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How to train a single-cell model with scEmbed

This example walks you through training an scembed region2vec model on a single-cell dataset. We start with data preparation, then train the model, and finally use the model to cluster the cells.

For this example we are using the 10x Genomics PBMC 10k dataset. The dataset contains 10,000 peripheral blood mononuclear cells (PBMCs) from a healthy donor.


Simply install the parent package geniml from PyPi:

pip install geniml

Then import scEmbed from geniml:

from geniml.scembed import ScEmbed

Data preparation

scembed requires that the input data is in the AnnData format. Moreover, the .var attribute of this object must have chr, start, and end values. The reason is two fold: 1) we can track which vectors belong to which genmomic regions, and 2) region vectors are now reusable. We ned three files: 1) The barcodes.txt file, 2) the peaks.bed file, and 3) the matrix.mtx file. These will be used to create the AnnData object. To begin, download the data from the 10x Genomics website:

tar -xzf 10k_pbmc_ATACv2_nextgem_Chromium_Controller_raw_peak_bc_matrix.tar.gz

Your files will be inside filtered_peak_bc_matrix/. Assuming you've installed the proper dependencies, you can now use python to build the AnnData object:

import pandas as pd
import scanpy as sc

from import mmread
from scipy.sparse import csr_matrix

barcodes = pd.read_csv("barcodes.tsv", sep="\t", header=None, names=["barcode"])
peaks = pd.read_csv("peaks.bed", sep="\t", header=None, names=["chr", "start", "end"])
mtx = mmread("matrix.mtx")
mtx_sparse = csr_matrix(mtx)
mtx_sparse = mtx_sparse.T

adata = sc.AnnData(X=mtx_sparse, obs=barcodes, var=peaks)

We will use the pbmc.h5ad file for downstream work.


Training an scEmbed model requires two key steps: 1) pre-tokenizing the data, and 2) training the model.

Pre-tokenizing the data

To learn more about pre-tokenizing the data, see the pre-tokenization tutorial. Pre-tokenization offers many benefits, the two most important being 1) speeding up training, and 2) lower resource requirements. The pre-tokenization process is simple and can be done with a combination of geniml and genimtools utilities. Here is an example of how to pre-tokenize the 10x Genomics PBMC 10k dataset:

from genimtools.utils import write_tokens_to_gtok
from geniml.tokenization import ITTokenizer

adata = sc.read_h5ad("path/to/adata.h5ad")
tokenizer = ITTokenizer("peaks.bed")

tokens = tokenizer(adata)

for i, t in enumerate(tokens):
    file = f"tokens{i}.gtok"
    write_tokens_to_gtok(t, file)

Training the model

Now that the data is pre-tokenized, we can train the model. The scEmbed model is designed to be used with scanpy. Here is an example of how to train the model:

from geniml.region2vec.utils import Region2VecDataset

dataset = Region2VecDataset("path/to/tokens")

model = ScEmbed(

We can then export the model for upload to huggingface:


Get embeddings of single-cells

scEmbed is simple to use and designed to be used with scanpy. Here is a simple example of how to train a model and get cell embeddings:

model = ScEmbed.from_pretrained("path/to/model")
model = ScEmbed("databio/scembed-pbmc10k")

adata = sc.read_h5ad("path/to/adata.h5ad")
embeddings = model.encode(adata)

adata.obsm["scembed_X"] = embeddings

Clustering the cells

With the model now trained, and cell-embeddings obtained, we can get embeddings of our individual cells. You can use scanpy utilities to cluster the cells:

sc.pp.neighbors(adata, use_rep="scembed_X") # or louvain

And visualize with UMAP, color="leiden")