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NVIDIA-BioNeMo

8 indexed repositories · View on GitHub

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

Python · 857 stars
bionemo-agent-toolkit
Turn any agent into a life science expert with NVIDIA BioNeMo skills.

Python · 462 stars
Proteina-Complexa
Generative model for protein binder design for protein and small molecule targets. Combines a pretrained flow-based generative model (bui...

Python · 432 stars
nvMolKit
A high-performance, GPU-accelerated library for key computational chemistry tasks, such as molecular similarity, conformer generation, an...

Cuda · 276 stars
KERMT
KERMT is a pretrained graph neural network model for molecular property prediction.

Python · 99 stars
BioNeMo-Inference-Runtime
Easy, fast, and memory-efficient structure prediction inference

Python · 60 stars
boltz-cp
Context Parallelism Code for Boltz-2

Python · 59 stars
cuik-molmaker
cuik-molmaker is a specialized package designed for molecular featurization, converting chemical structures into formats that can be effe...

C++ · 36 stars

Beginner friendly Everything

Open All

[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

NVIDIA-BioNeMo

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