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BioNeMo Framework
SUMMARY
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    NVIDIA/bionemo-framework
    • Home
    • User Guide
    • Models
    • Datasets
    • API
    NVIDIA/bionemo-framework
    • Home
    • User Guide
        • Hardware and Software Prerequisites
        • Access and Startup
        • Initialization Guide
        • Development
        • Training Models
        • NeMo2 Parallelism
        • Megatron Dataset Considerations
          • bionemo-amplify
          • bionemo-core
          • bionemo-esm2
          • bionemo-evo2
          • bionemo example model Overview
          • bionemo-fw
          • bionemo-geneformer
          • bionemo-geometric
          • bionemo-llm
          • Modular Co-Design (MoCo) Interpolants
          • bionemo-noodles
          • BioNeMo-SCDL: Single Cell Data Loading for Scalable Training of Single Cell Foundation Models.
          • bionemo-size-aware-batching
          • bionemo-testing
          • bionemo-webdatamodule
        • Conftest
          • ESM-2 Fine-tuning
          • ESM-2 Inference
          • Zero-Shot Protein Design Using ESM-2
          • ESM-2 Pretraining
          • Fine tuning tutorial
          • Zero-shot prediction of BRCA1 variant effects with Evo 2
          • Geneformer Cell Type Classification Benchmark
          • BioNeMo - Geneformer inferencing for single cell downstream tasks
          • 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
          • Example notebook
        • Code Review
        • Contributing Guidelines
        • Sub package dependency graph
        • Writing Documentation
          • Jupyter Notebook Support
          • MkDocs
        • Frequently Asked Questions
        • Release Notes
    • Models
      • Amplify
      • Evo2
      • Geneformer
      • ESM 2
        • Pre-trained Checkpoints
    • Datasets
      • CELLxGENE
      • UniProt Dataset
    • API
          • Convert
          • Datamodule
          • Dataset
          • Hf rotary
          • Infer amplify
          • Model
          • Tokenizer
          • Train amplify
          • Api
          • Data
            • Api
            • Load
            • Multi epoch dataset
            • Permute
            • Resamplers
            • Resource
            • Config
            • Batching utils
            • Dtypes
            • Random utils
          • Api
            • Datamodule
            • Dataset
            • Tokenizer
            • Convert
            • Embedding
            • Model
              • Datamodule
              • Dataset
              • Loss
              • Peft
              • Sequence model
              • Token model
            • Config models
            • Main
            • Recipes
          • Scripts
            • Finetune esm2
            • Infer esm2
            • Train esm2
            • Compare
          • Data
            • Fasta dataset
            • Preprocess
            • Tokenizer
            • Transcript extraction
            • Infer
            • Predict
            • Train
            • Config
            • Checkpoint
              • Convert checkpoint model parallel evo2
              • Convert to nemo
              • Convert zero3 to zero1
              • Params
              • Zero3 conversion lib
            • Lightning basic
            • Finetune mnist
            • Predict mnist
            • Pretrain mnist
          • Dependency graph
          • Api
            • Preprocess
              • Datamodule
              • Dataset
              • Preprocess
              • Utils
            • Finetune token regressor
            • Config models
            • Main
            • Recipes
          • Scripts
            • Infer geneformer
            • Train geneformer
            • Gene tokenizer
          • Atom featurizers
          • Base featurizer
          • Bond featurizers
          • Molecule featurizers
          • Api
          • Lightning
          • Train
            • Collate
            • Datamodule
            • Label2id tokenizer
            • Masking
            • Types
            • Config
            • Layers
            • Loss
            • Lr scheduler
              • Lightning
              • Model
              • Testing utils
              • Transformer specs
            • Config models
            • Callbacks
            • Datamodule utils
            • Iomixin utils
            • Logger utils
            • Megatron utils
            • Remote
            • Weight utils
              • Distribution
                • Gaussian
                • Harmonic
                • Utils
                • Custom
                • Mask
                • Uniform
              • Beta
              • Distribution
              • Logit normal
              • Uniform
              • Utils
            • Base interpolant
            • Batch augmentation
                • Continuous flow matching
                • Vdm
                  • Augmentation types
                  • Equivariant ot sampler
                  • Kabsch augmentation
                  • Ot sampler
                • Discrete flow matching
                • Mdlm
              • Utils
                • Ddpm
                • D3pm
            • Inference time schedules
            • Utils
              • Continuous noise transforms
              • Continuous snr transforms
              • Discrete noise schedules
            • Parallel test utils
          • Nvfaidx
            • Single cell row dataset
            • Row feature index
            • Single cell collection
            • Single cell memmap dataset
            • Convert h5ad to scdl
            • Async worker queue
            • Torch dataloader utils
          • Sampler
          • Utils
          • Callbacks
          • Lightning
          • Megatron dataset compatibility
          • Megatron parallel state utils
          • Subprocess utils
          • Testing callbacks
          • Torch
          • Utils
            • Esm2
            • Fasta
            • Load
            • Resource
            • Mode
            • Stop and go
          • Datamodule
          • Utils

    SUMMARY

    • What is BioNeMo?
    • Getting Started
    • Background
    • Developer Guide
    • Tutorials
    • Developer Guide
    • Contributing
    • Appendix
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