Uncertainty Quantification (Optional)

Uncertainty quantification in CASSIA helps assess annotation reliability through multiple analysis iterations and similarity scoring. This process is crucial for:

• Identifying robust cell type assignments
• Detecting mixed or ambiguous clusters
• Quantifying annotation confidence
• Understanding prediction variability

Multiple Iteration Analysis

Basic Usage

# Run multiple analyses
runCASSIA_batch_n_times(
    # Core parameters
    n = 5, #number of iteratioins
    marker = marker_data,
    output_name = "my_annottaion_repeat",
    
    # Model settings
    model = "gpt-4o,
    provider = "openai",
    
    # Context information
    tissue = "brain",
    species = "human",
    additional_info = NULL,


    # Processing control
    max_workers = 4,        # Total parallel workers
    batch_max_workers = 2   # Workers per batch
)
R

⚠️ Cost Warning: Running multiple iterations with LLM models can incur significant costs. Each iteration makes separate API calls, so the total cost will be approximately n times the cost of a single run. Consider starting with a smaller number of iterations for testing purposes.

Parameter Details

1. Iteration Control:

   • n: Number of analysis iterations
   • Recommended: 5 iterations for standard analysis
   • Consider more iterations for critical applications

2. Resource Management:

   • max_workers: Overall parallel processing limit
   • batch_max_workers: Workers per iteration
   • max_workers * batch_max_workers to match your number of cores.

Similarity Score Calculation

Running Similarity Analysis

# Calculate similarity scores
runCASSIA_similarity_score_batch(
    # Input parameters
    marker = marker_data,
    file_pattern = "my_annottaion_repeat_*_full.csv",
    output_name = "similarity_results",
    
    
    # Processing parameters
    max_workers = 4,
    model = "anthropic/claude-3.5-sonnet",
    provider = "openrouter",
    
    # Scoring weights
    main_weight = 0.5, # Weight for main cell type
    sub_weight = 0.5  # Weight for subtypes
)
R

Scoring Parameters

1. Weight Configuration:

   • main_weight: Importance of main cell type match (0-1)
   • sub_weight: Importance of subtype match (0-1)
   • Weights should sum to 1.0

2. File Management:

   • file_pattern: Pattern to match iteration results
   • Uses * to match iteration numbers
   • Example: if you have "my_annottaion_repeat_1_full.csv", "my_annottaion_repeat_2_full.csv", and "my_annottaion_repeat_3_full.csv", use "my_annottaion_repeat__full.csv" to match the pattern.

Output Interpretation

1. Similarity Scores:
   • Range: 0 (completely different) to 1 (identical)
   • Interpretation guidelines:
     • 0.9: High consistency
     • 0.75-0.9: Moderate consistency
     • <0.75: Low consistency

Troubleshooting

1. Performance Issues:

   • Reduce worker counts
   • Process in smaller batches

2. Low Similarity Scores:

   • Review marker gene quality
   • Use Annotation Boost function
   • Review cluster heterogeneity
   • Consider biological variability
   • Increase iteration count
   • Try subclustering