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NVIDIA BioNeMo Framework
GETTING STARTED
What is BioNeMo?
Hardware and Software Prerequisites
Access and Startup
Initialization Guide
BioNeMo Framework Tutorials
BioNeMo CORE
Fundamentals
Data Module
Validation with a Downstream Task
Inference with Nvidia Triton Server
Example of PyTriton Inference
BEST PRACTICES
Hyperparameter Usage and Tuning
Training Parallelism
MODELS
DiffDock
DNABERT
DSMBind
EquiDock
ESM-1nv
ESM-2nv
Geneformer
MegaMolBART
MolMIM
OpenFold
Prott5nv
Model Benchmarks
DATASETS
UniProt Dataset
CELLxGENE
ZINC-15 Dataset
The Protein Data Bank (PDB)
Human Reference Genome Version GRCh38.p13
OpenProteinSet
MoleculeNet Physical Chemistry Datasets - Lipophilicity, FreeSolv, ESOL
TUTORIALS
DiffDock: Preparing Workspace and Data for Pre-training
Zero-Shot Protein Design Using ESM-2nv
BioNeMo - MegaMolBART Inferencing for Generative Chemistry
MolMIM Inferencing for Generative Chemistry and Downstream Prediction
ZINC Training Dataset Setup for small molecule language models
Finetune pre-trained models in BioNeMo
MolMIM Property Guided Molecular Optimization Using CMA-ES
Adding the OAS Dataset: Modifying the Dataset Class
Adding the OAS Dataset: Customizing Dataset Object and Dataloader Functions
Adding the OAS Dataset: Downloading and Preprocessing
Encoder Fine-tuning
DiffDock Model Training using BioNeMo
EquiDock Model Training using BioNeMo
ESM1nv Model Training using BioNeMo
ESM-2nv: Data Preprocessing and Model Training Using BioNeMo
MegaMolBART Model Training using BioNeMo
Train MolMIM from scratch on your own data using the BioNeMo Framework
Finetuning LLM in BioNeMo for a Downstream Task
Generating Embeddings for Protein Clustering
Training LLM for a Custom Downstram Task: Retrosynthesis Prediction using MegaMolBART
Fine-Tune ESM-2nv on FLIP Data for Sequence-Level Classification, Regression, Token-Level Classification, and with LoRA Adapters
Performing inference on OAS sequences with ESM-2nv
Pretrain from Scratch, Continue Training from an Existing Checkpoint, and Fine-tune ESM-2nv on Custom Data
Generating and visualizing embeddings with DNABert
Pretrain, Fine-tune, and Perform Inference with DNABERT for Splice Site Prediction
APPENDIX
Frequently Asked Questions (FAQ)
Bibliography
Release Notes
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