config.json

{
  "task_description": "Your task is to develop a predictive model that accurately estimates gene expression profiles of individual K562 cells following CRISPR interference (CRISPRi), using the dataset from Norman et al. (2019, Science).\n\nTask Definition:\n- Input: Baseline gene expression profile of an unperturbed K562 cell and the identity of the target gene(s) for perturbation\n- Output: Predicted gene expression profile after perturbation\n\nEvaluation Scenarios:\n1. Unseen Perturbations: Predict effects of gene perturbations not present during training\n2. Unseen Cell Contexts: Predict responses in cells with gene expression profiles not observed during training\n\nEvaluation Metrics:\n- Mean Squared Error (MSE): Measures the average squared difference between predicted and observed gene expression.\n- Pearson Correlation Coefficient (PCC): Quantifies linear correlation between predicted and observed profiles.\n- R² (Coefficient of Determination): Represents the proportion of variance in the observed gene expression that can be explained by the predicted values.\n- MSE for Differentially Expressed (DE) Genes (MSE_DE): Same as MSE but computed specifically for genes identified as differentially expressed.\n- PCC for Differentially Expressed (DE) Genes (PCC_DE): Same as PCC but computed specifically for genes identified as differentially expressed.\n- R² for Differentially Expressed (DE) Genes (R2_DE): Same as R² but computed specifically for genes identified as differentially expressed.",
  "dataset_path": "cellforge/data/datasets/",
  "output_dir": "results/",
  "llm_config": {
    "provider": "deepseek",
    "model": "deepseek-reasoner",
    "api_key": "loaded_from_env"
  },
  "workflow_phases": [
    "task_analysis",
    "method_design",
    "code_generation"
  ],
  "qdrant_config": {
    "CelloFrge": {
      "url": "https://f3c8d5c0-45a8-4166-b4a4-493166d91a16.europe-west3-0.gcp.cloud.qdrant.io:6333",
      "api_key": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJhY2Nlc3MiOiJtIn0.QQRWUndauiWv4-tjnKCmPY15UwzLR4JenAe6N9c2nsU"
    },
    "cellforge_tmp": {
      "url": "https://0a898751-2b0a-4c96-b64d-e0961f386ae3.us-west-1-0.aws.cloud.qdrant.io:6333",
      "api_key": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJhY2Nlc3MiOiJtIn0.C_ktv2cjHwyh2la4vgHEvLL0CdJjBeDns3H78SVZYFU"
    }
  }
}