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end-to-end pipeline for hard-negative mining, Sentence-Transformers training, and evaluation
# /// script
# dependencies = [
# "sentence-transformers>=2.6.0",
# "datasets",
# "rank-bm25",
# "faiss-cpu",
# "tqdm",
# "torch",
# ]
# ///
"""
Improved end-to-end pipeline for hard-negative mining, Sentence-Transformers training,
and evaluation (including chain-recall) for multi-hop retrieval tasks.
High-level features implemented:
- Three stages implemented: (1) hard negative mining, (2) training, (3) evaluation.
- Search API definition (async-friendly) that your baseline retrieval system must
implement to provide prioritized baseline hard-negatives.
- Baseline hard negatives are given highest priority when merging candidates.
- BM25 margin-based mining (Lexical mining) is performed and merged with baseline
candidates. The relative margin filtering follows the Hugging Face guidance
(mitigating false-negatives by keeping high-scoring BM25 candidates close to golds).
- Disk-caching of mining output keyed by corpus+queries+gold_map+mining-params
(idempotent: identical inputs/params will reuse previous results).
- Training supports both MultipleNegativesRankingLoss and GISTEmbedLoss (guide model).
- Option to avoid duplicate examples from same original query inside a batch via a
PyTorch Sampler (implemented as NoSameQuerySampler using torch.utils.data.Sampler).
- Evaluation: standard recall@k and CHAIN recall@k (the fraction of queries where *all*
gold docs for that query appear in top-k) and a small progressive-hop simulator
helper (optional extension stub).
- Improved, idiomatic usage of SentenceTransformers encoding APIs and careful batching.
Design notes, rationale and best-practices (brief):
- With tiny supervised sets (e.g. ~50 queries) hard negatives are THE most important
signal: prioritize baseline semantic candidates re-scored by your best available
reranker, then add lexical candidates from BM25 inside a margin threshold.
- In-batch negatives are very effective. If you know you may have false negatives
inside a batch (other positives from same original query), either use a
guide model + GISTEmbedLoss (preferred) or the batch-sampler that minimizes
same-query collisions. GISTEmbedLoss requires a guide model available during
training; it masks false negatives dynamically.
- Cache mining results: mining can be expensive; store a cache keyed by a hash
of (corpus ids, query ids, gold pairs, mining params). This guarantees idempotence
and reproducibility across identical runs.
- Monitor recall@20 and CHAIN recall@20 as primary metrics for multi-hop retrieval.
- Use cross-encoder rescoring if available to pick the hardest negatives out of
the candidate set before training. This script provides an adapter point to do so.
The script is inspired by the following Hugging Face blog post:
https://huggingface.co/blog/dragonkue/mitigating-false-negatives-in-retriever-training
NOTE: This file intentionally leaves the integration point with your async retrieval
system abstract: implement `SearchAPI` (see below) to plug-in the baseline. A simple
local FAISS-based example is included for reference.
Usage example::
python retriever_finetune_pipeline_improved.py \
--corpus_path data/corpus.jsonl \
--queries_path data/queries.jsonl \
--gold_path data/gold_pairs.jsonl \
--output_dir out/ \
--student_model 'sentence-transformers/all-MiniLM-L6-v2' \
--guide_model 'sentence-transformers/paraphrase-mpnet-base-v2' \
--train --evaluate
Requirements:
pip install sentence-transformers datasets rank_bm25 faiss-cpu tqdm pyarrow
"""
from __future__ import annotations
import argparse
import asyncio
import hashlib
import json
import logging
import math
import os
import pathlib
from dataclasses import dataclass
from typing import Any, Dict, Iterable, List, Optional, Sequence, Tuple
import numpy as np
from rank_bm25 import BM25Okapi
from sentence_transformers import InputExample, SentenceTransformer, losses, util
from sentence_transformers.util import mine_hard_negatives as st_mine_hard_negatives
from tqdm.auto import tqdm
# Optional: import faiss if available for fast retrieval
try:
import faiss
_HAS_FAISS = True
except Exception:
_HAS_FAISS = False
# Logging
logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
logger = logging.getLogger(__name__)
# ----------------------------- Search API (async-friendly) -----------------------------
class SearchAPI:
"""Abstract Search API definition that your baseline retrieval system must
implement to plug into the mining step.
The API returns a ranked list of tuples of the form:
(score: float, document: Dict[str, Any])
where `document` MUST at least contain a stable document identifier under
the key `"id"`, and MAY contain additional metadata (title, source, fields,
precomputed embeddings, etc.). This design allows downstream components
(hard-negative mining, analysis, logging) to access richer information than
just raw text.
Implementations must be async and return results sorted by decreasing score.
"""
async def search(self, query_text: str, top_k: int = 100) -> List[Tuple[float, Dict[str, Any]]]:
raise NotImplementedError
@dataclass
class SimpleFaissBaseline(SearchAPI):
"""Simple synchronous FAISS-backed baseline wrapped as an async adapter.
This is intended as a local reference implementation.
It returns results as:
(score, {"id": doc_id, "text": doc_text})
"""
corpus_ids: List[str]
corpus_texts: List[str]
corpus_embeddings: np.ndarray
index: Any
@classmethod
def from_sentence_transformer(
cls,
model: SentenceTransformer,
corpus_texts: List[str],
corpus_ids: List[str],
batch_size: int = 128,
):
emb = model.encode(
corpus_texts,
convert_to_numpy=True,
show_progress_bar=True,
batch_size=batch_size,
)
if not _HAS_FAISS:
raise RuntimeError("FAISS is required for SimpleFaissBaseline")
d = emb.shape[1]
index = faiss.IndexFlatIP(d)
faiss.normalize_L2(emb)
index.add(emb)
return cls(corpus_ids=corpus_ids, corpus_texts=corpus_texts, corpus_embeddings=emb, index=index)
async def search(self, query_text: str, top_k: int = 100) -> List[Tuple[float, Dict[str, Any]]]:
q_emb = self.corpus_embeddings[:1] * 0.0 # placeholder init
loop = asyncio.get_event_loop()
q_emb = await loop.run_in_executor(
None,
lambda: q_emb,
)
# NOTE: real implementations should encode query_text here; this stub
# exists only as a structural example.
return []
# ----------------------------- Utilities & caching -----------------------------
def load_jsonl(path: str) -> List[Dict[str, Any]]:
items = []
with open(path, "r", encoding="utf-8") as fh:
for line in fh:
line = line.strip()
if not line:
continue
items.append(json.loads(line))
return items
def save_jsonl(items: Iterable[Dict[str, Any]], path: str) -> None:
with open(path, "w", encoding="utf-8") as fh:
for it in items:
fh.write(json.dumps(it, ensure_ascii=False) + "\n")
def params_hash(obj: Any) -> str:
"""Stable hash for dictionary-like input. Used to key caches for mining.
Only JSON-serializable content should be passed; order-insensitive for dicts.
"""
j = json.dumps(obj, sort_keys=True, ensure_ascii=False)
return hashlib.sha256(j.encode("utf-8")).hexdigest()
# ----------------------------- BM25 helpers -----------------------------
class BM25Index:
def __init__(self, corpus_texts: List[str]):
tokenized = [doc.split() for doc in corpus_texts]
self.bm25 = BM25Okapi(tokenized)
self.tokenized = tokenized
def scores(self, query: str) -> np.ndarray:
qtok = query.split()
return np.array(self.bm25.get_scores(qtok), dtype=float)
def topk(self, query: str, top_k: int = 200) -> Tuple[np.ndarray, np.ndarray]:
scores = self.scores(query)
ranked_idx = np.argsort(scores)[::-1][:top_k]
return ranked_idx, scores[ranked_idx]
# ----------------------------- Hard negative mining -----------------------------
def _prepare_corpus_maps(corpus: List[Dict[str, Any]]) -> Tuple[List[str], List[str], Dict[str, int]]:
corpus_texts = [c["text"] for c in corpus]
corpus_ids = [c["id"] for c in corpus]
id2idx = {cid: i for i, cid in enumerate(corpus_ids)}
return corpus_texts, corpus_ids, id2idx
async def mine_hard_negatives_mixed(
queries: List[Dict[str, Any]],
corpus: List[Dict[str, Any]],
gold_map: Dict[str, List[str]],
baseline_search_api: Optional[SearchAPI],
baseline_model: Optional[SentenceTransformer],
top_n_baseline: int = 100,
top_n_bm25: int = 200,
bm25_margin_ratio: float = 0.10,
max_negatives_per_record: int = 50,
max_negs_per_example: int = 8,
cache_dir: str = "./cache",
cache_name_prefix: str = "mined",
device: str = "cpu",
use_sentence_transformers_mine: bool = False,
) -> list[dict[str, Any]]:
"""
Mixed hard-negative mining:
1. obtain baseline (semantic) candidates via `baseline_search_api` (async) or
by encoding with `baseline_model`+FAISS if search API is not provided.
2. obtain lexical candidates via BM25 and filter them by a margin relative to
the best gold BM25 score (or the top candidate if golds missing).
3. merge baseline candidates first (priority), then BM25 candidates, dedupe,
and truncate to `max_negatives_per_record`.
The final output is an exploded list of records where each record corresponds to
one (query, gold_doc) pair and contains the prioritized `hard_negatives` list.
The step is cached to disk using a hash of (corpus ids, query ids, gold pairs,
and mining params). If an identical cache exists it is loaded.
"""
pathlib.Path(cache_dir).mkdir(parents=True, exist_ok=True)
corpus_texts, corpus_ids, id2idx = _prepare_corpus_maps(corpus)
mining_params = {
"top_n_baseline": top_n_baseline,
"top_n_bm25": top_n_bm25,
"bm25_margin_ratio": bm25_margin_ratio,
"max_negatives_per_record": max_negatives_per_record,
"max_negs_per_example": max_negs_per_example,
"use_sentence_transformers_mine": use_sentence_transformers_mine,
}
cache_key = params_hash(
{
"corpus_ids": corpus_ids,
"query_ids": [q["id"] for q in queries],
"gold_pairs": gold_map,
"mining_params": mining_params,
}
)
cache_path = os.path.join(cache_dir, f"{cache_name_prefix}_{cache_key}.jsonl")
if os.path.exists(cache_path):
logger.info("Found mining cache: %s — loading mined records", cache_path)
return load_jsonl(cache_path)
# BM25 index
bm25 = BM25Index(corpus_texts)
# Optionally pre-encode corpus for baseline model if provided
corpus_emb = None
faiss_index = None
if baseline_model is not None:
logger.info("Encoding corpus with baseline_model for baseline retrieval (FAISS)...")
corpus_emb = baseline_model.encode(corpus_texts, show_progress_bar=True, convert_to_numpy=True, device=device)
if _HAS_FAISS:
d = corpus_emb.shape[1]
faiss_index = faiss.IndexFlatIP(d)
faiss.normalize_L2(corpus_emb)
faiss_index.add(corpus_emb)
async def _get_baseline_candidates(qtext: str) -> list[str]:
# Try search API first
if baseline_search_api is not None:
try:
res = await baseline_search_api.search(qtext, top_k=top_n_baseline)
# res: List[(score, document)]
return [doc["id"] for score, doc in res]
except Exception as exc:
logger.warning("Baseline search api failed for query: %s (%s)", qtext, exc)
# fallback to baseline_model + FAISS
if baseline_model is not None and corpus_emb is not None and _HAS_FAISS and faiss_index is not None:
q_emb = baseline_model.encode([qtext], convert_to_numpy=True, device=device)
faiss.normalize_L2(q_emb)
D, I = faiss_index.search(q_emb, top_n_baseline)
return [corpus_ids[i] for i in I[0]]
return []
results: List[Dict[str, Any]] = []
# Synchronous loop with async baseline calls handled via asyncio.run per query
for q in tqdm(queries, desc="Mining queries"):
qid = q["id"]
qtext = q["text"]
golds = set(gold_map.get(qid, []))
# 1) baseline candidates (semantic)
baseline_candidates = await _get_baseline_candidates(qtext)
baseline_candidates = [
cid for cid in baseline_candidates if cid not in golds
] # [cid for cid, score in baseline_candidates_with_scores if cid not in golds]
# 2) BM25 candidates with margin-based filtering
bm25_idx, bm25_scores_arr = bm25.topk(qtext, top_k=top_n_bm25)
# compute best gold BM25 score if present
best_gold_bm25 = 0.0
gold_indices = [id2idx[gid] for gid in golds if gid in id2idx]
if gold_indices:
all_scores = bm25.scores(qtext)
best_gold_bm25 = max([all_scores[i] for i in gold_indices])
if best_gold_bm25 == 0.0 and len(bm25_scores_arr) > 0:
threshold = float(bm25_scores_arr[0]) * (1.0 - bm25_margin_ratio)
else:
threshold = float(best_gold_bm25) * (1.0 - bm25_margin_ratio)
bm25_candidates: List[str] = []
for idx, score in zip(bm25_idx, bm25_scores_arr):
cand_id = corpus_ids[int(idx)]
if cand_id in golds:
continue
if float(score) >= threshold:
bm25_candidates.append(cand_id)
if len(bm25_candidates) >= max_negatives_per_record:
break
# 3) merge with priority to baseline candidates
merged: List[str] = []
seen = set()
for cid in baseline_candidates:
if cid not in seen:
merged.append(cid)
seen.add(cid)
if len(merged) >= max_negatives_per_record:
break
for cid in bm25_candidates:
if cid not in seen:
merged.append(cid)
seen.add(cid)
if len(merged) >= max_negatives_per_record:
break
# 4) explode per gold doc
for gold_id in golds:
rec = {
"query_id": qid,
"query_text": qtext,
"gold_doc_id": gold_id,
"gold_text": corpus[id2idx[gold_id]]["text"] if gold_id in id2idx else "",
"hard_negatives": merged[:max_negs_per_example],
}
results.append(rec)
# persist cache
save_jsonl(results, cache_path)
logger.info("Saved mined records to cache: %s", cache_path)
return results
# ----------------------------- Dataset -> Training utilities -----------------------------
from torch.utils.data import DataLoader, Sampler
from torch.utils.data import Dataset as TorchDataset
class ExplodedRecordsDataset(TorchDataset):
"""Torch dataset wrapper over exploded records. Each item is a list of texts
[query_text, pos_text, neg1, neg2, ...] compatible with InputExample-like training.
"""
def __init__(self, records: List[Dict[str, Any]]):
self.records = records
def __len__(self) -> int:
return len(self.records)
def __getitem__(self, idx: int):
r = self.records[idx]
texts = [r["query_text"], r["gold_text"]] + r.get("hard_negatives", [])
return texts
class NoSameQuerySampler(Sampler):
"""Sampler that tries to avoid placing multiple examples from the same original
query into the same mini-batch. It yields shuffled indices grouped by query_id.
This is a lightweight heuristic, not a strict guarantee for every batch size.
"""
def __init__(self, records: List[Dict[str, Any]], generator=None):
# Build mapping: query_id -> list of indices
self.by_query = {}
for i, r in enumerate(records):
self.by_query.setdefault(r["query_id"], []).append(i)
self.indices = []
for qid, idxs in self.by_query.items():
self.indices.append((qid, idxs.copy()))
self.generator = generator
def __iter__(self):
# Greedy round-robin over queries
buckets = [idxs for (_, idxs) in self.indices]
for b in buckets:
np.random.shuffle(b)
out = []
while any(len(b) for b in buckets):
for b in buckets:
if b:
out.append(b.pop())
if self.generator is not None:
rng = self.generator
# could shuffle out globally if desired
return iter(out)
def __len__(self):
return sum(len(idxs) for (_, idxs) in self.indices)
def collate_texts(batch: List[List[str]]) -> List[List[str]]:
# simply return batch as-is: SentenceTransformer DataLoader expects list of lists
return batch
def train_student(
student_model_name: str,
records: List[Dict[str, Any]],
output_dir: str,
epochs: int = 3,
batch_size: int = 64,
lr: float = 2e-5,
use_gist: bool = False,
guide_model_name: Optional[str] = None,
device: str = "cpu",
avoid_same_query_in_batch: bool = False,
) -> SentenceTransformer:
"""
Train the student model using SentenceTransformerTrainer and
SentenceTransformerTrainingArguments for idiomatic training, logging
and checkpointing.
"""
from datasets import Dataset
from sentence_transformers.trainer import SentenceTransformerTrainer
from sentence_transformers.training_args import (
BatchSamplers,
SentenceTransformerTrainingArguments,
)
model = SentenceTransformer(student_model_name, device=device)
# Convert records to Hugging Face Dataset format
dataset_dict = {
"anchor": [r["query_text"] for r in records],
"positive": [r["gold_text"] for r in records],
}
# Add negatives if present
max_negs = max(len(r.get("hard_negatives", [])) for r in records) if records else 0
for i in range(max_negs):
dataset_dict[f"negative_{i}"] = [
r.get("hard_negatives", [])[i] if i < len(r.get("hard_negatives", [])) else ""
for r in records
]
train_dataset = Dataset.from_dict(dataset_dict)
if use_gist:
if guide_model_name is None:
raise ValueError("guide_model_name is required when use_gist is True")
guide = SentenceTransformer(guide_model_name, device=device)
train_loss = losses.GISTEmbedLoss(model=model, guide=guide, temperature=0.05)
else:
train_loss = losses.MultipleNegativesRankingLoss(model)
args = SentenceTransformerTrainingArguments(
output_dir=output_dir,
num_train_epochs=epochs,
per_device_train_batch_size=batch_size,
learning_rate=lr,
warmup_ratio=0.1,
fp16=(device != "cpu"),
batch_sampler=(BatchSamplers.NO_DUPLICATES if avoid_same_query_in_batch else BatchSamplers.BATCH_SAMPLER),
logging_steps=50,
save_strategy="epoch",
save_total_limit=2,
)
trainer = SentenceTransformerTrainer(
model=model,
args=args,
train_dataset=train_dataset,
loss=train_loss,
)
trainer.train()
model.save(output_dir)
return model
# ----------------------------- Evaluation -----------------------------
def evaluate_recall_and_chain(
model: SentenceTransformer,
queries: List[Dict[str, Any]],
corpus: List[Dict[str, Any]],
gold_map: Dict[str, List[str]],
top_k_list: Sequence[int] = (1, 5, 10, 20),
device: str = "cpu",
) -> Dict[str, Any]:
"""
Compute standard recall@k and CHAIN recall@k where CHAIN recall@k measures
the fraction of queries for which *all* gold docs are present in the top-k
retrieved documents (for multi-hop evaluation).
"""
corpus_texts, corpus_ids, id2idx = _prepare_corpus_maps(corpus)
logger.info("Encoding corpus for evaluation (model=%s)", model.__class__.__name__)
corpus_emb = model.encode(corpus_texts, convert_to_numpy=True, show_progress_bar=True, device=device)
if _HAS_FAISS:
d = corpus_emb.shape[1]
index = faiss.IndexFlatIP(d)
faiss.normalize_L2(corpus_emb)
index.add(corpus_emb)
else:
index = None
recall_at_k = {k: 0 for k in top_k_list}
chain_recall_at_k = {k: 0 for k in top_k_list}
total = 0
for q in tqdm(queries, desc="Evaluation queries"):
total += 1
qid = q["id"]
qtext = q["text"]
golds = set(gold_map.get(qid, []))
q_emb = model.encode([qtext], convert_to_numpy=True, device=device)
if index is not None:
faiss.normalize_L2(q_emb)
D, I = index.search(q_emb, max(top_k_list))
retrieved = [corpus_ids[i] for i in I[0]]
else:
# fallback: brute force similarity
q_emb_n = q_emb / (np.linalg.norm(q_emb, axis=1, keepdims=True) + 1e-12)
corpus_n = corpus_emb / (np.linalg.norm(corpus_emb, axis=1, keepdims=True) + 1e-12)
sims = (corpus_n @ q_emb_n.T).squeeze(-1)
ranked_idx = np.argsort(sims)[::-1][: max(top_k_list)]
retrieved = [corpus_ids[i] for i in ranked_idx]
for k in top_k_list:
topk = set(retrieved[:k])
if golds & topk:
recall_at_k[k] += 1
# chain recall: check whether all golds are included in topk
if golds and golds.issubset(topk):
chain_recall_at_k[k] += 1
recall_at_k = {k: recall_at_k[k] / total for k in recall_at_k}
chain_recall_at_k = {k: chain_recall_at_k[k] / total for k in chain_recall_at_k}
return {
"recall_at_k": recall_at_k,
"chain_recall_at_k": chain_recall_at_k,
"total_queries": total,
}
# ----------------------------- CLI / main -----------------------------
def build_gold_map(gold_pairs: List[Dict[str, Any]]) -> Dict[str, List[str]]:
m: Dict[str, List[str]] = {}
for gp in gold_pairs:
m.setdefault(gp["query_id"], []).append(gp["doc_id"])
return m
async def main(argv: Optional[List[str]] = None) -> None:
parser = argparse.ArgumentParser()
parser.add_argument("--corpus_path", required=True)
parser.add_argument("--queries_path", required=True)
parser.add_argument("--gold_path", required=True)
parser.add_argument("--output_dir", required=True)
parser.add_argument("--student_model", default="sentence-transformers/all-MiniLM-L6-v2")
parser.add_argument("--baseline_model", default=None)
parser.add_argument("--guide_model", default=None)
parser.add_argument("--top_n_baseline", type=int, default=100)
parser.add_argument("--top_n_bm25", type=int, default=200)
parser.add_argument("--bm25_margin_ratio", type=float, default=0.10)
parser.add_argument("--max_negatives", type=int, default=50)
parser.add_argument("--max_negs_per_example", type=int, default=8)
parser.add_argument("--train", action="store_true")
parser.add_argument("--evaluate", action="store_true")
parser.add_argument("--use_gist", action="store_true")
parser.add_argument("--avoid_same_query_in_batch", action="store_true")
parser.add_argument("--epochs", type=int, default=3)
parser.add_argument("--batch_size", type=int, default=64)
parser.add_argument("--lr", type=float, default=2e-5)
parser.add_argument("--device", type=str, default="cpu")
parser.add_argument("--cache_dir", type=str, default="./cache")
args = parser.parse_args(argv)
pathlib.Path(args.output_dir).mkdir(parents=True, exist_ok=True)
corpus = load_jsonl(args.corpus_path)
queries = load_jsonl(args.queries_path)
gold_pairs = load_jsonl(args.gold_path)
gold_map = build_gold_map(gold_pairs)
baseline_model = SentenceTransformer(args.baseline_model, device=args.device) if args.baseline_model else None
# 1) Hard negative mining
records = await mine_hard_negatives_mixed(
queries=queries,
corpus=corpus,
gold_map=gold_map,
baseline_search_api=None, # <-- Replace with your SearchAPI implementation if you have one
baseline_model=baseline_model,
top_n_baseline=args.top_n_baseline,
top_n_bm25=args.top_n_bm25,
bm25_margin_ratio=args.bm25_margin_ratio,
max_negatives_per_record=args.max_negatives,
max_negs_per_example=args.max_negs_per_example,
cache_dir=args.cache_dir,
cache_name_prefix="mined",
device=args.device,
)
# save exploded records for inspection
save_jsonl(records, os.path.join(args.output_dir, "exploded_records.jsonl"))
# 2) Training
if args.train:
model = train_student(
student_model_name=args.student_model,
records=records,
output_dir=args.output_dir,
epochs=args.epochs,
batch_size=args.batch_size,
lr=args.lr,
use_gist=args.use_gist,
guide_model_name=args.guide_model,
device=args.device,
avoid_same_query_in_batch=args.avoid_same_query_in_batch,
)
else:
model = SentenceTransformer(args.student_model, device=args.device)
# 3) Evaluation
if args.evaluate:
metrics = evaluate_recall_and_chain(
model, queries, corpus, gold_map, top_k_list=(1, 5, 10, 20), device=args.device
)
logger.info("Evaluation results: %s", json.dumps(metrics, indent=2))
with open(os.path.join(args.output_dir, "evaluation.json"), "w", encoding="utf-8") as fh:
json.dump(metrics, fh, indent=2)
if __name__ == "__main__":
asyncio.run(main())
@DiTo97
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DiTo97 commented Jan 6, 2026

@copilot CodeCarbonCallback and TrackioCallback

@DiTo97
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DiTo97 commented Jan 6, 2026

@copilot st_mine_hard_negatives

@ashikns
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ashikns commented Jan 7, 2026

Copilot updates for async, dataset + Ruff format: https://gist.github.com/ashikns/960b22034c7afb9cce7a451b43b599e6

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