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BioNeMo
NVIDIA-BioNeMo/bionemo-framework
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BioNeMo Recipes
BioNeMo Recipes
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About
Overview
Get Started
Get Started
Hardware and Software Prerequisites
Initialization Guide
Development
Training Models
Using SLURM
Recipes
Recipes
Models
Models
Models Directory
Amplify
Amplify
Codonfm
Codonfm
Tests
Tests
Common
Common
Esm2
Esm2
Tests
Tests
Common
Common
Geneformer
Geneformer
Model readme
Llama3
Llama3
Tests
Tests
Common
Common
Mixtral
Mixtral
Tests
Tests
Common
Common
Qwen
Qwen
Tests
Tests
Common
Common
Recipes
Recipes
Recipes Directory
Context Parallelism
Codonfm native te
Codonfm native te
Hydra config
Hydra config
Codonfm ptl te
Codonfm ptl te
Data scripts
Data scripts
Data curation
Data curation
Notebooks
Notebooks
0-Zero-Shot-Mutation-Cancer-Hotspot
Mutation Datasets Preprocessing
000 Annotation File Processing
1-Zero-Shot-Mutation-Variant-DDD-ASD
2-Zero-Shot-Mutation-Variant-Clinvar-Alphamissense
3-Zero-Shot-Mutation-Variant-Clinvar-Synonymous
Tutorial 4: RiboNN Translation Efficiency Prediction with Encodon
Tutorial 5: mRFP Expression Prediction with Encodon
Tutorial 6: mRNA Stability Prediction with Encodon
Eden megatron
Eden megatron
Src
Src
Bionemo
Bionemo
Eden
Eden
Data
Data
Utils
Utils
Checkpoint
Checkpoint
Tokenizers
Tokenizers
Nucleotide fast tokenizer 256
Nucleotide fast tokenizer 256
Nucleotide fast tokenizer 512
Nucleotide fast tokenizer 512
Esm2 accelerate te
Esm2 accelerate te
Example 8m checkpoint
Example 8m checkpoint
Hydra config
Hydra config
Esm2 native te
Esm2 native te
Hydra config
Hydra config
Esm2 peft te
Esm2 peft te
Example 8m checkpoint
Example 8m checkpoint
Hydra config
Hydra config
Evo2 megatron
Evo2 megatron
Examples
Examples
Evaluating Evo2 with GFMBench-API (BioNeMo Recipe)
Fine tuning tutorial
Lora fine tuning tutorial
Zero-shot prediction of BRCA1 variant effects with Evo 2
Configs
Configs
Src
Src
Bionemo
Bionemo
Evo2
Evo2
Data
Data
Utils
Utils
Checkpoint
Checkpoint
Tokenizers
Tokenizers
Nucleotide fast tokenizer 256
Nucleotide fast tokenizer 256
Nucleotide fast tokenizer 512
Nucleotide fast tokenizer 512
Fp8 analysis
Fp8 analysis
Geneformer native te mfsdp fp8
Geneformer native te mfsdp fp8
Hydra config
Hydra config
Model
Model
Llama3 native te
Llama3 native te
Hydra config
Hydra config
Tokenizers
Tokenizers
Nucleotide fast tokenizer
Nucleotide fast tokenizer
Opengenome2 llama native te
Opengenome2 llama native te
OpenGenome2 Metagenome Dataset: Sharding, Shuffling, and Tokenization in the LlaMA 3 Recipe
Hydra config
Hydra config
Tokenizers
Tokenizers
Nucleotide fast tokenizer
Nucleotide fast tokenizer
Vit
Vit
Config
Config
Vllm inference
Vllm inference
Esm2
Esm2
Tutorials
Tutorials
Data Sets
Data Sets
CELLxGENE
UniProt Dataset
Contributing
Contributing
Code Review
Contributing
Writing Documentation
Writing Documentation
Jupyter Notebook Support
MkDocs
Frequently Asked Questions
Models
Models
Amplify
Evo2
Geneformer
ESM 2
ESM 2
Pre-trained Checkpoints
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BioNeMo Recipes
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Generated Tutorials
Tutorials generated from recipe notebooks are listed in this section.
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