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import argparse
import json
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from experiments.common import ARTIFACT_DIR
from featurelens.stats import (
bootstrap_mean_ci,
paired_bootstrap_difference_ci,
paired_sign_flip_pvalue,
)
def parse_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(
description="Build a truthful experiment report from saved metrics."
)
parser.add_argument("--artifact-dir", type=Path, default=ARTIFACT_DIR)
return parser.parse_args()
def _selected_features(catalog: pd.DataFrame) -> pd.DataFrame:
scored = catalog.copy()
scored["activation_contrast"] = (
scored["activation_rate_pos"] - scored["activation_rate_neg"]
)
ordered = scored.sort_values(
["concept", "train_auroc", "activation_contrast"],
ascending=[True, False, False],
)
return ordered.groupby("concept", as_index=False).first()
def _effect_column(frame: pd.DataFrame) -> str:
if "target_mean_logprob_delta" in frame.columns:
return "target_mean_logprob_delta"
return "target_logprob_delta"
def _causal_file(artifact_dir: Path, policy: str) -> Path:
if policy == "final_token":
name = "causal_results_final_token.csv"
else:
name = "causal_results_max_active.csv"
path = artifact_dir / name
if path.exists():
return path
legacy = artifact_dir / "causal_results.csv"
if policy == "final_token" and legacy.exists():
return legacy
return path
def _task_level_stats(
frame: pd.DataFrame,
*,
seed: int,
active_only: bool = False,
) -> dict:
metric = _effect_column(frame)
sae_rows = frame[frame["condition"] == "sae_feature"].copy()
if active_only:
if "feature_active_at_intervention" in frame.columns:
active_col = "feature_active_at_intervention"
else:
active_col = "feature_activation"
active_mask = (
pd.to_numeric(sae_rows[active_col], errors="coerce").fillna(0) > 0
)
active_ids = sae_rows.loc[active_mask, "task_id"].unique()
frame = frame[frame["task_id"].isin(active_ids)].copy()
sae_rows = frame[frame["condition"] == "sae_feature"].copy()
sae = (
sae_rows.assign(
_abs=lambda data: np.abs(
pd.to_numeric(data[metric], errors="coerce")
)
)
.groupby("task_id", as_index=False)
.agg(sae_abs=("_abs", "mean"))
)
random = (
frame[frame["condition"] == "random_norm_matched"]
.assign(
_abs=lambda data: np.abs(
pd.to_numeric(data[metric], errors="coerce")
)
)
.groupby(["task_id", "intervention"], as_index=False)["_abs"]
.mean()
.groupby("task_id", as_index=False)["_abs"]
.mean()
.rename(columns={"_abs": "random_abs"})
)
paired = sae.merge(random, on="task_id", how="inner")
if paired.empty:
nan = float("nan")
return {
"sae_abs": nan,
"random_abs": nan,
"ratio": nan,
"advantage": nan,
"ci": [nan, nan],
"pvalue": nan,
"n_tasks": 0,
}
sae_effect = paired["sae_abs"].to_numpy(float)
random_effect = paired["random_abs"].to_numpy(float)
low, high = paired_bootstrap_difference_ci(
sae_effect,
random_effect,
seed=seed,
)
return {
"sae_abs": float(sae_effect.mean()),
"random_abs": float(random_effect.mean()),
"ratio": float(
sae_effect.mean() / max(float(random_effect.mean()), 1e-12)
),
"advantage": float((sae_effect - random_effect).mean()),
"ci": [float(low), float(high)],
"pvalue": float(
paired_sign_flip_pvalue(
sae_effect,
random_effect,
seed=seed + 1,
)
),
"n_tasks": int(len(paired)),
}
def _paired_stats(
frame: pd.DataFrame,
*,
index: list[str],
sae_condition: str,
random_condition: str,
seed: int,
) -> dict[str, float | list[float]]:
"""Legacy helper retained for report-control regression tests."""
metric = _effect_column(frame)
sae = (
frame[frame["condition"] == sae_condition]
.groupby(index, as_index=False)[metric]
.first()
.rename(columns={metric: "sae_effect"})
)
random = (
frame[frame["condition"] == random_condition]
.assign(
_abs_effect=lambda data: np.abs(
pd.to_numeric(data[metric], errors="coerce")
)
)
.groupby(index, as_index=False)["_abs_effect"]
.mean()
.rename(columns={"_abs_effect": "random_abs_effect"})
)
paired = sae.merge(random, on=index, how="inner")
sae_effect = np.abs(paired["sae_effect"].to_numpy(dtype=float))
random_effect = paired["random_abs_effect"].to_numpy(dtype=float)
if sae_effect.size == 0:
nan = float("nan")
return {
"sae_abs": nan,
"random_abs": nan,
"ratio": nan,
"paired_advantage": nan,
"ci": [nan, nan],
"pvalue": nan,
"n_pairs": 0,
}
low, high = paired_bootstrap_difference_ci(
sae_effect,
random_effect,
seed=seed,
)
return {
"sae_abs": float(sae_effect.mean()),
"random_abs": float(random_effect.mean()),
"ratio": float(
sae_effect.mean() / max(float(random_effect.mean()), 1e-12)
),
"paired_advantage": float((sae_effect - random_effect).mean()),
"ci": [float(low), float(high)],
"pvalue": float(
paired_sign_flip_pvalue(
sae_effect,
random_effect,
seed=seed + 1,
)
),
"n_pairs": int(sae_effect.size),
}
def _feature_set_stats(frame: pd.DataFrame, *, seed: int) -> dict:
metric = _effect_column(frame)
sae = (
frame[frame["condition"] == "sae_feature_set"]
.groupby("task_id", as_index=False)[metric]
.first()
.rename(columns={metric: "sae"})
)
random = (
frame[frame["condition"] == "random_norm_matched"]
.assign(
_abs=lambda data: np.abs(
pd.to_numeric(data[metric], errors="coerce")
)
)
.groupby("task_id", as_index=False)["_abs"]
.mean()
.rename(columns={"_abs": "random"})
)
paired = sae.merge(random, on="task_id")
sae_effect = np.abs(paired["sae"].to_numpy(float))
random_effect = paired["random"].to_numpy(float)
if sae_effect.size == 0:
return {}
low, high = paired_bootstrap_difference_ci(
sae_effect,
random_effect,
seed=seed,
)
return {
"sae_abs": float(sae_effect.mean()),
"random_abs": float(random_effect.mean()),
"ratio": float(
sae_effect.mean() / max(float(random_effect.mean()), 1e-12)
),
"advantage": float((sae_effect - random_effect).mean()),
"ci": [float(low), float(high)],
"pvalue": float(
paired_sign_flip_pvalue(
sae_effect,
random_effect,
seed=seed + 1,
)
),
"n_tasks": int(sae_effect.size),
}
def _save_figure(fig: plt.Figure, path: Path) -> None:
fig.tight_layout()
fig.savefig(path, dpi=160)
plt.close(fig)
def _save_plots(
artifact_dir: Path,
selected: pd.DataFrame,
layers: pd.DataFrame,
max_active: pd.DataFrame,
feature_sets: pd.DataFrame | None,
position: pd.DataFrame,
study: pd.DataFrame,
) -> None:
fig_dir = artifact_dir / "figures"
fig_dir.mkdir(parents=True, exist_ok=True)
fig = plt.figure(figsize=(7.5, 4.2))
ax = fig.add_subplot(111)
ordered = selected.sort_values("auroc")
ax.barh(ordered["concept"], ordered["auroc"])
ax.axvline(0.5, linewidth=1, linestyle="--")
ax.set_xlabel("Held-out AUROC")
ax.set_title("Selected SAE feature predictiveness")
_save_figure(fig, fig_dir / "feature_auroc.png")
fig = plt.figure(figsize=(7.0, 4.2))
ax = fig.add_subplot(111)
ax.plot(
layers["layer"],
layers["linear_probe_macro_auroc"],
marker="o",
label="Linear probe AUROC",
)
ax.plot(
layers["layer"],
layers["reconstruction_cosine"],
marker="o",
label="SAE reconstruction cosine",
)
ax.set_xlabel("Layer")
ax.set_ylim(0, 1.05)
ax.set_title("Layer-wise representation diagnostics")
ax.legend()
_save_figure(fig, fig_dir / "layer_diagnostics.png")
metric = _effect_column(max_active)
grouped = (
max_active.groupby(["intervention", "condition"])[metric]
.apply(lambda values: float(np.mean(np.abs(values))))
.reset_index(name="mean_abs_effect")
)
pivot = grouped.pivot(
index="intervention",
columns="condition",
values="mean_abs_effect",
)
fig = plt.figure(figsize=(7, 4.2))
ax = fig.add_subplot(111)
pivot.plot(kind="bar", ax=ax)
ax.set_ylabel("Mean |Δ mean log p/token|")
ax.set_title("Max-active SAE edits vs norm-matched controls")
ax.tick_params(axis="x", rotation=0)
_save_figure(fig, fig_dir / "causal_effects.png")
if feature_sets is not None and not feature_sets.empty:
feature_set_metric = _effect_column(feature_sets)
grouped_sets = (
feature_sets.groupby(["set_size", "condition"])[feature_set_metric]
.apply(lambda values: float(np.mean(np.abs(values))))
.reset_index(name="mean_abs_effect")
)
set_pivot = grouped_sets.pivot(
index="set_size",
columns="condition",
values="mean_abs_effect",
)
fig = plt.figure(figsize=(7, 4.2))
ax = fig.add_subplot(111)
set_pivot.plot(kind="line", marker="o", ax=ax)
ax.set_xlabel("Jointly ablated feature count")
ax.set_ylabel("Mean |Δ mean log p/token|")
ax.set_title("Final-token feature-set diagnostic")
_save_figure(fig, fig_dir / "feature_set_effects.png")
overall = position[position["concept"] == "__all__"].copy()
policy_order = ["final_token", "max_feature_activation"]
overall["position_policy"] = pd.Categorical(
overall["position_policy"],
categories=policy_order,
ordered=True,
)
overall = overall.sort_values("position_policy")
position_plot = pd.DataFrame(
{
"Policy": ["Final token", "Max feature activation"],
"SAE effect": overall["target_sae_abs_mean"].to_numpy(float),
"Random control": overall["target_random_abs_mean"].to_numpy(float),
}
)
fig = plt.figure(figsize=(7.2, 4.4))
ax = fig.add_subplot(111)
x_positions = np.arange(len(position_plot))
width = 0.34
ax.bar(
x_positions - width / 2,
position_plot["SAE effect"],
width,
label="SAE effect",
)
ax.bar(
x_positions + width / 2,
position_plot["Random control"],
width,
label="Random control",
)
ax.set_xticks(x_positions, position_plot["Policy"])
ax.set_ylabel("Task-level mean |Δ mean log p/token|")
ax.set_title("Causal position sensitivity")
ax.legend()
_save_figure(fig, fig_dir / "causal_position_sensitivity.png")
if not study.empty:
fig = plt.figure(figsize=(7.2, 4.6))
ax = fig.add_subplot(111)
ax.scatter(
study["heldout_auroc"],
study["max_active_target_specificity_ratio"],
)
for row in study.itertuples():
ax.annotate(
str(row.concept),
(row.heldout_auroc, row.max_active_target_specificity_ratio),
fontsize=8,
)
ax.set_xlabel("Held-out feature AUROC")
ax.set_ylabel("Max-active target specificity ratio")
ax.set_title("Association evidence vs max-active causality")
_save_figure(fig, fig_dir / "association_vs_causality.png")
def _coverage(
frame: pd.DataFrame,
column: str,
fallback: str = "feature_activation",
) -> float:
name = column if column in frame.columns else fallback
values = pd.to_numeric(frame[name], errors="coerce").fillna(0)
return float((values > 0).mean())
def _build_interpretation(
*,
max_stats: dict,
final_coverage: float,
max_coverage: float,
) -> str:
strong = (
max_stats["ratio"] >= 1.5
and max_stats["ci"][0] > 0
and max_stats["pvalue"] < 0.05
)
if strong:
interpretation = (
"Max-active interventions produced larger task-level target effects than "
"norm-matched random controls with paired uncertainty excluding zero. "
"Predictive SAE features therefore show causal specificity when intervened "
"where the selected feature is actually represented, while the final-token "
"baseline quantifies sensitivity to intervention location."
)
elif max_stats["ratio"] >= 1.5:
interpretation = (
"Max-active interventions had a larger point-estimate effect than norm-matched "
"random controls, but task-level paired uncertainty did not support a strong "
"significance claim. The result is therefore reported as suggestive causal "
"specificity rather than conclusive evidence."
)
else:
interpretation = (
"Held-out feature predictiveness was strong, but max-active causal effects were "
"only modest relative to norm-matched random controls. FeatureLens therefore "
"separates predictive association from causal control rather than treating them "
"as interchangeable."
)
if max_coverage > final_coverage + 0.1:
interpretation += (
" Moving from the final prompt token to the feature's maximum-activation token "
f"increased intervention coverage from {final_coverage:.1%} to "
f"{max_coverage:.1%}, showing that causal conclusions depend materially on "
"where the representation is tested."
)
return interpretation
def _build_report_lines(
*,
headline: str,
interpretation: str,
highlights: list[str],
feature_sets: pd.DataFrame | None,
study: pd.DataFrame,
) -> list[str]:
lines = [
"# FeatureLens experiment report",
"",
"## Research question",
"",
"**Do sparse features that predict a concept also causally influence model behaviour?**",
"",
"## Executive summary",
"",
headline,
"",
interpretation,
"",
"## Key measurements",
"",
*[f"- {item}" for item in highlights],
"",
"## Experimental design",
"",
"- Model: Qwen3-1.7B-Base.",
"- SAEs: Qwen-Scope residual-stream TopK SAEs at configured early/middle/late layers.",
"- Discovery evidence: prompt-wide maximum SAE activation across non-padding tokens; final-token activations are saved separately.",
"- Split discipline: paraphrase groups remain entirely in train or held-out test.",
"- Feature selection: training-split AUROC plus activation contrast; held-out AUROC/F1 are reported separately.",
"- Causal position policies: final prompt token and maximum selected-feature activation within the prompt. Max-active positions are selected from SAE activation only, never from behavioral outcomes.",
"- Primary causal statistical unit: causal task. Ablation and 2× amplification are averaged within task before paired bootstrap/sign-flip inference.",
"- Negative control: deterministic norm-matched random residual directions.",
"- Primary target metric: exact full continuation mean log probability per token under teacher forcing.",
"- Coverage and conditional-on-active effect strength are reported separately.",
"- Feature-set analysis remains a final-token diagnostic and is not conflated with the max-active single-feature study.",
"",
"## Figures",
"",
"",
"",
"",
"",
"",
"",
"",
]
if feature_sets is not None and not feature_sets.empty:
lines.extend(
[
"",
"",
]
)
if not study.empty:
lines.extend(
[
"",
"",
"",
"## Position sensitivity",
"",
"The final-token policy asks whether the selected feature matters at the conventional last-prompt-token intervention site. The max-active policy asks whether it matters where that same feature is most strongly represented in the prompt. Reporting both prevents low final-token coverage from being mistaken for evidence that a predictive feature is globally non-causal.",
"",
"## Association vs causality across concepts",
"",
"Cross-concept correlations use max-active random-normalized specificity and are descriptive because the study has seven controlled concepts.",
]
)
lines.extend(
[
"",
"## Interpretation guardrails",
"",
"High held-out AUROC is correlational evidence. Causal claims require downstream changes relative to norm-matched random controls. Max-active positions are chosen without reference to behavioral effect size. Task-level uncertainty treats ablation and amplification on the same causal prompt as repeated interventions, not independent experimental units.",
"",
"## Reproducibility",
"",
"Run `python -m experiments.run_all --resume` for a fresh full study. The causal-addendum notebook is retained as a migration utility for an already-completed final-token baseline.",
"",
]
)
return lines
def main() -> None:
args = parse_args()
artifact_dir = args.artifact_dir
catalog = pd.read_csv(artifact_dir / "feature_catalog.csv")
layers = pd.read_csv(artifact_dir / "layer_metrics.csv")
stability = pd.read_csv(artifact_dir / "stability.csv")
final = pd.read_csv(_causal_file(artifact_dir, "final_token"))
max_active = pd.read_csv(
_causal_file(artifact_dir, "max_feature_activation")
)
feature_set_path = artifact_dir / "feature_set_results.csv"
feature_sets = (
pd.read_csv(feature_set_path) if feature_set_path.exists() else None
)
study_path = artifact_dir / "study_feature_summary.csv"
study = pd.read_csv(study_path) if study_path.exists() else pd.DataFrame()
position = pd.read_csv(artifact_dir / "causal_position_summary.csv")
study_summary_path = artifact_dir / "study_summary.json"
if study_summary_path.exists():
study_summary = json.loads(study_summary_path.read_text())
else:
study_summary = {}
selected = _selected_features(catalog)
_save_plots(
artifact_dir,
selected,
layers,
max_active,
feature_sets,
position,
study,
)
mean_auc = float(selected["auroc"].mean())
median_auc = float(selected["auroc"].median())
auc_low, auc_high = bootstrap_mean_ci(
selected["auroc"].to_numpy(),
seed=42,
)
best = layers.sort_values(
"linear_probe_macro_auroc",
ascending=False,
).iloc[0]
mean_jaccard = float(stability["topk_jaccard"].mean())
mean_cosine = float(stability["sparse_cosine"].mean())
final_stats = _task_level_stats(final, seed=43)
final_active_stats = _task_level_stats(
final,
seed=44,
active_only=True,
)
max_stats = _task_level_stats(max_active, seed=45)
max_active_stats = _task_level_stats(
max_active,
seed=46,
active_only=True,
)
final_sae = final[final["condition"] == "sae_feature"]
max_sae = max_active[max_active["condition"] == "sae_feature"]
final_coverage = _coverage(
final_sae,
"feature_active_at_intervention",
)
anywhere_coverage = _coverage(
max_sae,
"feature_active_anywhere",
)
max_coverage = _coverage(
max_sae,
"feature_active_at_intervention",
)
set_summary: dict[int, dict] = {}
if feature_sets is not None and not feature_sets.empty:
sizes = sorted(int(value) for value in feature_sets["set_size"].unique())
for size in sizes:
subset = feature_sets[feature_sets["set_size"] == size]
set_summary[size] = _feature_set_stats(
subset,
seed=100 + size,
)
interpretation = _build_interpretation(
max_stats=max_stats,
final_coverage=final_coverage,
max_coverage=max_coverage,
)
headline = (
f"Selected SAE features averaged {mean_auc:.3f} held-out AUROC. "
f"Max-active interventions covered {max_coverage:.1%} of causal tasks and "
f"changed mean log p/token by {max_stats['sae_abs']:.3f} in absolute value "
f"on average versus {max_stats['random_abs']:.3f} for norm-matched random "
f"controls ({max_stats['ratio']:.2f}×)."
)
highlights = [
(
f"Median selected-feature held-out AUROC: {median_auc:.3f}; mean AUROC "
f"95% bootstrap CI [{auc_low:.3f}, {auc_high:.3f}]."
),
(
f"Best residual linear-probe layer: {int(best['layer'])} with macro AUROC "
f"{float(best['linear_probe_macro_auroc']):.3f}."
),
(
f"Mean paraphrase TopK Jaccard: {mean_jaccard:.3f}; sparse activation "
f"cosine: {mean_cosine:.3f}."
),
(
f"Feature coverage: final-token policy {final_coverage:.1%}; active "
f"anywhere in prompt {anywhere_coverage:.1%}; max-active intervention "
f"{max_coverage:.1%}."
),
(
f"Final-token task-level SAE/random ratio: {final_stats['ratio']:.2f}×; "
f"paired advantage {final_stats['advantage']:+.4f}, 95% CI "
f"[{final_stats['ci'][0]:+.4f}, {final_stats['ci'][1]:+.4f}], "
f"sign-flip p={final_stats['pvalue']:.4f}."
),
(
f"Max-active task-level SAE/random ratio: {max_stats['ratio']:.2f}×; "
f"paired advantage {max_stats['advantage']:+.4f}, 95% CI "
f"[{max_stats['ci'][0]:+.4f}, {max_stats['ci'][1]:+.4f}], "
f"sign-flip p={max_stats['pvalue']:.4f}."
),
(
"Conditional on feature-active tasks, max-active SAE/random ratio: "
f"{max_active_stats['ratio']:.2f}× "
f"(n={max_active_stats['n_tasks']})."
),
]
if set_summary:
max_size = max(set_summary)
set_stats = set_summary[max_size]
highlights.append(
f"Final-token top-{max_size} joint ablation SAE/random ratio: "
f"{set_stats['ratio']:.2f}×; paired advantage "
f"{set_stats['advantage']:+.4f}, 95% CI "
f"[{set_stats['ci'][0]:+.4f}, {set_stats['ci'][1]:+.4f}], "
f"sign-flip p={set_stats['pvalue']:.4f}."
)
correlations = study_summary.get("correlations", {})
target_corr = correlations.get(
"heldout_auroc_vs_max_active_target_specificity",
{},
)
js_corr = correlations.get(
"heldout_auroc_vs_max_active_js_specificity",
{},
)
if target_corr:
target_rho = float(target_corr.get("rho", float("nan")))
js_rho = float(js_corr.get("rho", float("nan")))
highlights.extend(
[
(
"Across seven concepts, held-out AUROC vs max-active target "
f"specificity Spearman ρ={target_rho:+.3f}; descriptive only."
),
(
"Held-out AUROC vs max-active JS specificity Spearman "
f"ρ={js_rho:+.3f}; descriptive only."
),
]
)
summary = {
"headline": headline,
"highlights": highlights,
"interpretation": interpretation,
"metrics": {
"mean_selected_feature_test_auroc": mean_auc,
"mean_selected_feature_test_auroc_bootstrap_ci_95": [
auc_low,
auc_high,
],
"median_selected_feature_test_auroc": median_auc,
"best_linear_probe_layer": int(best["layer"]),
"best_linear_probe_macro_auroc": float(
best["linear_probe_macro_auroc"]
),
"mean_paraphrase_topk_jaccard": mean_jaccard,
"mean_paraphrase_sparse_cosine": mean_cosine,
"final_token_feature_coverage": final_coverage,
"prompt_anywhere_feature_coverage": anywhere_coverage,
"max_active_feature_coverage": max_coverage,
"final_token_task_level": final_stats,
"final_token_active_only": final_active_stats,
"max_active_task_level": max_stats,
"max_active_active_only": max_active_stats,
"feature_set_results": {
str(key): value for key, value in set_summary.items()
},
"study_summary": study_summary,
},
}
(artifact_dir / "summary.json").write_text(
json.dumps(summary, indent=2),
encoding="utf-8",
)
report_lines = _build_report_lines(
headline=headline,
interpretation=interpretation,
highlights=highlights,
feature_sets=feature_sets,
study=study,
)
report_path = artifact_dir / "report.md"
report_path.write_text("\n".join(report_lines), encoding="utf-8")
print(headline)
print(f"Wrote {report_path}")
if __name__ == "__main__":
main()
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