CLI Options

Complete reference for run.sh command-line options.

Basic Options

Option	Description	Default
--model <name>	LLM model to use	Interactive selection
--dataset <name>	Dataset name	Interactive selection
--iterations <n>	Number of iterations	Prompted in interactive mode (default 5)
--val-metric <metric>	Validation metric to optimize	Task-based default (AUROC for classification, MAE for regression)
--timeout <seconds>	Time limit for entire run	None
--run-python-timeout <seconds>	Timeout in seconds for each run_python tool execution - this will determine the maximum training time	21600 (6 hours)

The run stops when either the iteration count is reached or the timeout expires.

Deployment Options

Option	Description
--pull-images	Pull pre-built Docker images from Docker Hub
--local	Run without Docker (uses conda)
--cpu-only	Disable GPU acceleration
--ollama	Use local Ollama for LLM

Listing Options

Option	Description
--list-models	Show available LLM models
--list-datasets	Show prepared datasets
--list-metrics	Show available validation metrics
--help	Show help message

Advanced Options

Option	Description
--user-prompt <text>	Custom prompt for the agent
--foundation-model-type <type>	Pre-download foundation models (dna, rna, protein, molecule, all)
--use-provisioning-key	Use OpenRouter temporary API key
--spend-limit <n>	Spend limit for provisioning key (requires --use-provisioning-key)
--split-allowed-iterations <n>	Iterations that can modify train/val split (default 1)
--exploration-iterations <n>	Baseline exploration iterations (default 4)
--run-python-timeout <seconds>	Per-training timeout for run_python tool (default 21600)

Examples

Basic Run

./run.sh --model openai/gpt-4 --dataset breast_cancer --iterations 10

Quick Start with Pre-built Images

./run.sh --pull-images

Local Mode

./run.sh --local --model openai/gpt-4 --dataset my_data

With Time Limit

./run.sh --timeout 3600 --model openai/gpt-4 --dataset my_data

Custom Optimization Goal

./run.sh --user-prompt "Focus on interpretable models only" --model openai/gpt-4

Using Ollama

./run.sh --ollama

CPU Only

./run.sh --cpu-only --model openai/gpt-4 --dataset my_data

Pre-download Foundation Models

./run.sh --foundation-model-type protein --model openai/gpt-4

Validation Metrics

Available metrics for --val-metric:

Classification:

• ACC - Accuracy
• AUROC - Area Under ROC Curve
• AUPRC - Area Under Precision-Recall Curve
• F1 - F1 Score (macro)
• LOG_LOSS - Log loss
• MCC - Matthews Correlation Coefficient

Regression:

• MSE - Mean Squared Error
• RMSE - Root Mean Squared Error
• MAE - Mean Absolute Error
• MAPE - Mean Absolute Percentage Error
• PEARSON - Pearson Correlation
• SPEARMAN - Spearman Correlation
• R2 - R-squared

Environment Variables

API keys and logging settings come from environment variables or .env. See Environment Variables.

Model Names

Model names are provider-specific. Use --list-models to see available models for your configured providers.

Exit Codes

Code	Meaning
0	Success
1	General error
2	Invalid arguments
130	Interrupted (Ctrl+C)