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NVIDIA/bionemo-framework

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BioNeMo

NVIDIA/bionemo-framework

Home
BioNeMo Framework
BioNeMo Framework
- About
  About
  - Overview
  - Background
    Background
    
    NeMo2
    
    Megatron Dataset Considerations
  - Release Notes
- Get Started
  Get Started
- Recipes
  Recipes
  - Models
    
    Models
    
    Models Directory
    
    Amplify
    
    Amplify
    
    Esm2
    
    Esm2
    
    Geneformer
    
    Geneformer
    
    Model readme
    
    Llama3
    
    Llama3
    
    Mixtral
    
    Mixtral
    
    Qwen
    
    Qwen
  - Recipes
    
    Recipes
    
    Recipes Directory
    
    Context Parallelism
    
    Codonfm native te
    
    Codonfm native te
    
    Codonfm ptl te
    
    Codonfm ptl te
    
    Notebooks
    Notebooks
    
    0-Zero-Shot-Mutation-Cancer-Hotspot
    
    Mutation Datasets Preprocessing
    
    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
    
    Esm2 accelerate te
    
    Esm2 accelerate te
    
    Esm2 native te
    
    Esm2 native te
    
    Esm2 peft te
    
    Esm2 peft te
    
    Evo2 megatron
    
    Evo2 megatron
    
    Examples
    Examples
    
    Fine tuning tutorial
    
    Zero-shot prediction of BRCA1 variant effects with Evo 2
    
    Configs
    
    Configs
    
    Fp8 analysis
    
    Fp8 analysis
    
    Geneformer native te mfsdp fp8
    
    Geneformer native te mfsdp fp8
    
    Llama3 native te
    
    Llama3 native te
    
    Opengenome2 llama native te
    
    Opengenome2 llama native te
    
    OpenGenome2 Metagenome Dataset: Sharding, Shuffling, and Tokenization in the LlaMA 3 Recipe
    
    Vit
    
    Vit
- Sub-packages
  Sub-packages
- Tutorials
  Tutorials
  - Evo2
    Evo2
    
    Examples
    Examples
    
    Fine tuning tutorial
    
    Zero-shot prediction of BRCA1 variant effects with Evo 2
    
    Configs
    
    Configs
  - CodonFM
    CodonFM
    
    Notebooks
    Notebooks
    
    0-Zero-Shot-Mutation-Cancer-Hotspot
    
    Mutation Datasets Preprocessing
    
    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
  - MoCo
    MoCo
    
    Examples
    Examples
    
    Building Generative Models for Continuous Data via Continuous Interpolants
    
    Building Generative Models for Continuous Data via Continuous Interpolants
    
    Building Generative Models for Continuous Data via Continuous Interpolants
    
    Building Generative Models for Discrete Data via Discrete Interpolants
    
    Entropic Flow Matching for Optimal Time Scheduling
    
    Optimal Transport Samplers Tutorial
  - SCDL
    SCDL
    
    Examples
    Examples
    
    Example notebook
- Data Sets
  Data Sets
  - CELLxGENE
  - UniProt Dataset
- Contributing
  Contributing
  - Code Review
  - Contributing Guidelines
  - Sub package dependency graph
  - Writing Documentation
    
    Writing Documentation
    
    Jupyter Notebook Support
    
    MkDocs
- References
  References
  - Frequently Asked Questions
  - API reference
    
    API reference
    
    Bionemo
    Bionemo
    
    Core
    Core
    
    Data
    
    Data
    
    Api Api
    Table of contents
    
    api
    
    Load
    
    Multi epoch dataset
    
    Permute
    
    Resamplers
    
    Resource
    
    Utils
    Utils
    
    Batching utils
    
    Dtypes
    
    Random utils
    
    Subprocess utils
    
    Moco
    Moco
    
    Distributions
    Distributions
    
    Prior
    Prior
    
    Distribution
    
    Continuous
    Continuous
    
    Gaussian
    
    Harmonic
    
    Utils
    
    Discrete
    Discrete
    
    Custom
    
    Mask
    
    Uniform
    
    Time
    Time
    
    Beta
    
    Distribution
    
    Logit normal
    
    Uniform
    
    Utils
    
    Interpolants
    Interpolants
    
    Base interpolant
    
    Batch augmentation
    
    Continuous time
    Continuous time
    
    Continuous
    Continuous
    
    Continuous flow matching
    
    Vdm
    
    Data augmentation
    Data augmentation
    
    Augmentation types
    
    Equivariant ot sampler
    
    Kabsch augmentation
    
    Ot sampler
    
    Discrete
    Discrete
    
    Discrete flow matching
    
    Mdlm
    
    Discrete time
    Discrete time
    
    Utils
    
    Continuous
    Continuous
    
    Ddpm
    
    Discrete
    Discrete
    
    D3pm
    
    Schedules
    Schedules
    
    Inference time schedules
    
    Utils
    
    Noise
    Noise
    
    Continuous noise transforms
    
    Continuous snr transforms
    
    Discrete noise schedules
    
    Testing
    Testing
    
    Parallel test utils
    
    Noodles
    Noodles
    
    Nvfaidx
    
    Recipeutils
    Recipeutils
    
    Checkpoint
    Checkpoint
    
    Remove optimizer
    
    Data
    Data
    
    Basecamp
    Basecamp
    
    Sharded dataset
    
    Utils
    
    Inference
    Inference
    
    Collation
    
    Io
    Io
    
    Fasta to jsonl
    
    Scdl
    Scdl
    
    Api
    Api
    
    Single cell row dataset
    
    Data
    Data
    
    Load
    
    Index
    Index
    
    Row feature index
    
    Io
    Io
    
    Single cell collection
    
    Single cell memmap dataset
    
    Schema
    Schema
    
    Header
    
    Headerutil
    
    Magic
    
    Version
    
    Scripts
    Scripts
    
    Convert h5ad to scdl
    
    Util
    Util
    
    Async worker queue
    
    Filecopyutil
    
    Memmap utils
    
    Scdl constants
    
    Torch dataloader utils
    
    Scspeedtest
    Scspeedtest
    
    Benchmark
    
    Common
    
    Size aware batching
    Size aware batching
    
    Sampler
    
    Utils
    
    Webdatamodule
    Webdatamodule
    
    Datamodule
    
    Utils
Models
Models
- Amplify
- Evo2
- Geneformer
- ESM 2
  ESM 2
  - Pre-trained Checkpoints

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