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BioNeMo Framework
NVIDIA/bionemo-framework
Home
User Guide
User Guide
Getting Started
Getting Started
Hardware and Software Prerequisites
Access and Startup
Initialization Guide
Development
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 Overview
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
ESM-2 Fine-Tuning
ESM-2 Pretraining
Bionemo geneformer
Bionemo geneformer
Geneformer Cell Type Classification Benchmark
Bionemo scdl
Bionemo scdl
Example notebook
Contributing
Contributing
Code Review
Contributing Guidelines
Writing Documentation
Writing Documentation
Jupyter Notebook Support
MkDocs
Appendix
Appendix
Frequently Asked Questions
Release Notes
Models
Models
ESM-2
Geneformer
Datasets
Datasets
CELLxGENE
UniProt Dataset
API
API
Bionemo
Bionemo
Core
Core
Api
Data
Data
Api
Load
Multi epoch dataset
Permute
Resamplers
Resource
Model
Model
Config
Utils
Utils
Batching utils
Dtypes
Random utils
Esm2
Esm2
Api
Data
Data
Datamodule
Dataset
Tokenizer
Tokenizer
Model
Model
Attention
Embedding
Model
Finetune
Finetune
Datamodule
Finetune regressor
Finetune token classifier
Infer
Peft
Train
Run
Run
Config models
Main
Recipes
Scripts
Scripts
Infer esm2
Train esm2
Example model
Example model
Lightning
Lightning
Lightning basic
Training scripts
Training scripts
Finetune mnist
Predict mnist
Pretrain mnist
Geneformer
Geneformer
Api
Data
Data
Preprocess
Singlecell
Singlecell
Datamodule
Dataset
Preprocess
Utils
Model
Model
Finetune token regressor
Run
Run
Config models
Main
Main
Table of contents
main
Recipes
Scripts
Scripts
Infer geneformer
Sc memmap
Train geneformer
Tokenizer
Tokenizer
Gene tokenizer
Llm
Llm
Api
Lightning
Train
Data
Data
Collate
Datamodule
Label2id tokenizer
Masking
Types
Model
Model
Config
Layers
Loss
Lr scheduler
Biobert
Biobert
Lightning
Model
Testing utils
Transformer specs
Run
Run
Config models
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
Torch
Utils
Data
Data
Esm2
Load
Resource
Harnesses
Harnesses
Mode
Stop and go
Webdatamodule
Webdatamodule
Datamodule
Utils
Table of contents
main
Main
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