scarches

name	scarches
description	Comprehensive skill for scARCHES - Deep learning library for single-cell analysis of chromatin accessibility data. Use for scATAC-seq data processing, model training, batch correction, integration with scRNA-seq, and spatial chromatin analysis.

Scarches Skill

Comprehensive assistance with scarches development, generated from official documentation.

When to Use This Skill

This skill should be triggered when you need to:

Data Analysis & Processing:

• Perform scATAC-seq data preprocessing and quality control
• Integrate multi-omics single-cell data (scRNA-seq + scATAC-seq)
• Map query datasets to reference atlases (e.g., Human Lung Cell Atlas)
• Apply batch correction across different single-cell experiments

Model Development & Training:

• Build and train scVI, SCANVI, TRVAE, or totalVI models
• Perform model surgery for adapting pre-trained models to new data
• Set up early stopping and hyperparameter optimization
• Handle raw count data vs. normalized data appropriately

Advanced Applications:

• Transfer cell type labels from reference to query datasets
• Work with multi-modal TCR data using mvTCR
• Perform spatial chromatin accessibility analysis
• Create comprehensive atlases and reference embeddings

Technical Implementation:

• Debug model training issues and convergence problems
• Optimize model architecture (layers, latent dimensions)
• Choose appropriate loss functions (nb, zinb, mse)
• Set up proper data preprocessing pipelines

Quick Reference

Essential Imports and Setup

import scanpy as sc
import torch
import scarches as sca
from scarches.dataset.trvae.data_handling import remove_sparsity
import matplotlib.pyplot as plt
import numpy as np
import gdown

# Configure scanpy settings
sc.settings.set_figure_params(dpi=200, frameon=False)
sc.set_figure_params(figsize=(4, 4))
torch.set_printoptions(precision=3, sci_mode=False, edgeitems=7)

Data Preparation for scARCHES

# Ensure count data is in adata.X for models using 'nb' or 'zinb' loss
# Remove sparsity for memory efficiency
adata = remove_sparsity(adata)

# Remove obsm and varm matrices to prevent downstream errors
adata.obsm = {}
adata.varm = {}

# Check for integer count data
print(f"Data type: {adata.X.dtype}")

Model Configuration Examples

# TRVAE model with early stopping
condition_key = 'study'
cell_type_key = 'cell_type'
target_conditions = ['Pancreas CelSeq2', 'Pancreas SS2']

trvae_epochs = 500
surgery_epochs = 500

early_stopping_kwargs = {
    "early_stopping_metric": "val_unweighted_loss",
    "threshold": 0,
    "patience": 20,
    "reduce_lr": True,
    "lr_patience": 13,
    "lr_factor": 0.1,
}

# Create TRVAE model with NB loss (default)
trvae_model = sca.models.TRVAE(
    adata=adata,
    condition_key=condition_key,
    recon_loss='nb',  # Use 'mse' for normalized data, 'zinb' for zero-inflated
    beta=1.0,  # MMD regularization strength
    hidden_layers=[128, 128],
    latent_dim=10
)

SCVI Model for Integration

# Create SCVI model with ZINB loss (default)
scvi_model = sca.models.SCVI(
    adata=adata,
    gene_likelihood='zinb'  # Use 'nb' for negative binomial loss
)

# Train the model
scvi_model.train(max_epochs=400)

# Save for later use
scvi_model.save("scvi_model")

Model Surgery for Query Data

# Load pretrained model
scvi_model = sca.models.SCVI.load("scvi_model")

# Perform surgery to adapt to query data
query_model = sca.models.SCVI.load_query_data(
    scvi_model,
    adata_query,
    freeze_classifier=True  # Keep reference embeddings stable
)

# Train on query data with fewer epochs
query_model.train(max_epochs=200)

# Get latent representations
latent = query_model.get_latent_representation()
adata_query.obsm["X_scVI"] = latent

Setting Up Model Variables for Reference Mapping

# For HLCA (Human Lung Cell Atlas) mapping
batch_key = 'batch'           # How batches are identified
labels_key = 'cell_type'      # Cell type annotations
unlabeled_category = 'unlabeled'  # Category for unknown cells

# Set query batch (usually single batch per dataset)
adata_query.obs[batch_key] = 'my_dataset'

# Set all query cells as unlabeled for mapping
adata_query.obs[labels_key] = unlabeled_category

KNN Classification for Label Transfer

from sklearn.neighbors import KNeighborsClassifier
from sklearn.metrics import f1_score

# Train KNN on latent representations
knn = KNeighborsClassifier(n_neighbors=15)
knn.fit(reference_latent, reference_labels)

# Predict labels for query data
predicted_labels = knn.predict(query_latent)
adata_query.obs['predicted_cell_type'] = predicted_labels

# Calculate prediction confidence
confidence_scores = knn.predict_proba(query_latent)
adata_query.obs['prediction_confidence'] = np.max(confidence_scores, axis=1)

Training Tips and Hyperparameters

# Model architecture recommendations
hidden_layers = [128, 128]  # Default, good for most datasets
latent_dim = 10             # Default (10-20 recommended)
beta = 1.0                  # MMD strength for TRVAE

# Loss function selection
if has_raw_counts:
    recon_loss = 'nb' or 'zinb'  # For count data
else:
    recon_loss = 'mse'           # For normalized data

# Early stopping for TRVAE
early_stopping_kwargs = {
    "early_stopping_metric": "val_unweighted_loss",  # Best for TRVAE
    "threshold": 0,
    "patience": 20,
    "reduce_lr": True,
    "lr_patience": 13,
    "lr_factor": 0.1,
}

Key Concepts

Model Types

• SCVI: Single-cell Variational Inference for count data integration
• SCANVI: Semi-supervised extension with cell type labels
• TRVAE: Transfer VAE with MMD regularization for cross-dataset integration
• totalVI: Multi-modal model for RNA + protein data
• mvTCR: Multi-modal model for transcriptome + TCR data

Model Surgery

A technique to adapt pre-trained reference models to new query data by:

1. Loading the reference model
2. Adding new query-specific parameters
3. Freezing reference embeddings
4. Training only query adaptation layers

Loss Functions

• nb (Negative Binomial): Good for count data with overdispersion
• zinb (Zero-Inflated NB): Handles excess zeros in scATAC-seq
• mse (Mean Squared Error): Use for normalized/log-transformed data

Key Hyperparameters

• beta: MMD regularization strength (higher = more integration, lower = preserve biology)
• alpha_kl: KL divergence weight for SCVI/SCANVI
• latent_dim: Dimensionality of the latent space (10-20 recommended)
• early_stopping_metric: 'val_unweighted_loss' for TRVAE, 'elbo_validation' for SCVI

Reference Files

This skill includes comprehensive documentation in references/:

api_reference.md - Complete API Documentation

Contains detailed tutorials and walkthroughs:

• Unsupervised surgery pipeline with SCVI: Full workflow from data preparation to model adaptation
• Unsupervised surgery pipeline with TRVAE: Alternative approach with MMD regularization
• Mapping to Human Lung Cell Atlas: Step-by-step guide for reference mapping and label transfer
• Code examples for each major use case
• Data preprocessing and preparation instructions
• Model saving and loading procedures

models.md - Model Architecture and Training

Essential information for model development:

• Training tips: Loss function selection based on data type
• Architecture recommendations: Hidden layers, latent dimensions for different dataset complexities
• Hyperparameter tuning: Beta values, early stopping criteria, regularization parameters
• Performance guidelines: When to increase model capacity vs. regularization
• Best practices: Variable gene selection, count data requirements

other.md - Specialized Applications

Advanced use cases and domain-specific methods:

• mvTCR Tutorial: Multi-modal integration of transcriptome and TCR data for tumor-infiltrating lymphocytes
• Tissue origin inference using learned representations
• KNN classification on latent embeddings for downstream tasks
• Cancer type prediction from TIL data

Use view to read specific reference files when detailed information is needed.

Working with This Skill

For Beginners

1. Start with basic data preprocessing: Read the api_reference.md for essential imports and data setup
2. Choose your first model: Begin with SCVI for count data integration or TRVAE for cross-dataset mapping
3. Follow the complete tutorials: The SCVI and TRVAE surgery pipelines provide end-to-end workflows
4. Check model training tips: Review models.md for hyperparameter guidance

For Intermediate Users

1. Reference mapping: Use the HLCA mapping tutorial when integrating your data with existing atlases
2. Label transfer: Implement KNN classification for automated cell type annotation
3. Model surgery: Adapt pre-trained models to new datasets efficiently
4. Multi-modal analysis: Explore mvTCR for TCR-RNA integration or totalVI for protein-RNA data

For Advanced Users

1. Model architecture optimization: Experiment with deeper networks ([128,128,128]) for complex datasets
2. Custom loss functions: Modify reconstruction losses based on data characteristics
3. Large-scale atlases: Build comprehensive reference using the architecture and training guidelines
4. Spatial chromatin analysis: Apply to spatial transcriptomics data integration

Navigation Tips

• Data-first approach: Always start with understanding your data type (counts vs. normalized)
• Model selection flow: Choose SCVI/SCANVI for count data, TRVAE for batch correction, mvTCR for TCR
• Reference mapping workflow: Follow HLCA tutorial step-by-step for first-time users
• Troubleshooting: Check models.md for training tips if models don't converge

Resources

references/

Organized documentation extracted from official sources:

• Step-by-step tutorials with complete code workflows
• Real-world examples from published datasets
• Parameter tuning guides based on experimental results
• Best practice recommendations from core developers
• Links to original documentation for further reading

scripts/

Add your automation scripts here:

• Data preprocessing pipelines
• Model training and evaluation workflows
• Batch processing for multiple datasets
• Visualization and analysis utilities

assets/

Store templates and reference materials:

• Configuration file templates for common use cases
• Example dataset formats and metadata schemas
• Visualization templates for model results
• Documentation for custom preprocessing steps

Notes

Data Requirements

• Raw counts are required for 'nb' and 'zinb' loss functions
• Highly variable genes (2000-5000) recommended for model training
• Batch information should be stored in adata.obs columns
• Cell type labels needed for SCANVI training in semisupervised mode

Performance Considerations

• Use remove_sparsity() for better memory efficiency
• Implement early stopping to prevent overfitting
• Monitor training loss curves for convergence issues
• Adjust beta parameter based on integration quality vs. biological variation

Common Pitfalls

• Using normalized data with count-based loss functions (nb, zinb)
• Forgetting to set query cells to 'unlabeled' category for mapping
• Not checking that gene symbols/match between reference and query
• Overfitting when using too many latent dimensions (>50)

Updating

To refresh this skill with updated documentation:

1. Check the official scArches documentation at https://docs.scarches.org/
2. Re-run the scraper with updated source URLs if available
3. The skill will preserve existing structure while incorporating new examples and methods

For the most current information, always cross-reference with the official scArches documentation and GitHub repository.