaborator • Draft
5 tasks
2
Add Evo2 1B SAE recipe + fix Savanna weights_only loading
#1579 opened May 21, 2026 by polinabinder1 Collaborator Loading…
3 tasks
2
interpretability/sae: add bionemo-sae-recipe Claude skill
#1578 opened May 21, 2026 by polinabinder1 Collaborator Loading…
9 tasks
2
fix: guard division-by-zero and uninitialized state in metrics/masking code
#1576 opened May 18, 2026 by mooreneural Loading…
4 tasks
5
[WIP] codonfm recipe
#1573 opened May 13, 2026 by balvisio Collaborator Loading…
9 tasks
1
Jwilber/cd image up4 ciflow:skip Skip all CI tests for this PR
#1569 opened May 4, 2026 by jwilber Collaborator Loading…
@jwilber
3
[draft] Add notebooks for codonfm sae tasks ciflow:skip Skip all CI tests for this PR
#1558 opened Apr 21, 2026 by jwilber Collaborator Loading…
@jwilber
2
Mixtral recipes
#1551 opened Apr 15, 2026 by trvachov Collaborator Loading…
4 of 9 tasks
7
init conversion demo
#1549 opened Apr 8, 2026 by lbliii Loading…
1
Generalize MFU/FLOPs module across recipes with log_mfu training hook
#1548 opened Apr 4, 2026 by gagank1 Contributor Loading…
1 of 9 tasks
@gagank1
66
[DRAFT] DO NOT MERGE Esm2 minifold
#1541 opened Apr 1, 2026 by jomitchellnv Collaborator Loading…
9 tasks
2
Remove BIONEMO-2840 sm120 fused attention workarounds
#1538 opened Mar 30, 2026 by pstjohn Collaborator Loading…
3
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