paper-writing

Paper Writing Skill

Generate a markdown research paper pre-populated with methods tables, results tables, and figure references from SWARM experiment data.

Prerequisites

• sqlite3 (Python stdlib) for reading runs database
• pandas>=2.0 for data manipulation
• Experiment data in SQLite database or CSV files

Procedure

1. Query the runs database

import sqlite3
import pandas as pd

def load_runs(db_path, scenario_ids=None):
    """Load scenario runs from SQLite database."""
    conn = sqlite3.connect(db_path)
    
    if scenario_ids:
        placeholders = ",".join("?" * len(scenario_ids))
        query = f"SELECT * FROM scenario_runs WHERE scenario_id IN ({placeholders})"
        df = pd.read_sql_query(query, conn, params=scenario_ids)
    else:
        df = pd.read_sql_query("SELECT * FROM scenario_runs", conn)
    
    conn.close()
    return df

2. Build the methods table

def build_methods_table(df):
    """Generate a markdown table of experimental scenarios."""
    scenarios = df.groupby("scenario_id").first().reset_index()
    
    lines = ["| Scenario | Agents | Governance | Seeds | Epochs |",
             "|----------|--------|-----------|-------|--------|"]
    
    for _, row in scenarios.iterrows():
        lines.append(
            f"| {row['scenario_id']} | {row.get('n_agents', 'N/A')} | "
            f"{row.get('governance_desc', 'default')} | "
            f"{row.get('n_seeds', 'N/A')} | {row.get('n_epochs', 'N/A')} |"
        )
    
    return "\n".join(lines)

3. Build the results table

def build_results_table(df):
    """Generate a cross-scenario summary results table."""
    summary = df.groupby("scenario_id").agg({
        "welfare": ["mean", "std"],
        "toxicity_rate": ["mean", "std"],
        "quality_gap": ["mean", "std"],
    }).reset_index()
    
    lines = ["| Scenario | Welfare (mean±std) | Toxicity (mean±std) | Quality Gap (mean±std) |",
             "|----------|-------------------|--------------------|-----------------------|"]
    
    for _, row in summary.iterrows():
        lines.append(
            f"| {row[('scenario_id', '')]} | "
            f"{row[('welfare', 'mean')]:.3f}±{row[('welfare', 'std')]:.3f} | "
            f"{row[('toxicity_rate', 'mean')]:.3f}±{row[('toxicity_rate', 'std')]:.3f} | "
            f"{row[('quality_gap', 'mean')]:.3f}±{row[('quality_gap', 'std')]:.3f} |"
        )
    
    return "\n".join(lines)