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BioNeMo 框架

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BioNeMo 框架

NVIDIA/bionemo-framework

首页
用户指南
用户指南
- 入门
  入门
- 背景
  背景
  - NeMo2 并行性
  - Megatron 数据集注意事项
- 开发者指南
  开发者指南
  - Bionemo core
    Bionemo core
    
    bionemo-core
  - Bionemo esm2
    Bionemo esm2
    
    bionemo-esm2
  - Bionemo example model
    Bionemo example model
    
    bionemo example model 概述
  - Bionemo fw
    Bionemo fw
    
    bionemo-fw
  - Bionemo geneformer
    Bionemo geneformer
    
    bionemo-geneformer
  - Bionemo geometric
    Bionemo geometric
    
    bionemo-geometric
  - Bionemo llm
    Bionemo llm
    
    bionemo-llm
  - Bionemo moco
    Bionemo moco
    
    模块化协同设计 (MoCo) 插值器
  - Bionemo noodles
    Bionemo noodles
    
    bionemo-noodles
  - Bionemo scdl
    Bionemo scdl
    
    BioNemo-SCDL：用于可扩展训练单细胞基础模型的单细胞数据加载。
  - Bionemo size aware batching
    Bionemo size aware batching
    
    bionemo-size-aware-batching
  - Bionemo testing
    Bionemo testing
    
    bionemo-testing
  - Bionemo webdatamodule
    Bionemo webdatamodule
    
    bionemo-webdatamodule
- 教程
  教程
  - Conftest
  - Bionemo esm2
    Bionemo esm2
    
    ESM-2 微调
    
    ESM-2 推理
    
    使用 ESM-2 的零样本蛋白质设计
    
    ESM-2 预训练
  - Bionemo geneformer
    Bionemo geneformer
    
    Geneformer 细胞类型分类基准测试
  - Bionemo moco
    Bionemo moco
    
    通过连续插值器构建连续数据生成模型
    
    通过离散插值器构建离散数据生成模型
    
    最优传输采样器教程
  - Bionemo scdl
    Bionemo scdl
    
    示例笔记本
- 贡献
  贡献
  - 贡献
  - 代码审查
  - 编写文档
    
    编写文档
    
    Jupyter Notebook 支持
    
    MkDocs
- 附录
  附录
  - 常见问题
  - 发行说明
模型
模型
- Geneformer
- ESM 2
  ESM 2
  - 预训练检查点
数据集
数据集
- CELLxGENE
- UniProt 数据集
API
API
- Bionemo
  Bionemo
  - Core
    Core
    
    Api
    
    Data
    
    Data
    
    Api
    
    Load
    
    多周期数据集
    
    Permute
    
    Resamplers
    
    Resource
    
    Model
    Model
    
    Config
    
    Utils
    Utils
    
    Batching utils
    
    Dtypes
    
    Random utils
  - Esm2
    Esm2
    
    Api
    
    Data
    Data
    
    Datamodule
    
    Dataset
    
    Tokenizer
    
    Tokenizer
    
    Model
    Model
    
    Embedding
    
    Model
    
    Finetune
    Finetune
    
    Datamodule
    
    Finetune regressor
    
    Finetune token classifier
    
    Peft
    
    Train
    
    Run
    Run
    
    Config models
    
    Main
    
    Recipes
    
    Scripts
    
    Scripts
    
    Infer esm2
    
    Train esm2
  - Example model
    Example model
    
    Lightning
    Lightning
    
    Lightning basic
    
    Training scripts
    Training scripts
    
    Finetune mnist
    
    Predict mnist
    
    Pretrain mnist
  - 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
    
    回调
    
    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
    
    Optimal transport
    Optimal transport
    
    Equivariant ot sampler
    
    Kabsch augmentation
    
    Ot sampler
    
    Ot types
    
    Discrete
    Discrete
    
    Discrete flow matching
    
    Mdlm
    
    Discrete time
    Discrete time
    
    Utils
    
    Continuous
    Continuous
    
    Ddpm
    
    Discrete
    Discrete
    
    D3pm
    
    Schedules
    Schedules
    
    Discrete noise schedules
    
    Inference time schedules
    
    Utils
    
    Noise
    Noise
    
    Continuous noise transforms
    
    Continuous snr transforms
    
    Discrete noise schedules
  - 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
    
    Torch dataloader utils
  - Size aware batching
    Size aware batching
    
    Sampler
    
    Utils
  - Testing
    Testing
    
    Callbacks 回调
    目录
    
    callbacks
    
    Lightning
    
    Megatron 数据集兼容性
    
    Megatron 并行状态工具
    
    测试回调
    
    Torch
    
    Utils
    
    Data
    Data
    
    Esm2
    
    Load
    
    Resource
    
    Harnesses
    Harnesses
    
    Mode
    
    Stop and go
  - Webdatamodule
    Webdatamodule
    
    Datamodule
    
    Utils