Single Cell Foundation Model Geneformer

Geneformer

Use This Skill When

Use this skill when the task involves official Geneformer workflows such as:

• converting raw scRNA-seq data into Geneformer tokenized datasets
• fine-tuning Geneformer for cell or gene classification
• extracting cell or gene embeddings
• generating state embeddings for downstream perturbation analysis
• running in silico perturbation or in silico treatment style analyses
• distinguishing pretrained zero-shot usage from fine-tuned classifier usage

This skill is for Geneformer-specific workflows, not generic single-cell model use.

Start Here

1. Confirm the input is raw-count scRNA-seq data and still suitable for tokenization.
2. Check that ensembl_id and n_counts are available.
3. Tokenize first unless the user already has a Geneformer .dataset.
4. Decide whether the task is classification, embedding extraction, or in silico perturbation.

Choose A Path

Tokenization

Use TranscriptomeTokenizer first for almost every Geneformer workflow. This step converts raw-count .loom or .h5ad data into tokenized datasets used by the downstream APIs.

Geneformer expects:

• row attribute ensembl_id
• cell attribute n_counts

Optional metadata can be passed through during tokenization.

Classification

Use Classifier for:

• cell state classification
• cell type annotation
• gene classification tasks

The input is a tokenized Geneformer .dataset object, not raw AnnData.

Embedding extraction

Use EmbExtractor when the task is to:

• extract CLS, cell, or gene embeddings
• plot or inspect cell embeddings
• generate state embeddings for later perturbation analysis

In silico perturbation

Use InSilicoPerturber for zero-shot or model-based perturbation analyses such as:

• deleting or shifting genes
• modeling start and goal cell states
• ranking perturbations by movement toward a desired cell state

This is one of Geneformer's defining workflows and should be treated as more than ordinary classifier inference.

Guardrails

• Do not pass feature-selected matrices into the tokenizer; the docs expect raw counts without feature selection.
• Do not use gene symbols where the tokenizer expects ensembl_id.
• Do not confuse tokenized .dataset files with AnnData objects.
• Do not skip tokenization and jump directly to classifiers or perturbation APIs.
• For perturbation tasks, be explicit about model type, embedding mode, and target cell states.

Official Workflow Surface

Read More Only If Needed

• For operational usage and required input fields, read references/workflows.md.
• For official source locations and model-specific notes, read references/sources-and-notes.md.