Add RAG rewrite, 60-session experiment scripts, and analysis tools

- RAG rewrite adapter and vector preference pipeline in personalized_llm
- 60-session experiment queue scripts (reflection, rag, rag_vector, rag_rewrite)
- Vector-preference correlation analysis and visualization scripts
- Local reward model batch processing improvements
- Updated CLAUDE.md with full experiment documentation and notes

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

1 files changed, 407 insertions, 0 deletions

diff --git a/collaborativeagents/scripts/visualize_user_vectors.py b/collaborativeagents/scripts/visualize_user_vectors.py
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index 0000000..203cb68
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+++ b/collaborativeagents/scripts/visualize_user_vectors.py
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+#!/usr/bin/env python3
+"""
+User Vector Visualization Script
+
+Visualizes learned user vectors using t-SNE and PCA for dimensionality reduction.
+Supports multiple coloring schemes to analyze user clusters.
+
+Usage:
+    python visualize_user_vectors.py --results-dir ../results/fullrun_3methods
+    python visualize_user_vectors.py --vectors-file user_vectors.npy --profiles-file profiles.json
+"""
+
+import argparse
+import json
+import numpy as np
+import matplotlib.pyplot as plt
+from pathlib import Path
+from typing import Dict, List, Optional, Tuple
+from sklearn.manifold import TSNE
+from sklearn.decomposition import PCA
+from sklearn.preprocessing import StandardScaler
+import warnings
+warnings.filterwarnings('ignore')
+
+
+def load_user_vectors(results_dir: Path) -> Tuple[np.ndarray, List[int]]:
+    """Load user vectors from experiment results."""
+    vectors = []
+    user_ids = []
+
+    # Try to find user vectors in different locations
+    possible_paths = [
+        results_dir / "user_vectors.npy",
+        results_dir / "rag_vector" / "user_vectors.npy",
+        results_dir / "checkpoints" / "user_vectors.npy",
+    ]
+
+    for path in possible_paths:
+        if path.exists():
+            data = np.load(path, allow_pickle=True)
+            if isinstance(data, np.ndarray):
+                if data.dtype == object:
+                    # Dictionary format
+                    data = data.item()
+                    for uid, vec in data.items():
+                        user_ids.append(int(uid))
+                        vectors.append(vec)
+                else:
+                    # Direct array format
+                    vectors = data
+                    user_ids = list(range(len(data)))
+            print(f"Loaded {len(vectors)} user vectors from {path}")
+            return np.array(vectors), user_ids
+
+    # Try to extract from results.json
+    results_files = list(results_dir.glob("**/results.json"))
+    for rf in results_files:
+        try:
+            with open(rf) as f:
+                data = json.load(f)
+            # Extract user vectors if stored in results
+            if isinstance(data, dict) and "user_vectors" in data:
+                for uid, vec in data["user_vectors"].items():
+                    user_ids.append(int(uid))
+                    vectors.append(np.array(vec))
+                print(f"Loaded {len(vectors)} user vectors from {rf}")
+                return np.array(vectors), user_ids
+        except:
+            continue
+
+    raise FileNotFoundError(f"No user vectors found in {results_dir}")
+
+
+def load_profiles(profiles_path: Path) -> List[Dict]:
+    """Load user profiles for labeling."""
+    if profiles_path.suffix == '.jsonl':
+        profiles = []
+        with open(profiles_path) as f:
+            for line in f:
+                profiles.append(json.loads(line))
+        return profiles
+    else:
+        with open(profiles_path) as f:
+            return json.load(f)
+
+
+def extract_profile_features(profiles: List[Dict]) -> Dict[str, List]:
+    """Extract features from profiles for coloring."""
+    features = {
+        "categories": [],
+        "n_preferences": [],
+        "persona_length": [],
+    }
+
+    for p in profiles:
+        # Extract categories if available
+        cats = p.get("categories", [])
+        features["categories"].append(cats[0] if cats else "unknown")
+
+        # Number of preferences
+        prefs = p.get("preferences", [])
+        features["n_preferences"].append(len(prefs))
+
+        # Persona length
+        persona = p.get("persona", "")
+        features["persona_length"].append(len(persona))
+
+    return features
+
+
+def apply_tsne(vectors: np.ndarray, perplexity: int = 30, max_iter: int = 1000) -> np.ndarray:
+    """Apply t-SNE dimensionality reduction."""
+    # Standardize vectors
+    scaler = StandardScaler()
+    vectors_scaled = scaler.fit_transform(vectors)
+
+    # Adjust perplexity if needed
+    n_samples = len(vectors)
+    perplexity = min(perplexity, n_samples - 1)
+
+    tsne = TSNE(
+        n_components=2,
+        perplexity=perplexity,
+        max_iter=max_iter,
+        random_state=42,
+        init='pca',
+        learning_rate='auto'
+    )
+    return tsne.fit_transform(vectors_scaled)
+
+
+def apply_pca(vectors: np.ndarray) -> Tuple[np.ndarray, np.ndarray]:
+    """Apply PCA dimensionality reduction. Returns (2D projection, explained variance)."""
+    scaler = StandardScaler()
+    vectors_scaled = scaler.fit_transform(vectors)
+
+    pca = PCA(n_components=min(10, vectors.shape[1]))
+    transformed = pca.fit_transform(vectors_scaled)
+
+    return transformed[:, :2], pca.explained_variance_ratio_
+
+
+def plot_comparison(
+    vectors: np.ndarray,
+    user_ids: List[int],
+    profiles: Optional[List[Dict]] = None,
+    output_path: Optional[Path] = None,
+    title_prefix: str = ""
+):
+    """Create side-by-side t-SNE and PCA plots."""
+
+    # Apply dimensionality reduction
+    print("Applying t-SNE...")
+    tsne_2d = apply_tsne(vectors)
+
+    print("Applying PCA...")
+    pca_2d, pca_variance = apply_pca(vectors)
+
+    # Prepare coloring
+    if profiles and len(profiles) >= len(user_ids):
+        features = extract_profile_features(profiles)
+        color_by = features["n_preferences"]
+        color_label = "Number of Preferences"
+    else:
+        color_by = user_ids
+        color_label = "User ID"
+
+    # Create figure
+    fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+
+    # t-SNE plot
+    ax1 = axes[0]
+    scatter1 = ax1.scatter(
+        tsne_2d[:, 0], tsne_2d[:, 1],
+        c=color_by, cmap='viridis', alpha=0.7, s=50
+    )
+    ax1.set_xlabel('t-SNE Dimension 1')
+    ax1.set_ylabel('t-SNE Dimension 2')
+    ax1.set_title(f'{title_prefix}t-SNE Visualization\n({len(vectors)} users)')
+    plt.colorbar(scatter1, ax=ax1, label=color_label)
+
+    # PCA plot
+    ax2 = axes[1]
+    scatter2 = ax2.scatter(
+        pca_2d[:, 0], pca_2d[:, 1],
+        c=color_by, cmap='viridis', alpha=0.7, s=50
+    )
+    ax2.set_xlabel(f'PC1 ({pca_variance[0]*100:.1f}% variance)')
+    ax2.set_ylabel(f'PC2 ({pca_variance[1]*100:.1f}% variance)')
+    ax2.set_title(f'{title_prefix}PCA Visualization\n(Top 2 components: {(pca_variance[0]+pca_variance[1])*100:.1f}% variance)')
+    plt.colorbar(scatter2, ax=ax2, label=color_label)
+
+    plt.tight_layout()
+
+    if output_path:
+        plt.savefig(output_path, dpi=150, bbox_inches='tight')
+        print(f"Saved comparison plot to {output_path}")
+
+    plt.show()
+
+    return tsne_2d, pca_2d, pca_variance
+
+
+def plot_by_category(
+    vectors: np.ndarray,
+    user_ids: List[int],
+    profiles: List[Dict],
+    output_path: Optional[Path] = None
+):
+    """Create plots colored by preference category."""
+
+    features = extract_profile_features(profiles)
+    categories = features["categories"]
+    unique_cats = list(set(categories))
+    cat_to_idx = {c: i for i, c in enumerate(unique_cats)}
+    cat_colors = [cat_to_idx[c] for c in categories[:len(user_ids)]]
+
+    # Apply reductions
+    tsne_2d = apply_tsne(vectors)
+    pca_2d, pca_variance = apply_pca(vectors)
+
+    fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+
+    # t-SNE by category
+    ax1 = axes[0]
+    scatter1 = ax1.scatter(
+        tsne_2d[:, 0], tsne_2d[:, 1],
+        c=cat_colors, cmap='tab10', alpha=0.7, s=50
+    )
+    ax1.set_xlabel('t-SNE Dimension 1')
+    ax1.set_ylabel('t-SNE Dimension 2')
+    ax1.set_title('t-SNE by Preference Category')
+
+    # PCA by category
+    ax2 = axes[1]
+    scatter2 = ax2.scatter(
+        pca_2d[:, 0], pca_2d[:, 1],
+        c=cat_colors, cmap='tab10', alpha=0.7, s=50
+    )
+    ax2.set_xlabel(f'PC1 ({pca_variance[0]*100:.1f}%)')
+    ax2.set_ylabel(f'PC2 ({pca_variance[1]*100:.1f}%)')
+    ax2.set_title('PCA by Preference Category')
+
+    # Add legend
+    handles = [plt.scatter([], [], c=[cat_to_idx[c]], cmap='tab10', label=c)
+               for c in unique_cats[:10]]  # Limit to 10 categories
+    fig.legend(handles, unique_cats[:10], loc='center right', title='Category')
+
+    plt.tight_layout()
+    plt.subplots_adjust(right=0.85)
+
+    if output_path:
+        plt.savefig(output_path, dpi=150, bbox_inches='tight')
+        print(f"Saved category plot to {output_path}")
+
+    plt.show()
+
+
+def plot_pca_variance(vectors: np.ndarray, output_path: Optional[Path] = None):
+    """Plot PCA explained variance to understand dimensionality."""
+    scaler = StandardScaler()
+    vectors_scaled = scaler.fit_transform(vectors)
+
+    n_components = min(50, vectors.shape[1], vectors.shape[0])
+    pca = PCA(n_components=n_components)
+    pca.fit(vectors_scaled)
+
+    fig, axes = plt.subplots(1, 2, figsize=(14, 5))
+
+    # Individual variance
+    ax1 = axes[0]
+    ax1.bar(range(1, n_components + 1), pca.explained_variance_ratio_ * 100)
+    ax1.set_xlabel('Principal Component')
+    ax1.set_ylabel('Explained Variance (%)')
+    ax1.set_title('PCA Explained Variance by Component')
+    ax1.set_xlim(0, n_components + 1)
+
+    # Cumulative variance
+    ax2 = axes[1]
+    cumvar = np.cumsum(pca.explained_variance_ratio_) * 100
+    ax2.plot(range(1, n_components + 1), cumvar, 'b-o', markersize=4)
+    ax2.axhline(y=90, color='r', linestyle='--', label='90% variance')
+    ax2.axhline(y=95, color='g', linestyle='--', label='95% variance')
+    ax2.set_xlabel('Number of Components')
+    ax2.set_ylabel('Cumulative Explained Variance (%)')
+    ax2.set_title('PCA Cumulative Explained Variance')
+    ax2.legend()
+    ax2.set_xlim(0, n_components + 1)
+    ax2.set_ylim(0, 105)
+
+    # Find components needed for 90% and 95% variance
+    n_90 = np.argmax(cumvar >= 90) + 1
+    n_95 = np.argmax(cumvar >= 95) + 1
+    print(f"Components for 90% variance: {n_90}")
+    print(f"Components for 95% variance: {n_95}")
+
+    plt.tight_layout()
+
+    if output_path:
+        plt.savefig(output_path, dpi=150, bbox_inches='tight')
+        print(f"Saved variance plot to {output_path}")
+
+    plt.show()
+
+    return pca.explained_variance_ratio_
+
+
+def generate_synthetic_vectors(n_users: int = 200, dim: int = 64) -> np.ndarray:
+    """Generate synthetic user vectors for testing visualization."""
+    np.random.seed(42)
+
+    # Create 5 clusters of users
+    n_clusters = 5
+    cluster_size = n_users // n_clusters
+    vectors = []
+
+    for i in range(n_clusters):
+        # Each cluster has a different center
+        center = np.random.randn(dim) * 2
+        # Users in cluster are variations around center
+        cluster_vectors = center + np.random.randn(cluster_size, dim) * 0.5
+        vectors.append(cluster_vectors)
+
+    # Add remaining users
+    remaining = n_users - n_clusters * cluster_size
+    if remaining > 0:
+        vectors.append(np.random.randn(remaining, dim))
+
+    return np.vstack(vectors)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Visualize user vectors with t-SNE and PCA")
+    parser.add_argument("--results-dir", type=str, help="Path to experiment results directory")
+    parser.add_argument("--vectors-file", type=str, help="Path to user vectors .npy file")
+    parser.add_argument("--profiles-file", type=str, help="Path to user profiles JSON file")
+    parser.add_argument("--output-dir", type=str, default=".", help="Output directory for plots")
+    parser.add_argument("--demo", action="store_true", help="Run demo with synthetic data")
+    args = parser.parse_args()
+
+    output_dir = Path(args.output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    if args.demo:
+        print("Running demo with synthetic user vectors...")
+        vectors = generate_synthetic_vectors(200, 64)
+        user_ids = list(range(200))
+        profiles = None
+        title_prefix = "[Demo] "
+    elif args.vectors_file:
+        vectors = np.load(args.vectors_file)
+        user_ids = list(range(len(vectors)))
+        profiles = None
+        if args.profiles_file:
+            profiles = load_profiles(Path(args.profiles_file))
+        title_prefix = ""
+    elif args.results_dir:
+        results_dir = Path(args.results_dir)
+        vectors, user_ids = load_user_vectors(results_dir)
+
+        # Try to find profiles
+        profiles = None
+        profile_paths = [
+            results_dir / "generated_profiles.json",
+            results_dir.parent / "profiles.json",
+            Path("../data/complex_profiles_v2/profiles_200.jsonl"),
+        ]
+        for pp in profile_paths:
+            if pp.exists():
+                profiles = load_profiles(pp)
+                print(f"Loaded {len(profiles)} profiles from {pp}")
+                break
+        title_prefix = ""
+    else:
+        print("Please provide --results-dir, --vectors-file, or --demo")
+        return
+
+    print(f"\nUser vectors shape: {vectors.shape}")
+    print(f"Number of users: {len(user_ids)}")
+
+    # Generate plots
+    print("\n=== Generating comparison plot ===")
+    plot_comparison(
+        vectors, user_ids, profiles,
+        output_path=output_dir / "user_vectors_comparison.png",
+        title_prefix=title_prefix
+    )
+
+    print("\n=== Generating PCA variance plot ===")
+    plot_pca_variance(
+        vectors,
+        output_path=output_dir / "user_vectors_pca_variance.png"
+    )
+
+    if profiles and len(profiles) >= len(user_ids):
+        print("\n=== Generating category plot ===")
+        plot_by_category(
+            vectors, user_ids, profiles,
+            output_path=output_dir / "user_vectors_by_category.png"
+        )
+
+    print("\n=== Done! ===")
+    print(f"Plots saved to {output_dir}")
+
+
+if __name__ == "__main__":
+    main()