预训练single-cell大模型文档

Contents:

• 安装
  • 安装scGPT运行环境
• 教程
  • 数据预处理
  • 预训练scGPT
  • 精调scGPT
• 贡献
  • 对于GHDDI的同事

Indices and tables

• 索引

• 模块索引

• 搜索页面

API

APIs

• scgpt package
  • Modules
    • scgpt.model
      • Submodules
      • scgpt.model.dsbn
      • scgpt.model.flash_layers
      • scgpt.model.generation_model
      • scgpt.model.grad_reverse
      • scgpt.model.layers
      • scgpt.model.model
    • scgpt.scbank package
      • scgpt.scbank.data
      • scgpt.scbank.databank
      • scgpt.scbank.monitor
      • scgpt.scbank.setting
      • Module contents
    • scgpt.tasks package
      • scgpt.tasks.grn
      • Module contents
    • scgpt.tokenizer package
      • Submodules
      • scgpt.tokenizer.gene_tokenizer
      • Module contents
    • scgpt.utils package
      • scgpt.utils.util
      • Module contents
  • scgpt.data_collator
    • DataCollator
      • DataCollator.data_style
      • DataCollator.do_binning
      • DataCollator.do_mlm
      • DataCollator.do_padding
      • DataCollator.get_mlm_probability()
      • DataCollator.keep_first_n_tokens
      • DataCollator.mask_value
      • DataCollator.max_length
      • DataCollator.mlm_probability
      • DataCollator.pad_token_id
      • DataCollator.pad_value
      • DataCollator.reserve_keys
      • DataCollator.sampling
  • scgpt.data_sampler
    • SubsetSequentialSampler
    • SubsetsBatchSampler
  • scgpt.loss
    • criterion_neg_log_bernoulli()
    • masked_mse_loss()
    • masked_relative_error()
  • scgpt.preprocess
    • Preprocessor
      • Preprocessor.check_logged()
    • binning()
  • scgpt.trainer
    • SeqDataset
    • define_wandb_metrcis()
    • eval_testdata()
    • evaluate()
    • predict()
    • prepare_data()
    • prepare_dataloader()
    • test()
    • train()