BioNeMo Framework
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BioNeMo Framework
NVIDIA/bionemo-framework
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BioNeMo Documentation
BioNeMo Documentation
About
About
Overview
Background
Background
NeMo2 Parallelism
Megatron Dataset Considerations
Release Notes
Get Started
Get Started
Hardware and Software Prerequisites
Access and Startup
Initialization Guide
Development
Training Models
Developer Guide
Developer Guide
bionemo-amplify
bionemo-core
bionemo-esm2
bionemo-evo2
bionemo-example-model
bionemo-fw
bionemo-geneformer
bionemo-geometric
bionemo-llm
bionemo-moco
bionemo-noodles
bionemo-scdl
bionemo-size-aware-batching
bionemo-testing
bionemo-webdatamodule
Tutorials
Tutorials
ESM-2
ESM-2
ESM-2 Fine-tuning
ESM-2 Inference
Zero-Shot Protein Design Using ESM-2
ESM-2 Pretraining
Evo2
Evo2
Fine tuning tutorial
Zero-shot prediction of BRCA1 variant effects with Evo 2
Geneformer
Geneformer
Geneformer Cell Type Classification Benchmark
Geneformer gene embeddings extraction and building a gene co-expression/regulation network (GRN)
BioNeMo - Geneformer inferencing for single cell downstream tasks
MoCo
MoCo
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
Optimal Transport Samplers Tutorial
SCDL
SCDL
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
Amplify
Amplify
Convert
Datamodule
Dataset
Hf rotary
Infer amplify
Model
Tokenizer
Train amplify
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
Convert
Embedding
Model
Finetune
Finetune
Datamodule
Dataset
Loss
Peft
Sequence model
Token model
Run
Run
Config models
Main
Recipes
Scripts
Scripts
Finetune esm2
Infer esm2
Train esm2
Testing
Testing
Compare
Evo2
Evo2
Data
Data
Fasta dataset
Preprocess
Tokenizer
Transcript extraction
Run
Run
Infer
Predict
Train
Utils
Utils
Config
Checkpoint
Checkpoint
Convert checkpoint model parallel evo2
Convert to nemo
Convert zero3 to zero1
Params
Zero3 conversion lib
Example model
Example model
Lightning
Lightning
Lightning basic
Training scripts
Training scripts
Finetune mnist
Predict mnist
Pretrain mnist
Fw
Fw
Dependency graph
Geneformer
Geneformer
Api
Data
Data
Preprocess
Singlecell
Singlecell
Datamodule
Dataset
Preprocess
Utils
Model
Model
Finetune token regressor
Run
Run
Config models
Main
Recipes
Scripts
Scripts
Infer geneformer
Train geneformer
Tokenizer
Tokenizer
Gene tokenizer
Geometric
Geometric
Atom featurizers
Base featurizer
Bond featurizers
Molecule featurizers
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
Callbacks
Datamodule utils
Iomixin utils
Logger utils
Megatron utils
Remote
Weight 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
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
Filecopyutil
Torch dataloader utils
Size aware batching
Size aware batching
Sampler
Utils
Testing
Testing
Callbacks
Lightning
Megatron dataset compatibility
Megatron parallel state utils
Subprocess utils
Testing callbacks
Torch
Utils
Data
Data
Esm2
Fasta
Load
Resource
Harnesses
Harnesses
Mode
Stop and go
Webdatamodule
Webdatamodule
Datamodule
Utils
Models
Models
Amplify
Evo2
Geneformer
ESM 2
ESM 2
Pre-trained Checkpoints
SUMMARY
Overview
Background
Release Notes
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