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BioNeMo Framework
索引
初始化搜索
NVIDIA/bionemo-framework
首页
用户指南
模型
数据集
API
BioNeMo Framework
NVIDIA/bionemo-framework
首页
用户指南
用户指南
入门指南
入门指南
硬件和软件先决条件
访问和启动
初始化指南
开发
训练模型
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:用于可扩展单细胞基础模型训练的单细胞数据加载。
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
Callbacks
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
Lightning
Megatron dataset compatibility
Megatron parallel state utils
Testing callbacks
Torch
Utils
Data
Data
Esm2
Load
Resource
Harnesses
Harnesses
Mode
Stop and go
Webdatamodule
Webdatamodule
Datamodule
Utils
目录
ESM2 脚本目录
索引
ESM2 脚本目录
这是一个可通过命令行运行的单次脚本集合。有关如何生成这些脚本,请参阅 pyproject.toml 文件的
[project.scripts]
部分。
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