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- assets
- css
- images
- amplify
- cellxgene
- esm2
- evo2
- geneformer
- megatron_background
- recipes
- sub_package_graphs
- wandb_tips_tricks
- javascripts
- lunr
- min
- workers
- stylesheets
- main
- SUMMARY
- about
- SUMMARY
- background
- SUMMARY
- megatron_datasets
- nemo2
- overview
- releasenotes-fw
- contributing
- Writing Documentation
- jupyter-notebooks
- mkdocs
- code-review
- contributing
- sub-package_dependency_graph
- datasets
- CELLxGENE
- uniprot
- developer-guide
- SUMMARY
- bionemo-core/bionemo-core-Overview
- bionemo-evo2
- assets
- bionemo-evo2-Overview
- bionemo-example_model/bionemo-example_model-Overview
- bionemo-llm/bionemo-llm-Overview
- bionemo-moco/bionemo-moco-Overview
- bionemo-noodles/bionemo-noodles-Overview
- bionemo-scdl
- assets
- bionemo-scdl-Overview
- bionemo-scspeedtest/bionemo-scspeedtest-Overview
- bionemo-size-aware-batching/bionemo-size-aware-batching-Overview
- bionemo-testing/bionemo-testing-Overview
- bionemo-webdatamodule/bionemo-webdatamodule-Overview
- examples
- SUMMARY
- bionemo-evo2
- fine-tuning-tutorial
- zeroshot_brca1
- bionemo-moco
- continuous_data_interpolant_tutorial_cfm
- continuous_data_interpolant_tutorial_ddpm
- continuous_data_interpolant_tutorial_vdm
- discrete_data_interpolant_tutorial
- entropic_time_scheduler_tutorial_cfm
- ot_sampler_tutorial
- bionemo-scdl/example_notebook
- conftest
- getting-started
- SUMMARY
- access-startup
- development
- initialization-guide
- pre-reqs
- training-models
- using-slurm
- recipes
- SUMMARY
- models
- amplify/amplify
- esm2/esm2
- geneformer/geneformer
- llama3/llama3
- recipes
- codonfm_ptl_te
- assets/images
- codonfm_ptl_te
- esm2_accelerate_te/esm2_accelerate_te
- esm2_native_te/esm2_native_te
- esm2_peft_te/esm2_peft_te
- evo2_megatron
- assets
- evo2_megatron
- fp8_analysis/fp8_analysis
- geneformer_native_te_mfsdp_fp8/geneformer_native_te_mfsdp_fp8
- llama3_native_te/llama3_native_te
- vit/vit
- references
- API_reference
- bionemo
- core
- api
- data
- api
- load
- multi_epoch_dataset
- permute
- resamplers
- resource
- model/config
- utils
- batching_utils
- dtypes
- random_utils
- subprocess_utils
- evo2
- data
- fasta_dataset
- preprocess
- sharded_eden_dataloader
- tokenizer
- transcript_extraction
- models
- llama
- mamba
- peft
- run
- infer
- predict
- train
- utils
- utils
- callbacks
- checkpoint
- convert_checkpoint_model_parallel_evo2
- convert_to_nemo
- convert_zero3_to_zero1
- evo2_remove_optimizer
- nemo2_to_hf
- params
- zero3_conversion_lib
- config
- logging/callbacks
- loss/embedding_variance
- example_model
- lightning/lightning_basic
- training_scripts
- finetune_mnist
- predict_mnist
- pretrain_mnist
- llm
- api
- data
- collate
- datamodule
- label2id_tokenizer
- masking
- types
- lightning
- model
- biobert
- lightning
- model
- testing_utils
- transformer_specs
- config
- layers
- loss
- lr_scheduler
- run/config_models
- train
- utils
- callbacks
- datamodule_utils
- iomixin_utils
- logger_utils
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- remote
- weight_utils
- moco
- distributions
- prior
- continuous
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- utils
- discrete
- custom
- mask
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- distribution
- time
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- logit_normal
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- utils
- interpolants
- base_interpolant
- batch_augmentation
- continuous_time
- continuous
- continuous_flow_matching
- data_augmentation
- augmentation_types
- equivariant_ot_sampler
- kabsch_augmentation
- ot_sampler
- vdm
- discrete
- discrete_flow_matching
- mdlm
- discrete_time
- continuous/ddpm
- discrete/d3pm
- utils
- schedules
- inference_time_schedules
- noise
- continuous_noise_transforms
- continuous_snr_transforms
- discrete_noise_schedules
- utils
- testing/parallel_test_utils
- noodles/nvfaidx
- scdl
- api/single_cell_row_dataset
- data/load
- index/row_feature_index
- io
- single_cell_collection
- single_cell_memmap_dataset
- schema
- headerutil
- header
- magic
- version
- scripts/convert_h5ad_to_scdl
- util
- async_worker_queue
- filecopyutil
- memmap_utils
- scdl_constants
- torch_dataloader_utils
- scspeedtest
- benchmark
- common
- size_aware_batching
- sampler
- utils
- testing
- assert_optimizer_grads_match
- callbacks
- data
- esm2
- fasta
- load
- resource
- harnesses
- mode
- stop_and_go
- lightning
- megatron_dataset_compatibility
- megatron_parallel_state_utils
- subprocess_utils
- tensorboard
- testing_callbacks
- torch
- utils
- webdatamodule
- datamodule
- utils
- FAQ
- models
- ESM-2
- SUMMARY
- pre-training
- amplify
- evo2
- geneformer
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