feat: fix financebench
This commit is contained in:
Andy Lee
File diff suppressed because it is too large
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@@ -5,6 +5,7 @@ Downloads all PDFs and builds full LEANN datastore
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"""
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import argparse
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import os
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import re
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import time
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from concurrent.futures import ThreadPoolExecutor, as_completed
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@@ -139,14 +140,15 @@ class FinanceBenchSetup:
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start_time = time.time()
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# Initialize builder
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# Initialize builder with standard compact configuration
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builder = LeannBuilder(
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backend_name=backend,
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embedding_model=embedding_model,
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embedding_mode="sentence-transformers",
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graph_degree=32,
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complexity=64,
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is_recompute=False, # Store embeddings for speed
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is_recompute=True, # Enable recompute (no stored embeddings)
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is_compact=True, # Enable compact storage (pruned)
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num_threads=4,
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)
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@@ -185,6 +187,87 @@ class FinanceBenchSetup:
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return str(index_path)
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def build_faiss_flat_baseline(self, index_path: str, output_dir: str = "baseline"):
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"""Build FAISS flat baseline using the same embeddings as LEANN index"""
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print("🔨 Building FAISS Flat baseline...")
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import os
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import pickle
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import numpy as np
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from leann.api import compute_embeddings
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from leann_backend_hnsw import faiss
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os.makedirs(output_dir, exist_ok=True)
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baseline_path = os.path.join(output_dir, "faiss_flat.index")
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metadata_path = os.path.join(output_dir, "metadata.pkl")
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if os.path.exists(baseline_path) and os.path.exists(metadata_path):
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print(f"✅ Baseline already exists at {baseline_path}")
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return baseline_path
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# Read metadata from the built index
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meta_path = f"{index_path}.meta.json"
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with open(meta_path) as f:
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import json
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meta = json.loads(f.read())
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embedding_model = meta["embedding_model"]
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passage_source = meta["passage_sources"][0]
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passage_file = passage_source["path"]
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# Convert relative path to absolute
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if not os.path.isabs(passage_file):
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index_dir = os.path.dirname(index_path)
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passage_file = os.path.join(index_dir, os.path.basename(passage_file))
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print(f"📊 Loading passages from {passage_file}...")
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print(f"🤖 Using embedding model: {embedding_model}")
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# Load all passages for baseline
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passages = []
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passage_ids = []
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with open(passage_file, encoding="utf-8") as f:
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for line in f:
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if line.strip():
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data = json.loads(line)
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passages.append(data["text"])
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passage_ids.append(data["id"])
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print(f"📄 Loaded {len(passages)} passages")
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# Compute embeddings using the same method as LEANN
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print("🧮 Computing embeddings...")
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embeddings = compute_embeddings(
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passages,
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embedding_model,
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mode="sentence-transformers",
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use_server=False,
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)
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print(f"📐 Embedding shape: {embeddings.shape}")
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# Build FAISS flat index
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print("🏗️ Building FAISS IndexFlatIP...")
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dimension = embeddings.shape[1]
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index = faiss.IndexFlatIP(dimension)
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# Add embeddings to flat index
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embeddings_f32 = embeddings.astype(np.float32)
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index.add(embeddings_f32.shape[0], faiss.swig_ptr(embeddings_f32))
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# Save index and metadata
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faiss.write_index(index, baseline_path)
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with open(metadata_path, "wb") as f:
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pickle.dump(passage_ids, f)
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print(f"✅ FAISS baseline saved to {baseline_path}")
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print(f"✅ Metadata saved to {metadata_path}")
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print(f"📊 Total vectors: {index.ntotal}")
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return baseline_path
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def extract_pdf_text(self, pdf_path: Path) -> list[dict]:
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"""Extract and chunk text from a PDF file"""
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chunks = []
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@@ -300,6 +383,11 @@ def main():
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parser.add_argument("--max-workers", type=int, default=5, help="Parallel download workers")
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parser.add_argument("--skip-download", action="store_true", help="Skip PDF download")
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parser.add_argument("--skip-build", action="store_true", help="Skip index building")
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parser.add_argument(
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"--build-baseline-only",
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action="store_true",
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help="Only build FAISS baseline from existing index",
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)
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args = parser.parse_args()
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@@ -309,6 +397,24 @@ def main():
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setup = FinanceBenchSetup(args.data_dir)
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try:
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if args.build_baseline_only:
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# Only build baseline from existing index
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index_path = setup.index_dir / f"financebench_full_{args.backend}"
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index_file = f"{index_path}.index"
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meta_file = f"{index_path}.leann.meta.json"
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if not os.path.exists(index_file) or not os.path.exists(meta_file):
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print("❌ Index files not found:")
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print(f" Index: {index_file}")
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print(f" Meta: {meta_file}")
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print("💡 Run without --build-baseline-only to build the index first")
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exit(1)
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print(f"🔨 Building baseline from existing index: {index_path}")
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baseline_path = setup.build_faiss_flat_baseline(str(index_path))
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print(f"✅ Baseline built at {baseline_path}")
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return
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# Step 1: Download dataset
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setup.download_dataset()
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@@ -324,7 +430,12 @@ def main():
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backend=args.backend, embedding_model=args.embedding_model
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)
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# Step 4: Verify setup
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# Step 4: Build FAISS flat baseline
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print("\n🔨 Building FAISS flat baseline...")
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baseline_path = setup.build_faiss_flat_baseline(index_path)
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print(f"✅ Baseline built at {baseline_path}")
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# Step 5: Verify setup
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setup.verify_setup(index_path)
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else:
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print("⏭️ Skipping index building")
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214
benchmarks/financebench/verify_recall.py
Normal file
214
benchmarks/financebench/verify_recall.py
Normal file
@@ -0,0 +1,214 @@
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#!/usr/bin/env python3
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# /// script
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# requires-python = ">=3.9"
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# dependencies = [
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# "faiss-cpu",
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# "numpy",
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# "sentence-transformers",
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# "torch",
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# "tqdm",
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# ]
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# ///
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"""
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Independent recall verification script using standard FAISS.
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Creates two indexes (HNSW and Flat) and compares recall@3 at different complexities.
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"""
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import json
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import time
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from pathlib import Path
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import faiss
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import numpy as np
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from sentence_transformers import SentenceTransformer
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from tqdm import tqdm
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def compute_embeddings_direct(chunks: list[str], model_name: str) -> np.ndarray:
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"""
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Direct embedding computation using sentence-transformers.
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Copied logic to avoid dependency issues.
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"""
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print(f"Loading model: {model_name}")
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model = SentenceTransformer(model_name)
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print(f"Computing embeddings for {len(chunks)} chunks...")
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embeddings = model.encode(
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chunks,
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show_progress_bar=True,
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batch_size=32,
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convert_to_numpy=True,
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normalize_embeddings=False,
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)
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return embeddings.astype(np.float32)
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def load_financebench_queries(dataset_path: str, max_queries: int = 200) -> list[str]:
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"""Load FinanceBench queries from dataset"""
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queries = []
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with open(dataset_path, encoding="utf-8") as f:
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for line in f:
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if line.strip():
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data = json.loads(line)
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queries.append(data["question"])
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if len(queries) >= max_queries:
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break
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return queries
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def load_passages_from_leann_index(index_path: str) -> tuple[list[str], list[str]]:
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"""Load passages from LEANN index structure"""
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meta_path = f"{index_path}.meta.json"
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with open(meta_path) as f:
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meta = json.load(f)
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passage_source = meta["passage_sources"][0]
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passage_file = passage_source["path"]
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# Convert relative path to absolute
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if not Path(passage_file).is_absolute():
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index_dir = Path(index_path).parent
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passage_file = index_dir / Path(passage_file).name
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print(f"Loading passages from {passage_file}")
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passages = []
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passage_ids = []
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with open(passage_file, encoding="utf-8") as f:
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for line in tqdm(f, desc="Loading passages"):
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if line.strip():
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data = json.loads(line)
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passages.append(data["text"])
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passage_ids.append(data["id"])
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print(f"Loaded {len(passages)} passages")
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return passages, passage_ids
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def build_faiss_indexes(embeddings: np.ndarray) -> tuple[faiss.Index, faiss.Index]:
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"""Build FAISS indexes: Flat (ground truth) and HNSW"""
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dimension = embeddings.shape[1]
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# Build Flat index (ground truth)
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print("Building FAISS IndexFlatIP (ground truth)...")
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flat_index = faiss.IndexFlatIP(dimension)
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flat_index.add(embeddings)
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# Build HNSW index
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print("Building FAISS IndexHNSWFlat...")
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M = 32 # Same as LEANN default
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hnsw_index = faiss.IndexHNSWFlat(dimension, M, faiss.METRIC_INNER_PRODUCT)
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hnsw_index.hnsw.efConstruction = 200 # Same as LEANN default
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hnsw_index.add(embeddings)
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print(f"Built indexes with {flat_index.ntotal} vectors, dimension {dimension}")
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return flat_index, hnsw_index
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def evaluate_recall_at_k(
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query_embeddings: np.ndarray,
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flat_index: faiss.Index,
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hnsw_index: faiss.Index,
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passage_ids: list[str],
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k: int = 3,
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ef_search: int = 64,
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) -> float:
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"""Evaluate recall@k comparing HNSW vs Flat"""
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# Set search parameters for HNSW
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hnsw_index.hnsw.efSearch = ef_search
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total_recall = 0.0
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num_queries = query_embeddings.shape[0]
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for i in range(num_queries):
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query = query_embeddings[i : i + 1] # Keep 2D shape
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# Get ground truth from Flat index (standard FAISS API)
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flat_distances, flat_indices = flat_index.search(query, k)
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ground_truth_ids = {passage_ids[idx] for idx in flat_indices[0]}
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# Get results from HNSW index (standard FAISS API)
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hnsw_distances, hnsw_indices = hnsw_index.search(query, k)
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hnsw_ids = {passage_ids[idx] for idx in hnsw_indices[0]}
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# Calculate recall
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intersection = ground_truth_ids.intersection(hnsw_ids)
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recall = len(intersection) / k
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total_recall += recall
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if i < 3: # Show first few examples
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print(f" Query {i + 1}: Recall@{k} = {recall:.3f}")
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print(f" Flat: {list(ground_truth_ids)}")
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print(f" HNSW: {list(hnsw_ids)}")
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print(f" Intersection: {list(intersection)}")
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avg_recall = total_recall / num_queries
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return avg_recall
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def main():
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# Configuration
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dataset_path = "data/financebench_merged.jsonl"
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index_path = "data/index/financebench_full_hnsw.leann"
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embedding_model = "sentence-transformers/all-mpnet-base-v2"
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print("🔍 FAISS Recall Verification")
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print("=" * 50)
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# Check if files exist
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if not Path(dataset_path).exists():
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print(f"❌ Dataset not found: {dataset_path}")
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return
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if not Path(f"{index_path}.meta.json").exists():
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print(f"❌ Index metadata not found: {index_path}.meta.json")
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return
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# Load data
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print("📖 Loading FinanceBench queries...")
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queries = load_financebench_queries(dataset_path, max_queries=50)
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print(f"Loaded {len(queries)} queries")
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print("📄 Loading passages from LEANN index...")
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passages, passage_ids = load_passages_from_leann_index(index_path)
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# Compute embeddings
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print("🧮 Computing passage embeddings...")
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passage_embeddings = compute_embeddings_direct(passages, embedding_model)
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print("🧮 Computing query embeddings...")
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query_embeddings = compute_embeddings_direct(queries, embedding_model)
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# Build FAISS indexes
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print("🏗️ Building FAISS indexes...")
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flat_index, hnsw_index = build_faiss_indexes(passage_embeddings)
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# Test different efSearch values (equivalent to LEANN complexity)
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print("\n📊 Evaluating Recall@3 at different efSearch values...")
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ef_search_values = [16, 32, 64, 128, 256]
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for ef_search in ef_search_values:
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print(f"\n🧪 Testing efSearch = {ef_search}")
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start_time = time.time()
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recall = evaluate_recall_at_k(
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query_embeddings, flat_index, hnsw_index, passage_ids, k=3, ef_search=ef_search
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)
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elapsed = time.time() - start_time
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print(
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f"📈 efSearch {ef_search}: Recall@3 = {recall:.3f} ({recall * 100:.1f}%) in {elapsed:.2f}s"
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)
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print("\n✅ Verification completed!")
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print("\n📋 Summary:")
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print(" - Built independent FAISS Flat and HNSW indexes")
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print(" - Compared recall@3 at different efSearch values")
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print(" - Used same embedding model as LEANN")
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print(" - This validates LEANN's recall measurements")
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if __name__ == "__main__":
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main()
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@@ -46,6 +46,14 @@ dependencies = [
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"pathspec>=0.12.1",
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"nbconvert>=7.16.6",
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"gitignore-parser>=0.1.12",
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# AST-aware code chunking dependencies
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"astchunk>=0.1.0",
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"tree-sitter>=0.20.0",
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||||
"tree-sitter-python>=0.20.0",
|
||||
"tree-sitter-java>=0.20.0",
|
||||
"tree-sitter-c-sharp>=0.20.0",
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"tree-sitter-typescript>=0.20.0",
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"faiss-cpu>=1.12.0",
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]
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[project.optional-dependencies]
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|
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308
uv.lock
generated
308
uv.lock
generated
@@ -1,5 +1,5 @@
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version = 1
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revision = 2
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revision = 3
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requires-python = ">=3.9"
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resolution-markers = [
|
||||
"python_full_version >= '3.12'",
|
||||
@@ -198,6 +198,27 @@ wheels = [
|
||||
{ url = "https://files.pythonhosted.org/packages/81/29/5ecc3a15d5a33e31b26c11426c45c501e439cb865d0bff96315d86443b78/appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c", size = 4321, upload-time = "2024-02-06T09:43:09.663Z" },
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "astchunk"
|
||||
version = "0.1.0"
|
||||
source = { registry = "https://pypi.org/simple" }
|
||||
dependencies = [
|
||||
{ name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
|
||||
{ name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" },
|
||||
{ name = "numpy", version = "2.3.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
|
||||
{ name = "pyrsistent" },
|
||||
{ name = "tree-sitter", version = "0.23.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
|
||||
{ name = "tree-sitter", version = "0.25.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },
|
||||
{ name = "tree-sitter-c-sharp" },
|
||||
{ name = "tree-sitter-java" },
|
||||
{ name = "tree-sitter-python" },
|
||||
{ name = "tree-sitter-typescript" },
|
||||
]
|
||||
sdist = { url = "https://files.pythonhosted.org/packages/db/2a/7a35e2fac7d550265ae2ee40651425083b37555f921d1a1b77c3f525e0df/astchunk-0.1.0.tar.gz", hash = "sha256:f4dff0ef8b3b3bcfeac363384db1e153f74d4c825dc2e35864abfab027713be4", size = 18093, upload-time = "2025-06-19T04:37:25.34Z" }
|
||||
wheels = [
|
||||
{ url = "https://files.pythonhosted.org/packages/be/84/5433ab0e933b572750cb16fd7edf3d6c7902b069461a22ec670042752a4d/astchunk-0.1.0-py3-none-any.whl", hash = "sha256:33ada9fc3620807fdda5846fa1948af463f281a60e0d43d4f3782b6dbb416d24", size = 15396, upload-time = "2025-06-19T04:37:23.87Z" },
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "asttokens"
|
||||
version = "3.0.0"
|
||||
@@ -1147,6 +1168,74 @@ wheels = [
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Reference in New Issue
Block a user