Garfield 0.3.3

Garfield: Graph-based Contrastive Learning enable Fast Single-Cell Embedding

Garfield: Graph-based Contrastive Learning enable Fast Single-Cell Embedding

Installation

Please install Garfield from pypi with:

pip install Garfield

install from Github:

pip install git+https://github.com/zhou-1314/Garfield.git

or git clone and install:

git clone https://github.com/zhou-1314/Garfield.git
cd Garfield
python setup.py install

Garfield is implemented in Pytorch framework.

Usage

## load packages
import os
import Garfield as gf
import scanpy as sc
gf.__version__

# set workdir
workdir = 'garfield_multiome_10xbrain'
gf.settings.set_workdir(workdir)

### modify parameter
user_config = dict(
    ## Input options
    adata_list=mdata,  
    profile='multi-modal', 
    data_type='Paired',
    sub_data_type=['rna', 'atac'],
    sample_col=None, 
    weight=0.5,
    ## Preprocessing options
    graph_const_method='mu_std',
    genome='hg38',
    use_gene_weight=True,
    use_top_pcs=False,
    used_hvg=True,
    min_cells=3,
    min_features=0,
    keep_mt=False,
    target_sum=1e4,
    rna_n_top_features=3000,
    atac_n_top_features=100000,
    n_components=50,
    n_neighbors=5,
    metric='euclidean', 
    svd_solver='arpack',
    # datasets
    adj_key='connectivities',
    # data split parameters
    edge_val_ratio=0.1,
    edge_test_ratio=0.,
    node_val_ratio=0.1,
    node_test_ratio=0.,
    ## Model options
    augment_type='svd',
    svd_q=5,
    use_FCencoder=False,
    conv_type='GATv2Conv', # GAT or GATv2Conv or GCN
    gnn_layer=2,
    hidden_dims=[128, 128],
    bottle_neck_neurons=20,
    cluster_num=20,
    drop_feature_rate=0.2, 
    drop_edge_rate=0.2,
    num_heads=3,
    dropout=0.2,
    concat=True,
    used_edge_weight=False,
    used_DSBN=False,
    used_mmd=False,
    # data loader parameters
    num_neighbors=5,
    loaders_n_hops=2,
    edge_batch_size=4096,
    node_batch_size=128, # None
    # loss parameters
    include_edge_recon_loss=True,
    include_gene_expr_recon_loss=True,
    lambda_latent_contrastive_loss=1.0,
    lambda_gene_expr_recon=300.,
    lambda_edge_recon=500000.,
    lambda_omics_recon_mmd_loss=0.2,
    # train parameters
    n_epochs_no_edge_recon=0,
    learning_rate=0.001,
    weight_decay=1e-05,
    gradient_clipping=5,
    # other parameters
    latent_key='garfield_latent',
    reload_best_model=True,
    use_early_stopping=True,
    early_stopping_kwargs=None,
    monitor=True,
    seed=2024,
    verbose=True
)
dict_config = gf.settings.set_gf_params(user_config)

from Garfield.model import Garfield

# Initialize model
model = Garfield(dict_config)
# Train model
model.train()
# Compute latent neighbor graph
latent_key = 'garfield_latent'
sc.pp.neighbors(model.adata,
                use_rep=latent_key,
                key_added=latent_key)
# Compute UMAP embedding
sc.tl.umap(model.adata,
           neighbors_key=latent_key)
sc.pl.umap(model.adata, color=[ 'celltype'], show=True, size=3) 

model_folder_path = "./slideseqv2_mouse_hippocampus/model"
os.makedirs(figure_folder_path, exist_ok=True)
# Save trained model
model.save(dir_path=model_folder_path,
           overwrite=True,
           save_adata=True,
           adata_file_name="adata.h5ad")

Main Parameters of Garfield Model

Data Preprocessing Parameters

• adata_list: List of AnnData objects containing data from multiple batches or samples.
• profile: Specifies the data profile type (e.g., 'RNA', 'ATAC', 'ADT', 'multi-modal', 'spatial').
• data_type: Type of the multi-omics dataset (e.g., Paired, UnPaired) for preprocessing.
• sub_data_type: List of data types for multi-modal datasets (e.g., ['rna', 'atac'] or ['rna', 'adt']).
• sample_col: Column in the dataset that indicates batch or sample identifiers.
• weight: Weighting factor that determines the contribution of different modalities or types of graphs in multi-omics or spatial data.
  • For non-spatial single-cell multi-omics data (e.g., RNA + ATAC), weight specifies the contribution of the graph constructed from scRNA data. The remaining (1 - weight) represents the contribution from the other modality.
  • For spatial single-modality data, weight refers to the contribution of the graph constructed from the physical spatial information, while (1 - weight) reflects the contribution from the molecular graph (RNA graph).
• graph_const_method: Method for constructing the graph (e.g., 'mu_std', 'Radius', 'KNN', 'Squidpy').
• genome: Reference genome to use during preprocessing.
• use_gene_weight: Whether to apply gene weights in the preprocessing step.
• use_top_pcs: Whether to use the top principal components during dimensionality reduction.
• used_hvg: Whether to use highly variable genes (HVGs) for analysis.
• min_features: Minimum number of features required for a cell to be included in the dataset.
• min_cells: Minimum number of cells required for a feature to be retained in the dataset.
• keep_mt: Whether to retain mitochondrial genes in the analysis.
• target_sum: Target sum used for normalization (e.g., 1e4 for counts per cell).
• rna_n_top_features: Number of top features to retain for RNA datasets.
• atac_n_top_features: Number of top features to retain for ATAC datasets.
• n_components: Number of components to use for dimensionality reduction (e.g., PCA).
• n_neighbors: Number of neighbors to use in graph-based algorithms.
• metric: Distance metric used during graph construction.
• svd_solver: Solver for singular value decomposition (SVD).
• adj_key: Key in the AnnData object that holds the adjacency matrix.

Data Split Parameters

• edge_val_ratio: Ratio of edges to use for validation in edge-level tasks.
• edge_test_ratio: Ratio of edges to use for testing in edge-level tasks.
• node_val_ratio: Ratio of nodes to use for validation in node-level tasks.
• node_test_ratio: Ratio of nodes to use for testing in node-level tasks.

Model Architecture Parameters

• augment_type: Type of augmentation to use (e.g., 'dropout', 'svd').
• svd_q: Rank for the low-rank SVD approximation.
• use_FCencoder: Whether to use a fully connected encoder before the graph layers.
• hidden_dims: List of hidden layer dimensions for the encoder.
• bottle_neck_neurons: Number of neurons in the bottleneck (latent) layer.
• num_heads: Number of attention heads for each graph attention layer.
• dropout: Dropout rate applied during training.
• concat: Whether to concatenate attention heads or not.
• drop_feature_rate: Dropout rate applied to node features.
• drop_edge_rate: Dropout rate applied to edges during augmentation.
• used_edge_weight: Whether to use edge weights in the graph layers.
• used_DSBN: Whether to use domain-specific batch normalization.
• conv_type: Type of graph convolution to use ('GAT', 'GCN').
• gnn_layer: Number of times the graph neural network (GNN) encoder is repeated in the forward pass.
• cluster_num: Number of clusters for latent feature clustering.

Data Loader Parameters

• num_neighbors: Number of neighbors to sample for graph-based data loaders.
• loaders_n_hops: Number of hops for neighbors during graph construction.
• edge_batch_size: Batch size for edge-level tasks.
• node_batch_size: Batch size for node-level tasks.

Loss Function Parameters

• include_edge_recon_loss: Whether to include edge reconstruction loss in the training objective.
• include_gene_expr_recon_loss: Whether to include gene expression reconstruction loss in the training objective.
• used_mmd: Whether to use maximum mean discrepancy (MMD) for domain adaptation.
• lambda_latent_contrastive_instanceloss: Weight for the instance-level contrastive loss.
• lambda_latent_contrastive_clusterloss: Weight for the cluster-level contrastive loss.
• lambda_gene_expr_recon: Weight for the gene expression reconstruction loss.
• lambda_edge_recon: Weight for the edge reconstruction loss.
• lambda_omics_recon_mmd_loss: Weight for the MMD loss in omics reconstruction tasks.

Training Parameters

• n_epochs: Number of training epochs.
• n_epochs_no_edge_recon: Number of epochs without edge reconstruction loss.
• learning_rate: Learning rate for the optimizer.
• weight_decay: Weight decay (L2 regularization) for the optimizer.
• gradient_clipping: Maximum norm for gradient clipping.

Other Parameters

• latent_key: Key for storing latent features in the AnnData object.

• reload_best_model: Whether to reload the best model after training.

• use_early_stopping: Whether to use early stopping during training.

• early_stopping_kwargs: Arguments for configuring early stopping (e.g., patience, delta).

• monitor: Whether to print training progress.

• seed: Random seed for reproducibility.

• verbose: Whether to display detailed logs during training.

Support

Please submit issues or reach out to [e-mail].

Acknowledgment

Garfield uses and/or references the following libraries and packages:

• NicheCompass

• scArches

• SIMBA

• MaxFuse

• scanpy

Thanks for all their contributors and maintainers!

Citation

If you have used Garfiled for your work, please consider citing:

@misc{2024Garfield,
    title={Garfield: Graph-based Contrastive Learning enable Fast Single-Cell Embedding},
    author={Weige Zhou},
    howpublished = {\url{https://github.com/zhou-1314/Garfield}},
    year={2024}
}