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README.md

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+---
+library_name: perturblab
+tags:
+- biology
+- genomics
+- scfoundation
+- foundation-model
+license: apache-2.0
+base_model: biomap-research/scFoundation
+---
+
+# scfoundation-cell
+
+## Model Description
+This is the **cell embedding** model from scFoundation. It generates cell-level embeddings from single-cell RNA-seq data.
+
+Model weights were originally from the [biomap-research/scFoundation](https://github.com/biomap-research/scFoundation) repository and have been re-uploaded here for ease of use with the `perturblab` library.
+
+## Model Details
+- **Model Type**: Cell embedding model
+- **Architecture**: xTrimoGene with MAE (Masked Autoencoder), Performer/Transformer modules
+- **Parameters**: 100M parameters
+- **Training Data**: 50M+ human single-cell transcriptomics data
+- **Input**: Single-cell or bulk RNA-seq expression data (19,264 fixed genes)
+- **Output**: Cell-level embeddings
+
+## Source
+- **Original Repository**: [biomap-research/scFoundation](https://github.com/biomap-research/scFoundation)
+- **Paper**: [Large Scale Foundation Model on Single-cell Transcriptomics](https://www.nature.com/articles/s41592-024-02305-7) (_Nature Methods_, 2024)
+
+## Usage
+
+```python
+from perturblab.model.scfoundation import scFoundationModel
+
+# Load model
+model = scFoundationModel.from_pretrained('scfoundation-cell', device='cuda')
+
+# Generate cell embeddings
+cell_embeddings = model.predict_embedding(
+    adata, 
+    output_type='cell',
+    pool_type='all'
+)
+```
+
+## Note
+Intended for internal use with the PerturbLab framework.
+

config.json

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+{
+  "model_series": "scfoundation",
+  "model_name": "cell",
+  "model_type": "mae_autobin",
+  "num_tokens": 19264,
+  "encoder_hidden_dim": 768,
+  "decoder_hidden_dim": 512,
+  "encoder_depth": 12,
+  "decoder_depth": 6,
+  "encoder_heads": 12,
+  "decoder_heads": 8,
+  "encoder_dim_head": 64,
+  "decoder_dim_head": 64,
+  "bin_num": 100,
+  "bin_alpha": 1.0,
+  "pad_token_id": 103,
+  "mask_token_id": 102,
+  "encoder_module_type": "transformer",
+  "decoder_module_type": "performer",
+  "ff_dropout": 0.0,
+  "attn_dropout": 0.0
+}

model.pt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:2446c2fb99a0e183cdc9872b7e9e55ac74f7ec82db7ba0799c83be75cde66dc6
+size 477485967