NVIDIA-BioNeMo/bionemo-recipes

BioNeMo Recipes: For building and adapting AI models in drug discovery at scale

Stars: 857
Forks: 181
Open beginner issues: 0
Indexed issues: 36
Avg merge: 1d 6h
Merged PRs (30d): 14

Dominant language: Python
License: No license data
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

36 open issues indexed

[ALERT] Access to NVIDIA's Self-Hosted Runners is Expiring Open

nvidia-runners

Difficulty 1/5 Under an hour Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1726 · Opened Aug 30, 2026
Flaky test: CUDA error: initialization error in DataLoader workers (esm2_native_te) Open

bug ESM2

Difficulty 4/5 3-5 days Newbie friendliness 48/100

NVIDIA-BioNeMo/bionemo-recipes#1698 · Opened Jul 29, 2026
[Feature] Inference-side PTQ / weight-compression recipe for bio models (ESM-2 / Geneformer / Evo2) — wanted? where should it live? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1681 · Opened Jul 11, 2026
[BUG] Evo2 doesnt work in Bionemo V3.0.0 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

NVIDIA-BioNeMo/bionemo-recipes#1669 · 1 comment · Opened Jul 1, 2026
[Feature] Reflect vortex prefill improvements from PR 77 Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

NVIDIA-BioNeMo/bionemo-recipes#1647 · Opened Jun 16, 2026
[Feature] Support `.obsm` arrays in `SingleCellMemMapDataset` for spatial transcriptomics Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

NVIDIA-BioNeMo/bionemo-recipes#1577 · Opened May 21, 2026
MFU tracking: `pad_to_multiple_of` path inflates useful-work Σ(Lᵢ²) by the mock-sequence contribution Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

NVIDIA-BioNeMo/bionemo-recipes#1561 · Opened Apr 24, 2026
[Feature] Support loading & writing zarr files in scdl Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

NVIDIA-BioNeMo/bionemo-recipes#1560 · Opened Apr 22, 2026
[BUG] Investigate non-determinism in evo2 recipe data preprocessing script and/or test Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 32/100

NVIDIA-BioNeMo/bionemo-recipes#1493 · 1 comment · Opened Mar 4, 2026
Remove CUDA Sync Workaround in Evo2 Training Script Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1301 · 3 comments · Opened Oct 31, 2025
[BUG] Incorrect documentation for Continuous Flow matching augmentation Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

NVIDIA-BioNeMo/bionemo-recipes#1272 · Opened Oct 24, 2025
[BUG] EVO2 7b_arc_longcontext can't use context parallelism (2 GPUs) for long sequence prediction: shape mismatch Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1268 · 2 reactions · Opened Oct 22, 2025
[Feature] Tensor + Sequence parallel test coverage for evo2 inference. Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

NVIDIA-BioNeMo/bionemo-recipes#1243 · Opened Oct 10, 2025
[Feature] Can I use bionemo framework to extract the embeddings of evo2_40b model？ Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/bionemo-recipes#1200 · 2 comments · 1 reaction · Opened Sep 28, 2025
Add a classification / regression finetuning head to evo2 Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#1170 · 8 comments · 1 reaction · Opened Sep 22, 2025
[Feature] Support batched generation (inference) in evo2. Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/bionemo-recipes#1152 · 1 reaction · Opened Sep 16, 2025
[BUG] Evo2 finetune with LoRA does not work Open

bug Evo2

NVIDIA-BioNeMo/bionemo-recipes#1136 · 9 comments · 1 reaction · 1 assignee · Opened Sep 9, 2025
Obsolete references to `--experiment-dir` removed evo2 parameter Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

NVIDIA-BioNeMo/bionemo-recipes#1128 · 1 comment · Opened Sep 8, 2025
[Feature] Highlight contribution requirements to make contributing easier. Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

NVIDIA-BioNeMo/bionemo-recipes#1004 · 1 comment · Opened Jul 28, 2025
How to Transfer the Evo2-Bionemo checkpoint to the pytorch version and load it locally Open

Difficulty 5/5 Over a week Newbie friendliness 18/100

NVIDIA-BioNeMo/bionemo-recipes#967 · 8 comments · 1 reaction · Opened Jul 2, 2025
Evo2 distributed checkpoint to huggingface conversion Open

NVIDIA-BioNeMo/bionemo-recipes#920 · 7 comments · 1 assignee · Opened Jun 4, 2025
[Feature] Replace all instances of TimingCallback with DeltaTimingCallback to avoid global_step re-use Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

NVIDIA-BioNeMo/bionemo-recipes#917 · 1 comment · Opened Jun 3, 2025
Try out NBTest: A smarter tool for testing jupyter notebooks Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

NVIDIA-BioNeMo/bionemo-recipes#882 · 5 comments · Opened May 16, 2025
[Feature] Add Regressor Head Option to Evo2 Fine-Tuning Script for Numerical Label Prediction Open

enhancement

NVIDIA-BioNeMo/bionemo-recipes#881 · 12 comments · 2 reactions · 1 assignee · Opened May 15, 2025
[BUG] Evo2 training does not work with tp>1 when num_attention_heads is not divisible by tp Open

bug Evo2

Difficulty 4/5 3-5 days Newbie friendliness 32/100

NVIDIA-BioNeMo/bionemo-recipes#814 · 2 comments · Opened Apr 9, 2025
[Feature] Allow early training termination at specific step using Trainer.max_steps without modifying LR schedule ie from full convergence run Open

Evo2

NVIDIA-BioNeMo/bionemo-recipes#749 · 1 assignee · Opened Mar 12, 2025
[Feature] Flash attention v3 support Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#735 · 1 reaction · Opened Mar 8, 2025
Use faster direct call of train/predict methods in test scripts. Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

NVIDIA-BioNeMo/bionemo-recipes#720 · 1 comment · Opened Mar 5, 2025
Clean up and document scripts in the evo2/utils/ subdirectories. Split out useful functions. Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

NVIDIA-BioNeMo/bionemo-recipes#719 · Opened Mar 5, 2025
Split padding logic out of the batch collate function. Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#718 · Opened Mar 5, 2025
[Feature] Add golden value for metric logging in ESM2 finetuning Open

NVIDIA-BioNeMo/bionemo-recipes#684 · 2 comments · 1 assignee · Opened Feb 10, 2025
test DDP parallelism without usage of mock Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#680 · Opened Feb 6, 2025
Add descriptions for the params in the config YAML file of MolMIM Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

NVIDIA-BioNeMo/bionemo-recipes#612 · 1 comment · Opened Jan 16, 2025
Enable extraction of gene embeddings from geneformer (averaging of gene embeddings across all cells) Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

NVIDIA-BioNeMo/bionemo-recipes#452 · 11 comments · Opened Nov 19, 2024
Support virtual pipeline parallel in global batch size calculation Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

NVIDIA-BioNeMo/bionemo-recipes#286 · 3 comments · Opened Oct 8, 2024
Add a `pip-licenses` test Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

NVIDIA-BioNeMo/bionemo-recipes#82 · 1 comment · Opened Aug 7, 2024

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