scFoundation

✅ Status: ready | Version: xTrimoGene

Overview

Large-scale asymmetric transformer (xTrimoGene), custom 19264 gene vocabulary, pre-trained for perturbation/drug response

!!! tip “When to choose scFoundation”

User needs perturbation prediction, drug response modeling, or works with the xTrimoGene gene vocabulary

Specifications

Property

Value

Model

scFoundation

Version

xTrimoGene

Tasks

embed, integrate

Modalities

RNA

Species

human

Gene IDs

custom (19,264 gene set)

Embedding Dim

512

GPU Required

Yes

Min VRAM

16 GB

Recommended VRAM

32 GB

CPU Fallback

No

Adapter Status

✅ ready

Quick Start

import omicverse as ov

# 1. Check model spec
info = ov.fm.describe_model("scfoundation")

# 2. Profile your data
profile = ov.fm.profile_data("your_data.h5ad")

# 3. Validate compatibility
check = ov.fm.preprocess_validate("your_data.h5ad", "scfoundation", "embed")

# 4. Run inference
result = ov.fm.run(
    task="embed",
    model_name="scfoundation",
    adata_path="your_data.h5ad",
    output_path="output_scfoundation.h5ad",
    device="auto",
)

# 5. Interpret results
metrics = ov.fm.interpret_results("output_scfoundation.h5ad", task="embed")

Input Requirements

Requirement

Detail

Gene ID scheme

custom (19,264 gene set)

Preprocessing

Match genes to model vocabulary. Follow xTrimoGene preprocessing pipeline.

Data format

AnnData (.h5ad)

Batch key

.obs column for batch integration (optional)

Output Keys

After running ov.fm.run(), results are stored in the AnnData object:

Key

Location

Description

X_scfoundation

adata.obsm

Cell embeddings (512-dim)

scfoundation_pred

adata.obs

Predicted cell type labels

 
import scanpy as sc

adata = sc.read_h5ad("output_scfoundation.h5ad")
embeddings = adata.obsm["X_scfoundation"]  # shape: (n_cells, 512)

# Downstream analysis
sc.pp.neighbors(adata, use_rep="X_scfoundation")
sc.tl.umap(adata)
sc.tl.leiden(adata, resolution=0.5)
sc.pl.umap(adata, color=["leiden"])

Resources

Hands-On Tutorial

For a step-by-step walkthrough with code, see the scFoundation Tutorial Notebook.