claude-turing 2.0.0 → 2.2.0

package/templates/scripts/draft_paper_sections.py

@@ -0,0 +1,498 @@
+#!/usr/bin/env python3
+"""Paper section drafting from experiment logs.
+
+Drafts the mechanical sections of an ML paper directly from experiment
+data: experimental setup, results tables, ablation tables, and
+hyperparameter appendices. Eliminates transcription errors.
+
+Usage:
+    python scripts/draft_paper_sections.py                                    # All sections
+    python scripts/draft_paper_sections.py --sections setup,results           # Specific sections
+    python scripts/draft_paper_sections.py --format latex                     # LaTeX output
+    python scripts/draft_paper_sections.py --format markdown                  # Markdown output
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+from datetime import datetime, timezone
+from pathlib import Path
+
+import yaml
+
+from scripts.turing_io import load_config, load_experiments
+
+
+VALID_SECTIONS = ["setup", "results", "ablation", "hyperparameters"]
+DEFAULT_FORMAT = "latex"
+
+
+def load_seed_studies_for_paper(seed_dir: str = "experiments/seed_studies") -> dict[str, dict]:
+    """Load all seed studies indexed by experiment ID."""
+    path = Path(seed_dir)
+    studies = {}
+    if not path.exists():
+        return studies
+    for f in path.glob("*-seeds.yaml"):
+        try:
+            with open(f) as fh:
+                study = yaml.safe_load(fh)
+                if study and isinstance(study, dict) and "experiment_id" in study:
+                    studies[study["experiment_id"]] = study
+        except (yaml.YAMLError, OSError):
+            continue
+    return studies
+
+
+def load_ablation_studies(ablation_dir: str = "experiments/ablations") -> dict[str, dict]:
+    """Load all ablation studies indexed by experiment ID."""
+    path = Path(ablation_dir)
+    studies = {}
+    if not path.exists():
+        return studies
+    for f in path.glob("*-ablation.yaml"):
+        try:
+            with open(f) as fh:
+                study = yaml.safe_load(fh)
+                if study and isinstance(study, dict) and "experiment_id" in study:
+                    studies[study["experiment_id"]] = study
+        except (yaml.YAMLError, OSError):
+            continue
+    return studies
+
+
+def get_top_experiments(
+    experiments: list[dict],
+    metric: str,
+    lower_is_better: bool,
+    top_k: int = 10,
+) -> list[dict]:
+    """Get top-K kept experiments by primary metric."""
+    kept = [e for e in experiments if e.get("status") == "kept" and e.get("metrics", {}).get(metric) is not None]
+    kept.sort(key=lambda e: e["metrics"][metric], reverse=not lower_is_better)
+    return kept[:top_k]
+
+
+def group_by_model_type(experiments: list[dict]) -> dict[str, list[dict]]:
+    """Group experiments by model type, keeping best per type."""
+    groups: dict[str, list[dict]] = {}
+    for exp in experiments:
+        mt = exp.get("config", {}).get("model_type", "unknown")
+        groups.setdefault(mt, []).append(exp)
+    return groups
+
+
+def draft_setup_section(
+    config: dict,
+    experiments: list[dict],
+    seed_studies: dict[str, dict],
+    output_format: str = "latex",
+) -> str:
+    """Draft the experimental setup section."""
+    eval_cfg = config.get("evaluation", {})
+    data_cfg = config.get("data", {})
+    primary_metric = eval_cfg.get("primary_metric", "accuracy")
+    metrics = eval_cfg.get("metrics", [primary_metric])
+    lower_is_better = eval_cfg.get("lower_is_better", False)
+
+    task_desc = config.get("task_description", "the classification task")
+    data_source = data_cfg.get("source", "the provided dataset")
+    split_ratios = data_cfg.get("split_ratios", {})
+    random_state = data_cfg.get("random_state", 42)
+
+    # Determine seed study info
+    n_seeds = 0
+    for study in seed_studies.values():
+        n_seeds = max(n_seeds, len(study.get("seeds_run", [])))
+
+    # Build prose
+    split_text = ""
+    if split_ratios:
+        parts = [f"{int(v*100)}\\%" if output_format == "latex" else f"{int(v*100)}%" for v in split_ratios.values()]
+        split_names = list(split_ratios.keys())
+        split_text = "/".join(parts) + " " + "/".join(split_names) + " split"
+
+    direction = "lower" if lower_is_better else "higher"
+    metric_list = ", ".join(metrics)
+
+    if output_format == "latex":
+        lines = [
+            r"\subsection{Experimental Setup}",
+            "",
+            f"We evaluate on {data_source} using {metric_list} as evaluation metrics "
+            f"({direction} is better for {primary_metric}).",
+        ]
+        if split_text:
+            lines.append(f"Data is partitioned using a {split_text} with random state {random_state}.")
+        if n_seeds > 0:
+            lines.append(
+                f"Results are reported as mean $\\pm$ standard deviation over {n_seeds} random seeds "
+                f"to account for seed sensitivity."
+            )
+        lines.append(f"All experiments use {task_desc} as the target task.")
+    else:
+        lines = [
+            "## Experimental Setup",
+            "",
+            f"We evaluate on {data_source} using {metric_list} as evaluation metrics "
+            f"({direction} is better for {primary_metric}).",
+        ]
+        if split_text:
+            lines.append(f"Data is partitioned using a {split_text} with random state {random_state}.")
+        if n_seeds > 0:
+            lines.append(
+                f"Results are reported as mean +/- standard deviation over {n_seeds} random seeds "
+                f"to account for seed sensitivity."
+            )
+        lines.append(f"All experiments use {task_desc} as the target task.")
+
+    return "\n".join(lines)
+
+
+def draft_results_table(
+    experiments: list[dict],
+    metrics: list[str],
+    primary_metric: str,
+    lower_is_better: bool,
+    seed_studies: dict[str, dict],
+    output_format: str = "latex",
+    dataset_name: str = "the dataset",
+) -> str:
+    """Draft the results comparison table."""
+    # Group by model type, take best per type
+    groups = group_by_model_type(experiments)
+    rows = []
+    for mt, exps in groups.items():
+        # Best experiment per model type
+        best = exps[0]  # Already sorted by caller
+        row = {"model_type": mt, "experiment_id": best.get("experiment_id", "?")}
+        for m in metrics:
+            val = best.get("metrics", {}).get(m)
+            seed = seed_studies.get(best.get("experiment_id", ""))
+            if seed and seed.get("metric") == m:
+                row[m] = {"value": val, "mean": seed.get("mean"), "std": seed.get("std")}
+            else:
+                row[m] = {"value": val}
+        rows.append(row)
+
+    # Find best value per metric
+    best_per_metric = {}
+    for m in metrics:
+        values = [(r["model_type"], r[m].get("mean") or r[m].get("value")) for r in rows if r[m].get("value") is not None]
+        if values:
+            if lower_is_better:
+                best_per_metric[m] = min(values, key=lambda x: x[1] if x[1] is not None else float("inf"))[0]
+            else:
+                best_per_metric[m] = max(values, key=lambda x: x[1] if x[1] is not None else float("-inf"))[0]
+
+    if output_format == "latex":
+        return _format_results_latex(rows, metrics, best_per_metric, dataset_name)
+    else:
+        return _format_results_markdown(rows, metrics, best_per_metric, dataset_name)
+
+
+def _format_results_latex(rows: list[dict], metrics: list[str], best_per: dict, dataset: str) -> str:
+    """Format results as LaTeX table."""
+    n_cols = len(metrics)
+    col_spec = "l" + "c" * n_cols
+    metric_headers = " & ".join(m.replace("_", r"\_") for m in metrics)
+
+    lines = [
+        r"\begin{table}[h]",
+        r"\centering",
+        f"\\caption{{Comparison of model architectures on {dataset}.}}",
+        r"\label{tab:results}",
+        f"\\begin{{tabular}}{{{col_spec}}}",
+        r"\toprule",
+        f"Model & {metric_headers} \\\\",
+        r"\midrule",
+    ]
+
+    for row in rows:
+        mt = row["model_type"].replace("_", r"\_")
+        cells = [mt]
+        for m in metrics:
+            data = row[m]
+            val = data.get("mean") or data.get("value")
+            std = data.get("std")
+            if val is None:
+                cells.append("---")
+            elif std:
+                cell = f"{val:.3f} $\\pm$ {std:.3f}"
+                if best_per.get(m) == row["model_type"]:
+                    cell = f"\\textbf{{{cell}}}"
+                cells.append(cell)
+            else:
+                cell = f"{val:.4f}"
+                if best_per.get(m) == row["model_type"]:
+                    cell = f"\\textbf{{{cell}}}"
+                cells.append(cell)
+        lines.append(" & ".join(cells) + r" \\")
+
+    lines.extend([
+        r"\bottomrule",
+        r"\end{tabular}",
+        r"\end{table}",
+    ])
+    return "\n".join(lines)
+
+
+def _format_results_markdown(rows: list[dict], metrics: list[str], best_per: dict, dataset: str) -> str:
+    """Format results as markdown table."""
+    header = f"| Model |"
+    sep = "|-------|"
+    for m in metrics:
+        header += f" {m} |"
+        sep += f"{'---' * max(len(m) // 3, 1)}--|"
+
+    lines = [
+        f"## Results on {dataset}",
+        "",
+        header,
+        sep,
+    ]
+
+    for row in rows:
+        line = f"| {row['model_type']} |"
+        for m in metrics:
+            data = row[m]
+            val = data.get("mean") or data.get("value")
+            std = data.get("std")
+            if val is None:
+                line += " --- |"
+            elif std:
+                cell = f"{val:.3f} +/- {std:.3f}"
+                if best_per.get(m) == row["model_type"]:
+                    cell = f"**{cell}**"
+                line += f" {cell} |"
+            else:
+                cell = f"{val:.4f}"
+                if best_per.get(m) == row["model_type"]:
+                    cell = f"**{cell}**"
+                line += f" {cell} |"
+        lines.append(line)
+
+    return "\n".join(lines)
+
+
+def draft_ablation_table(
+    ablation_studies: dict[str, dict],
+    output_format: str = "latex",
+) -> str:
+    """Draft ablation table from ablation study results."""
+    if not ablation_studies:
+        return "No ablation studies available. Run `/turing:ablate` first."
+
+    # Use the most recent ablation study
+    study = list(ablation_studies.values())[-1]
+    metric = study.get("metric", "accuracy")
+    full_metric = study.get("full_model_metric", 0)
+    results = study.get("results", [])
+
+    if not results:
+        return "Ablation study has no results."
+
+    if output_format == "latex":
+        metric_escaped = metric.replace("_", r"\_")
+        lines = [
+            r"\begin{table}[h]",
+            r"\centering",
+            f"\\caption{{Ablation study results ({metric_escaped}).}}",
+            r"\label{tab:ablation}",
+            r"\begin{tabular}{lcc}",
+            r"\toprule",
+            f"Configuration & {metric_escaped} & $\\Delta$ from Full \\\\",
+            r"\midrule",
+            f"Full model & {full_metric:.4f} & --- \\\\",
+        ]
+        for r in results:
+            if r.get("status") == "failed":
+                continue
+            config = r.get("configuration", "?").replace("_", r"\_")
+            val = r.get("metric_value", 0)
+            delta = r.get("delta", 0)
+            delta_str = f"{delta:+.4f}" if delta is not None else "---"
+            lines.append(f"{config} & {val:.4f} & {delta_str} \\\\")
+        lines.extend([r"\bottomrule", r"\end{tabular}", r"\end{table}"])
+        return "\n".join(lines)
+    else:
+        lines = [
+            f"## Ablation Study ({metric})",
+            "",
+            f"| Configuration | {metric} | Delta from Full |",
+            f"|---------------|{'---' * max(len(metric) // 3, 1)}--|-----------------|",
+            f"| Full model | {full_metric:.4f} | --- |",
+        ]
+        for r in results:
+            if r.get("status") == "failed":
+                continue
+            config = r.get("configuration", "?")
+            val = r.get("metric_value", 0)
+            delta = r.get("delta", 0)
+            delta_str = f"{delta:+.4f}" if delta is not None else "---"
+            lines.append(f"| {config} | {val:.4f} | {delta_str} |")
+        return "\n".join(lines)
+
+
+def draft_hyperparameter_table(
+    experiments: list[dict],
+    output_format: str = "latex",
+) -> str:
+    """Draft hyperparameter appendix table."""
+    groups = group_by_model_type(experiments)
+
+    if output_format == "latex":
+        lines = [
+            r"\begin{table}[h]",
+            r"\centering",
+            r"\caption{Hyperparameters for reported models.}",
+            r"\label{tab:hyperparams}",
+            r"\begin{tabular}{llr}",
+            r"\toprule",
+            r"Model & Parameter & Value \\",
+            r"\midrule",
+        ]
+        for mt, exps in groups.items():
+            best = exps[0]
+            hyperparams = best.get("config", {}).get("hyperparams", {})
+            first = True
+            for param, value in sorted(hyperparams.items()):
+                model_col = mt.replace("_", r"\_") if first else ""
+                param_escaped = param.replace("_", r"\_")
+                lines.append(f"{model_col} & {param_escaped} & {value} \\\\")
+                first = False
+            lines.append(r"\midrule")
+        if lines[-1] == r"\midrule":
+            lines.pop()
+        lines.extend([r"\bottomrule", r"\end{tabular}", r"\end{table}"])
+        return "\n".join(lines)
+    else:
+        lines = [
+            "## Hyperparameters",
+            "",
+            "| Model | Parameter | Value |",
+            "|-------|-----------|-------|",
+        ]
+        for mt, exps in groups.items():
+            best = exps[0]
+            hyperparams = best.get("config", {}).get("hyperparams", {})
+            for param, value in sorted(hyperparams.items()):
+                lines.append(f"| {mt} | {param} | {value} |")
+        return "\n".join(lines)
+
+
+def save_paper_sections(sections: dict[str, str], output_dir: str = "paper/sections") -> list[Path]:
+    """Save each section to its own file."""
+    out_path = Path(output_dir)
+    out_path.mkdir(parents=True, exist_ok=True)
+
+    saved = []
+    for name, content in sections.items():
+        ext = ".tex" if r"\begin" in content else ".md"
+        filepath = out_path / f"{name}{ext}"
+        with open(filepath, "w") as f:
+            f.write(content)
+        saved.append(filepath)
+
+    return saved
+
+
+def draft_paper(
+    sections_str: str | None = None,
+    output_format: str = DEFAULT_FORMAT,
+    config_path: str = "config.yaml",
+    log_path: str = "experiments/log.jsonl",
+) -> dict:
+    """Draft all requested paper sections.
+
+    Args:
+        sections_str: Comma-separated section names (setup,results,ablation,hyperparameters).
+        output_format: "latex" or "markdown".
+        config_path: Path to config.yaml.
+        log_path: Path to experiment log.
+
+    Returns:
+        Dict with section name -> content mappings.
+    """
+    if sections_str:
+        sections = [s.strip() for s in sections_str.split(",")]
+    else:
+        sections = VALID_SECTIONS
+
+    config = load_config(config_path)
+    eval_cfg = config.get("evaluation", {})
+    primary_metric = eval_cfg.get("primary_metric", "accuracy")
+    all_metrics = eval_cfg.get("metrics", [primary_metric])
+    lower_is_better = eval_cfg.get("lower_is_better", False)
+
+    experiments = load_experiments(log_path)
+    top_exps = get_top_experiments(experiments, primary_metric, lower_is_better)
+
+    seed_studies = load_seed_studies_for_paper()
+    ablation_studies = load_ablation_studies()
+
+    dataset_name = config.get("data", {}).get("source", "the dataset")
+
+    result = {"format": output_format, "sections": {}}
+
+    for section in sections:
+        if section == "setup":
+            result["sections"]["setup"] = draft_setup_section(
+                config, experiments, seed_studies, output_format,
+            )
+        elif section == "results":
+            result["sections"]["results"] = draft_results_table(
+                top_exps, all_metrics, primary_metric, lower_is_better,
+                seed_studies, output_format, dataset_name,
+            )
+        elif section == "ablation":
+            result["sections"]["ablation"] = draft_ablation_table(
+                ablation_studies, output_format,
+            )
+        elif section == "hyperparameters":
+            result["sections"]["hyperparameters"] = draft_hyperparameter_table(
+                top_exps, output_format,
+            )
+
+    return result
+
+
+def main() -> None:
+    """CLI entry point."""
+    parser = argparse.ArgumentParser(description="Draft paper sections from experiment logs")
+    parser.add_argument("--sections", default=None, help="Comma-separated sections: setup,results,ablation,hyperparameters")
+    parser.add_argument("--format", default=DEFAULT_FORMAT, dest="output_format", choices=["latex", "markdown"])
+    parser.add_argument("--config", default="config.yaml", help="Path to config.yaml")
+    parser.add_argument("--log", default="experiments/log.jsonl", help="Path to experiment log")
+    parser.add_argument("--output", default="paper/sections", help="Output directory")
+    parser.add_argument("--json", action="store_true", help="Output raw JSON")
+    args = parser.parse_args()
+
+    result = draft_paper(
+        sections_str=args.sections,
+        output_format=args.output_format,
+        config_path=args.config,
+        log_path=args.log,
+    )
+
+    # Save sections
+    if result.get("sections"):
+        saved = save_paper_sections(result["sections"], args.output)
+        for f in saved:
+            print(f"Saved: {f}", file=sys.stderr)
+
+    if args.json:
+        print(json.dumps(result, indent=2, default=str))
+    else:
+        for name, content in result.get("sections", {}).items():
+            print(f"\n{'=' * 60}")
+            print(f"  {name.upper()}")
+            print(f"{'=' * 60}\n")
+            print(content)
+            print()
+
+
+if __name__ == "__main__":
+    main()