Skip to content

scPlantLLM

⚠️ Status: partial | Version: v1.0

Overview

Plant-specific single-cell model, handles polyploidy and plant gene nomenclature

When to choose scPlantLLM

User has plant single-cell data (Arabidopsis, rice, maize, etc.) or mentions polyploidy

Specifications

Property Value
Model scPlantLLM
Version v1.0
Tasks embed, integrate
Modalities RNA
Species plant (Arabidopsis, rice, maize, etc.)
Gene IDs symbol
Embedding Dim 512
GPU Required Yes
Min VRAM 16 GB
Recommended VRAM 32 GB
CPU Fallback No
Adapter Status ⚠️ partial

Quick Start

import omicverse as ov

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

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

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

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

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

Input Requirements

Requirement Detail
Gene ID scheme symbol
Preprocessing Standard preprocessing with plant gene nomenclature. Model handles polyploidy-specific challenges.
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_scplantllm adata.obsm Cell embeddings (512-dim) 
import scanpy as sc

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

# Downstream analysis
sc.pp.neighbors(adata, use_rep="X_scplantllm")
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 scPlantLLM Tutorial Notebook.