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BioNeMo Framework

bionemo-example_model

NVIDIA/bionemo-framework

BioNeMo Framework

NVIDIA/bionemo-framework

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User Guide
User Guide
- Getting Started
  Getting Started
- Background
  Background
  - NeMo2 Parallelism
  - Megatron Dataset Considerations
- Developer Guide
  Developer Guide
  - Bionemo core
    Bionemo core
    
    bionemo-core
  - Bionemo esm2
    Bionemo esm2
    
    bionemo-esm2
  - Bionemo example model
    Bionemo example model
    
    bionemo-example_model
  - Bionemo fw
    Bionemo fw
    
    bionemo-fw
  - Bionemo geneformer
    Bionemo geneformer
    
    bionemo-geneformer
  - Bionemo geometric
    Bionemo geometric
    
    bionemo-geometric
  - Bionemo llm
    Bionemo llm
    
    bionemo-llm
  - Bionemo scdl
    Bionemo scdl
    
    Bionemo-scdl: Single Cell Data Loading for Scalable Training of Single Cell Foundation Models.
  - Bionemo size aware batching
    Bionemo size aware batching
    
    bionemo-size-aware-batching
  - Bionemo testing
    Bionemo testing
    
    bionemo-testing
  - Bionemo webdatamodule
    Bionemo webdatamodule
    
    bionemo-webdatamodule
- Tutorials
  Tutorials
  - Bionemo esm2
    Bionemo esm2
    
    ESM2 Fine-Tuning
    
    ESM2 Pretraining
  - Bionemo scdl
    Bionemo scdl
    
    Example notebook
- Contributing
  Contributing
  - Contributing
  - Code Review
  - Writing Documentation
    
    Writing Documentation
    
    Jupyter Notebook Support
    
    MkDocs
- Appendix
  Appendix
  - Release Notes
Models
Models
- ESM-2
- Geneformer
Datasets
Datasets
- CELLxGENE
- UniProt Dataset
API
API
- Bionemo
  Bionemo
  - Core
    Core
    
    Api
    
    Data
    Data
    
    Api
    
    Multi epoch dataset
    
    Resamplers
    
    Model
    Model
    
    Config
    
    Utils
    Utils
    
    Batching utils
    
    Dtypes
    
    Random utils
  - Esm2
    Esm2
    
    Api
    
    Data
    Data
    
    Datamodule
    
    Dataset
    
    Tokenizer
    
    Tokenizer
    
    Model
    Model
    
    Attention
    
    Embedding
    
    Lr scheduler
    
    Model
    
    Finetune
    Finetune
    
    Datamodule
    
    Finetune regressor
    
    Finetune token classifier
    
    Infer
    
    Peft
    
    Train
  - Example model
    Example model
    
    Lightning basic
  - Geneformer
    Geneformer
    
    Api
    
    Data
    Data
    
    Preprocess
    
    Singlecell
    Singlecell
    
    Datamodule
    
    Dataset
    
    Preprocess
    
    Sc memmap
    
    Utils
    
    Model
    Model
    
    Finetune token regressor
    
    Tokenizer
    Tokenizer
    
    Gene tokenizer
  - Llm
    Llm
    
    Api
    
    Lightning
    
    Data
    Data
    
    Collate
    
    Label2id tokenizer
    
    Masking
    
    Types
    
    Model
    Model
    
    Config
    
    Layers
    
    Loss
    
    Biobert
    Biobert
    
    Lightning
    
    Model
    
    Testing utils
    
    Transformer specs
    
    Utils
    Utils
    
    Datamodule utils
    
    Iomixin utils
    
    Logger utils
    
    Megatron utils
    
    Remote
    
    Weight utils
  - Scdl
    Scdl
    
    Api
    Api
    
    Single cell row dataset
    
    Index
    Index
    
    Row feature index
    
    Io
    Io
    
    Single cell collection
    
    Single cell memmap dataset
    
    Scripts
    Scripts
    
    Convert h5ad to scdl
    
    Util
    Util
    
    Async worker queue
    
    Torch dataloader utils
  - Size aware batching
    Size aware batching
    
    Sampler
    
    Utils
  - Testing
    Testing
    
    Callbacks
    
    Lightning
    
    Megatron dataset compatibility
    
    Megatron parallel state utils
    
    Testing callbacks
    
    Utils
    
    Data
    
    Data
    
    Load
    
    Resource
    
    Harnesses
    Harnesses
    
    Stop and go
  - Webdatamodule
    Webdatamodule
    
    Datamodule
    
    Utils

bionemo-example_model

Minimalist package containing an example model that makes use of bionemo2/nemo conventions.

pip install -e .