SCVI Hyperparameter Screen

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SCVI Hyperparameter Screen

Dispatching the 8-arm scVI sweep to lab_cluster A100s — n_latent ∈ {10, 20, 30, 50} × n_layers ∈ {1, 2} , 40k cells × 2,000 HVGs, batch_key="sample_id" , 50 epochs, seed 0.

arm

n_latent

n_layers

label

Stephenson 2021 COVID PBMC — 40k cells, 2,000 batch-aware HVGs, no integration. Two UMAP panels: by sequencing site and by author cell type.

8 running · 16m 2s

Notebook

pbmc-pipeline

Shared with the agent

Live

[28]

python

Note to the agent. This kernel is the working pbmc-pipeline session. The reduced object covid_pbmc_40k_hvg.h5ad (counts + obs + var only) is on disk and loaded as a. All 8 scVI arms read from it; nothing else is mutated. Inspect a.obs and the HVG panel before adding a step.

Shared variables

aAnnData · 40,000 × 2,000

cleanAnnData · counts + obs + var

keep_obslist[str] · 8 columns

batch_keystr · "sample_id"

armslist · 8 scVI configs

output

wrote covid_pbmc_40k_hvg.h5ad

Python — pbmc-pipeline kernel

Connected to the agent’s live kernel — variables and state are shared. Type an expression and press Enter.