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NVIDIA BioNeMo Framework
GETTING STARTED
Introduction
Prerequisites for Using BioNeMo Framework
Quickstart Guide
Getting Started with BCP
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
ESM-1nv
ESM-2nv
Prott5nv
MegaMolBART
MolMIM
EquiDock
DiffDock
DNABERT
OpenFold
sc-FM
Model Benchmarks
DATASETS
UniProt Dataset
ZINC-15 Dataset
The Protein Data Bank (PDB)
Human Reference Genome Version GRCh38.p13
OpenProteinSet
MoleculeNet Physical Chemistry Datasets - Lipophilicity, FreeSolv, ESOL
Genecorpus-30M
PertNet 2022
TUTORIALS
DiffDoc: Preparing Workspace and Data for Pre-training
ESM2: Preparing Workspace and Data for Pre-training
BioNeMo - MegaMolBART Inferencing for Generative Chemistry
BioNeMo - MolMIM Inferencing for Generative Chemistry
MolMIM ZINC15 Training Dataset Setup
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
ESM2nv Model Training using BioNeMo
MegaMolBART Model Training using BioNeMo
MolMIM Model Training using BioNeMo
Finetuning LLM in BioNeMo for a Downstream Task
Generating Embeddings for Protein Clustering
Generating Embeddings for Protein Clustering
Training LLM for a Custom Downstram Task: Retrosynthesis Prediction using MegaMolBART
APPENDIX
Frequently Asked Questions (FAQ)
Bibliography
Release Notes
Index