concord-sc 1.0.13

CONCORD: Contrastive Learning for Cross-domain Reconciliation and Discovery

CONCORD: COntrastive learNing for Cross-dOmain Reconciliation and Discovery

Qin Zhu, Gartner Lab, UCSF

Description

Revealing the underlying cell-state landscape from single-cell data requires overcoming the critical obstacles of batch integration, denoising, and dimensionality reduction. We present CONCORD, a unified framework that simultaneously addresses these challenges within a single self-supervised model. At its core, CONCORD implements a unified probabilistic sampling strategy that corrects batch effects via dataset-aware sampling and enhances biological resolution through hard-negative sampling. Remarkably, using only a minimalist neural network with a single hidden layer and contrastive learning, CONCORD surpasses state-of-the-art performance without relying on deep architectures, auxiliary losses, or external supervision. It seamlessly integrates data across batches, technologies, and even species to generate high-resolution cell atlases. The resulting latent representations are denoised and biologically meaningful—capturing gene co-expression programs, revealing detailed lineage trajectories, and preserving both local geometric relationships and global topological structures. We demonstrate CONCORD’s broad applicability across diverse datasets, establishing it as a general-purpose framework for learning unified, high-fidelity representations of cellular identity and dynamics.

Full Documentation available at https://qinzhu.github.io/Concord_documentation/.

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Installation

It is recommended to use conda to create and set up a clean virtual environment for CONCORD.

1. Install PyTorch

You must install the correct version of PyTorch based on your system's CUDA setup. Follow the instructions on the official PyTorch website.

• For CPU:

  pip install torch torchvision torchaudio
  

• For CUDA (adjust based on your GPU version):

  pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
  

2. Install CONCORD (Stable or Development)

Stable Version (PyPI)

pip install concord-sc

Development Version (GitHub)

pip install git+https://github.com/Gartner-Lab/Concord.git

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Optional Installations

(Recommended) Enable Additional Functionalities

For GO enrichment, benchmarking, and R integration, install:

pip install "concord-sc[optional]"

(Optional) Install FAISS for Accelerated kNN mode

Note: If using Mac, you may need to disable FAISS when running Concord:

cur_ccd = ccd.Concord(adata=adata, input_feature=feature_list, use_faiss=False, device=device)

• FAISS with GPU:

  pip install faiss-gpu
  

• FAISS with CPU:

  pip install faiss-cpu
  

(Optional) Integration with VisCello

CONCORD integrates with the R package VisCello, a tool for interactive visualization.
To explore results interactively, visit VisCello GitHub for more details.

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Getting Started

Concord integrates seamlessly with anndata objects. Single-cell datasets, such as 10x Genomics outputs, can easily be loaded into an annData object using the Scanpy package. If you're using R and have data in a Seurat object, you can convert it to anndata format by following this tutorial. In this quick-start example, we'll demonstrate CONCORD using the pbmc3k dataset provided by the scanpy package.

Load package and data

# Load required packages
import concord as ccd
import scanpy as sc
import torch
# Load and prepare example data
adata = sc.datasets.pbmc3k_processed()
adata = adata.raw.to_adata()  # Assume starting from raw counts
# (Optional) Select top variably expressed/accessible features for analysis (other methods besides seurat_v3 available)
feature_list = ccd.ul.select_features(adata, n_top_features=2000, flavor='seurat_v3') # For complex dataset, increase n_top_features may be necessary
sc.pp.normalize_total(adata) # Normalize counts per cell
sc.pp.log1p(adata) # Log-transform data

Run CONCORD:

# Set device to cpu or to gpu (if your torch has been set up correctly to use GPU), for mac you can use either torch.device('mps') or torch.device('cpu')
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')

# Initialize Concord with an AnnData object, skip input_feature to use all features, set preload_dense=False if your data is very large
# Provide 'domain_key' if integrating across batches, see below
cur_ccd = ccd.Concord(adata=adata, input_feature=feature_list, device=device, preload_dense=True) 

# Encode data, saving the latent embedding in adata.obsm['Concord']
cur_ccd.fit_transform(output_key='Concord')

Batch Integration: To integrate data across different batches, provide the domain_key parameter (the column name in adata.obs containing batch labels).

Best Practice: Always use the most granular label available for your domain_key. For example, if a dataset contains multiple experiments from different labs, species or technologies, use the experiment ID rather than broad categories like lab, species or technology. This prevents the model from learning batch effects during contrasting.

# Not run for this example
# cur_ccd = ccd.Concord(adata=adata, input_feature=feature_list, domain_key='batch', device=device, preload_dense=True) 

Visualization:

CONCORD latent embeddings are designed for direct use in UMAP, t-SNE, or kNN graph construction.

• Use all dimensions: Unlike PCA, do not subset the latent space; use the full embedding for all downstream tasks.
• Use cosine distance: We strongly recommend using cosine distance (metric='cosine') rather than Euclidean distance to remain consistent with the contrastive objective used during training.

ccd.ul.run_umap(adata, source_key='Concord', result_key='Concord_UMAP', n_components=2, n_neighbors=30, min_dist=0.1, metric='cosine')

# Plot the UMAP embeddings
color_by = ['n_genes', 'louvain'] # Choose which variables you want to visualize
ccd.pl.plot_embedding(
    adata, basis='Concord_UMAP', color_by=color_by, figsize=(10, 5), dpi=600, ncols=2, font_size=6, point_size=10, legend_loc='on data',
    save_path='Concord_UMAP.png'
)

The latent space produced by CONCORD often capture complex biological structures that may not be fully visualized in 2D projections. We recommend exploring the latent space using a 3D UMAP to more effectively capture and examine the intricacies of the data. For example:

ccd.ul.run_umap(adata, source_key='Concord', result_key='Concord_UMAP_3D', n_components=3, n_neighbors=30, min_dist=0.1, metric='cosine')
# Plot the 3D UMAP embeddings
import plotly.io as pio
pio.renderers.default = 'notebook'
col = 'louvain'
fig = ccd.pl.plot_embedding_3d(
    adata, basis='Concord_UMAP_3D', color_by=col, 
    save_path='Concord_UMAP_3D.html',
    point_size=3, opacity=0.8, width=1500, height=1000
)

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License

This project is licensed under the MIT License.
See the LICENSE file for details.

Citation

If you use CONCORD in your research, please cite the following preprint:

"Revealing a coherent cell state landscape across single-cell datasets with CONCORD"
bioRxiv, 2025