Agent Skills: Embedding Comparison Skill

Embedding Comparison Skill

Evaluate and compare different embedding models on your actual data.

Overview

The default all-MiniLM-L6-v2 model is a good starting point, but may not be optimal for your specific content. This skill helps you:

• Benchmark different models on your data
• Compare retrieval quality
• Make informed model selection decisions

Why Compare Models?

| Factor | Impact | |--------|--------| | Domain vocabulary | Technical jargon may need specialized models | | Document length | Some models handle long text better | | Query style | Conversational vs keyword queries | | Speed requirements | Larger models = better quality but slower | | Memory constraints | Some models need significant RAM |

Candidate Models

General Purpose

| Model | Dimensions | Speed | Quality | Size | |-------|-----------|-------|---------|------| | all-MiniLM-L6-v2 | 384 | Fast | Good | 80MB | | all-MiniLM-L12-v2 | 384 | Medium | Better | 120MB | | all-mpnet-base-v2 | 768 | Slow | Best | 420MB |

Specialized

| Model | Best For | Dimensions | |-------|----------|-----------| | multi-qa-MiniLM-L6-cos-v1 | Question answering | 384 | | msmarco-MiniLM-L6-cos-v5 | Search/retrieval | 384 | | paraphrase-MiniLM-L6-v2 | Semantic similarity | 384 |

Code-Focused

| Model | Best For | Source | |-------|----------|--------| | krlvi/sentence-t5-base-nlpl-code_search_net | Code search | HuggingFace | | flax-sentence-embeddings/st-codesearch-distilroberta-base | Code + docs | HuggingFace |

Benchmarking Framework

Step 1: Create Test Dataset

#!/usr/bin/env python3
"""Create a test dataset for embedding comparison."""

from typing import List, Dict
import json

def create_test_dataset(
    documents: List[str],
    queries: List[str],
    relevance: Dict[str, List[int]]
) -> Dict:
    """
    Create a test dataset.

    Args:
        documents: List of documents to search
        queries: List of test queries
        relevance: Dict mapping query index to relevant document indices

    Returns:
        Test dataset dict
    """
    return {
        "documents": documents,
        "queries": queries,
        "relevance": relevance
    }


# Example: Create test dataset from your actual content
def create_from_qdrant(collection_name: str, sample_size: int = 50) -> Dict:
    """Create test dataset from existing Qdrant collection."""
    from qdrant_client import QdrantClient

    client = QdrantClient(url="http://localhost:6333")

    # Scroll through collection to get samples
    results = client.scroll(
        collection_name=collection_name,
        limit=sample_size,
        with_payload=True
    )

    documents = [p.payload.get("content", "") for p in results[0]]

    # You'll need to manually create queries and mark relevance
    # This is the ground truth that benchmarks against

    return {
        "documents": documents,
        "queries": [],  # Fill in manually
        "relevance": {}  # Fill in manually
    }


# Example test dataset
EXAMPLE_DATASET = {
    "documents": [
        "Python is a high-level programming language known for readability.",
        "FastAPI is a modern web framework for building APIs with Python.",
        "Qdrant is a vector database for AI applications.",
        "Docker containers provide isolated runtime environments.",
        "REST APIs use HTTP methods for client-server communication.",
    ],
    "queries": [
        "How do I build a web API?",
        "What is a vector database?",
        "How do I containerize my application?",
    ],
    "relevance": {
        "0": [1, 4],  # Query 0 is relevant to docs 1 and 4
        "1": [2],     # Query 1 is relevant to doc 2
        "2": [3],     # Query 2 is relevant to doc 3
    }
}

if __name__ == "__main__":
    with open("test_dataset.json", "w") as f:
        json.dump(EXAMPLE_DATASET, f, indent=2)
    print("Created test_dataset.json")

Step 2: Benchmark Script

#!/usr/bin/env python3
"""Benchmark embedding models on test dataset."""

import json
import time
from typing import Dict, List
import numpy as np
from sentence_transformers import SentenceTransformer

# Models to compare
MODELS = [
    "all-MiniLM-L6-v2",
    "all-MiniLM-L12-v2",
    "all-mpnet-base-v2",
    "multi-qa-MiniLM-L6-cos-v1",
    "msmarco-MiniLM-L6-cos-v5",
]


def cosine_similarity(a: np.ndarray, b: np.ndarray) -> float:
    """Compute cosine similarity between two vectors."""
    return np.dot(a, b) / (np.linalg.norm(a) * np.linalg.norm(b))


def compute_metrics(
    model: SentenceTransformer,
    documents: List[str],
    queries: List[str],
    relevance: Dict[str, List[int]],
    k: int = 3
) -> Dict:
    """
    Compute retrieval metrics for a model.

    Metrics:
    - Precision@k: Fraction of top-k results that are relevant
    - Recall@k: Fraction of relevant docs found in top-k
    - MRR: Mean Reciprocal Rank
    """
    # Encode documents
    doc_embeddings = model.encode(documents)

    precisions = []
    recalls = []
    reciprocal_ranks = []

    for q_idx, query in enumerate(queries):
        q_key = str(q_idx)
        if q_key not in relevance:
            continue

        relevant_docs = set(relevance[q_key])

        # Encode query and compute similarities
        q_embedding = model.encode([query])[0]
        similarities = [
            cosine_similarity(q_embedding, doc_emb)
            for doc_emb in doc_embeddings
        ]

        # Get top-k results
        top_k_indices = np.argsort(similarities)[-k:][::-1]

        # Precision@k
        hits = len(set(top_k_indices) & relevant_docs)
        precisions.append(hits / k)

        # Recall@k
        recalls.append(hits / len(relevant_docs))

        # MRR (reciprocal rank of first relevant result)
        for rank, idx in enumerate(top_k_indices, 1):
            if idx in relevant_docs:
                reciprocal_ranks.append(1 / rank)
                break
        else:
            reciprocal_ranks.append(0)

    return {
        "precision_at_k": np.mean(precisions),
        "recall_at_k": np.mean(recalls),
        "mrr": np.mean(reciprocal_ranks)
    }


def benchmark_model(model_name: str, dataset: Dict) -> Dict:
    """Benchmark a single model."""
    print(f"\nBenchmarking: {model_name}")

    # Load model (time it)
    load_start = time.perf_counter()
    model = SentenceTransformer(model_name)
    load_time = time.perf_counter() - load_start

    # Time encoding
    encode_start = time.perf_counter()
    _ = model.encode(dataset["documents"])
    encode_time = time.perf_counter() - encode_start

    # Compute retrieval metrics
    metrics = compute_metrics(
        model,
        dataset["documents"],
        dataset["queries"],
        dataset["relevance"]
    )

    # Get model info
    test_embedding = model.encode(["test"])[0]

    return {
        "model": model_name,
        "dimensions": len(test_embedding),
        "load_time_s": round(load_time, 2),
        "encode_time_s": round(encode_time, 3),
        "encode_per_doc_ms": round(encode_time / len(dataset["documents"]) * 1000, 2),
        **{k: round(v, 3) for k, v in metrics.items()}
    }


def run_benchmark(dataset_path: str = "test_dataset.json") -> List[Dict]:
    """Run full benchmark."""
    with open(dataset_path) as f:
        dataset = json.load(f)

    print(f"Dataset: {len(dataset['documents'])} docs, {len(dataset['queries'])} queries")

    results = []
    for model_name in MODELS:
        try:
            result = benchmark_model(model_name, dataset)
            results.append(result)
            print(f"  P@3: {result['precision_at_k']:.3f}, MRR: {result['mrr']:.3f}")
        except Exception as e:
            print(f"  Error: {e}")

    return results


def print_results_table(results: List[Dict]):
    """Print results as formatted table."""
    print("\n" + "=" * 80)
    print("BENCHMARK RESULTS")
    print("=" * 80)

    # Header
    print(f"{'Model':<35} {'Dim':>5} {'P@3':>6} {'R@3':>6} {'MRR':>6} {'ms/doc':>8}")
    print("-" * 80)

    # Sort by MRR (or your preferred metric)
    for r in sorted(results, key=lambda x: -x['mrr']):
        print(f"{r['model']:<35} {r['dimensions']:>5} {r['precision_at_k']:>6.3f} "
              f"{r['recall_at_k']:>6.3f} {r['mrr']:>6.3f} {r['encode_per_doc_ms']:>8.2f}")

    print("=" * 80)


if __name__ == "__main__":
    results = run_benchmark()
    print_results_table(results)

    # Save results
    with open("benchmark_results.json", "w") as f:
        json.dump(results, f, indent=2)
    print("\nResults saved to benchmark_results.json")

Decision Framework

When to Use Different Models

all-MiniLM-L6-v2 (default)
├── Fast enough for real-time
├── Good general quality
├── Low memory footprint
└── Use when: Starting out, general content

all-MiniLM-L12-v2
├── Slightly better quality
├── Still reasonably fast
└── Use when: Quality matters more than speed

all-mpnet-base-v2
├── Best quality
├── Significantly slower
├── Higher memory usage
└── Use when: Accuracy is critical, batch processing OK

multi-qa-MiniLM-L6-cos-v1
├── Optimized for Q&A
├── Better with question-form queries
└── Use when: Building Q&A system, FAQ retrieval

msmarco-MiniLM-L6-cos-v5
├── Optimized for search
├── Better with keyword-style queries
└── Use when: Building search engine, keyword queries

Quick Selection Guide

| Your Content | Recommended Model | |--------------|-------------------| | General documentation | all-MiniLM-L6-v2 | | Technical/code docs | msmarco-MiniLM-L6-cos-v5 | | Q&A / FAQ | multi-qa-MiniLM-L6-cos-v1 | | High-stakes retrieval | all-mpnet-base-v2 | | Mixed content | Run benchmark on your data |

Switching Models

After deciding on a model:

# 1. Update environment
export EMBEDDING_MODEL=all-mpnet-base-v2

# 2. Re-embed all collections (embeddings aren't portable between models!)
python scripts/reembed_collections.py

# 3. Rebuild router embeddings
python scripts/rebuild_router.py

Important: Different models produce different dimensional embeddings. You cannot mix embeddings from different models in the same collection!

Reembedding Script

#!/usr/bin/env python3
"""Re-embed all collections with a new model."""

import os
from qdrant_client import QdrantClient
from qdrant_client.models import Distance, VectorParams, PointStruct
from sentence_transformers import SentenceTransformer

NEW_MODEL = os.getenv("EMBEDDING_MODEL", "all-MiniLM-L6-v2")
QDRANT_URL = os.getenv("QDRANT_URL", "http://localhost:6333")

def reembed_collection(collection_name: str, model: SentenceTransformer, client: QdrantClient):
    """Re-embed a single collection."""

    # Get existing data
    results = client.scroll(
        collection_name=collection_name,
        limit=10000,
        with_payload=True
    )

    points = results[0]
    if not points:
        print(f"  {collection_name}: empty, skipping")
        return

    # Extract documents
    documents = [p.payload.get("content", "") for p in points]

    # Re-embed
    new_embeddings = model.encode(documents).tolist()
    vector_size = len(new_embeddings[0])

    # Delete and recreate collection
    client.delete_collection(collection_name)
    client.create_collection(
        collection_name=collection_name,
        vectors_config=VectorParams(size=vector_size, distance=Distance.COSINE)
    )

    # Re-add points
    new_points = [
        PointStruct(
            id=p.id,
            vector=new_embeddings[i],
            payload=p.payload
        )
        for i, p in enumerate(points)
    ]

    client.upsert(collection_name=collection_name, points=new_points)
    print(f"  {collection_name}: re-embedded {len(points)} documents")


def main():
    print(f"Re-embedding with model: {NEW_MODEL}")

    model = SentenceTransformer(NEW_MODEL)
    client = QdrantClient(url=QDRANT_URL)

    collections = client.get_collections().collections
    print(f"Found {len(collections)} collections")

    for coll in collections:
        reembed_collection(coll.name, model, client)

    print("✅ Re-embedding complete!")


if __name__ == "__main__":
    main()

Refinement Notes

Track findings from your benchmarks.

• [ ] Created test dataset from real content
• [ ] Ran benchmark on candidate models
• [ ] Selected optimal model for use case
• [ ] Re-embedded collections
• [ ] Verified retrieval quality improved