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{
"_name_or_path": "/jxm/cde/cde-small-v2/checkpoint-2635",
"architecture": "transductive",
"architectures": [
"ContextualDocumentEmbeddingTransformer"
],
"attn_implementation": null,
"auto_map": {
"AutoConfig": "model.ContextualModelConfig",
"AutoModel": "model.ContextualDocumentEmbeddingTransformer"
},
"autoregressive_backbone": false,
"cache_dir": null,
"config_name": null,
"dataset_backbone": null,
"disable_dropout": true,
"disable_transductive_rotary_embedding": true,
"embedder": "answerdotai/ModernBERT-base",
"embedder_rerank": "sentence-transformers/gtr-t5-base",
"embedding_output_dim": null,
"limit_layers": null,
"limit_layers_first_stage": null,
"logit_scale": 50.0,
"max_seq_length": 512,
"model_revision": "main",
"pool_ignore_contextual_tokens": true,
"pool_ignore_instruction_tokens": true,
"pooling_strategy": "mean",
"tokenizer_name": null,
"torch_dtype": "float32",
"transductive_corpus_size": 512,
"transductive_sequence_dropout_prob": 0.0,
"transductive_tie_token_embeddings": false,
"transductive_tokens_per_document": 1,
"transformers_version": "4.48.0.dev0"
}

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{
"__version__": {
"sentence_transformers": "3.1.0",
"transformers": "4.43.4",
"pytorch": "2.5.0.dev20240807+cu121"
},
"prompts": {
"query": "search_query: ",
"document": "search_document: "
},
"default_prompt_name": null,
"similarity_fn_name": "cosine"
}

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from typing import Dict, Iterable, List, Optional, Tuple, Union
import collections
import glob
import json
import hashlib
import itertools
import logging
import multiprocessing
import os
import pickle
import random
import requests
import sys
import zipfile
import datasets
import numpy as np
import torch
import tqdm
import transformers
from cde.lib.dist import get_num_proc, get_rank
def get_cde_cache_dir() -> str:
script_directory = os.path.normpath(
os.path.join(
os.path.dirname(os.path.abspath(__file__)),
os.pardir, os.pardir,
)
)
return os.path.join(script_directory, "data")
def get_cache_location_from_kwargs(**kwargs):
cache_location = os.path.join(
get_cde_cache_dir(), "cluster"
)
os.makedirs(cache_location, exist_ok=True)
return os.path.join(cache_location, md5_hash_kwargs(**kwargs))
def process_qrels_uncached(corpus: datasets.Dataset, qrels: datasets.Dataset) -> Tuple[Dict[str, List[float]], Dict[str, List[str]]]:
qrels_idxs = collections.defaultdict(list)
qrels_scores = collections.defaultdict(list)
corpus_ids = np.array(corpus['_id'])
skipped_qrels = 0
for ex in tqdm.tqdm(qrels, desc='processing qrels', colour='#964B00', leave=False):
#
# example:
# {
# 'query-id': 1,
# 'corpus-id': 'b0680508-2019-04-18T13:48:51Z-00002-000',
# 'score': 2
# }
#
q_id = str(ex['query-id'])
c_idxs = (corpus_ids == str(ex['corpus-id'])).nonzero()[0]
#
assert len(c_idxs) <= 1, f"error - duplicate corpus ID? (found {len(c_idxs)} matches)"
#
if len(c_idxs):
qrels_idxs[q_id].append(c_idxs[0])
qrels_scores[q_id].append(ex['score'])
else:
skipped_qrels += 1
#
if skipped_qrels > 0:
logging.warning(f'Warning: Skipped {skipped_qrels}/{len(qrels)} qrels.')
return qrels_idxs, qrels_scores
def process_qrels(
corpus: datasets.Dataset, qrels: datasets.Dataset,
use_cache: bool = True
) -> Tuple[Dict[str, List[float]], Dict[str, List[str]]]:
dataset_cache_file = '_'.join(
(corpus.cache_files[0]['filename'], qrels.cache_files[0]['filename'])
)
cache_file = strip_extension(dataset_cache_file) + '_processed_qrels.p'
os.makedirs(os.path.dirname(cache_file), exist_ok=True)
if not (use_cache and os.path.exists(cache_file)):
qrels_idxs, qrels_scores = process_qrels_uncached(
corpus=corpus, qrels=qrels
)
if use_cache:
pickle.dump((qrels_idxs, qrels_scores), open(cache_file, 'wb'))
else:
qrels_idxs, qrels_scores = pickle.load(open(cache_file, 'rb'))
return qrels_idxs, qrels_scores
def strip_extension(filename: str) -> str:
"""Strips file extension.
Ex:
>> strip_extension('/root/dir/sub/file.ext')
'/root/dir/sub/file'
"""
return os.path.splitext(filename)[0]
def md5_hash(t: Tuple[str]) -> str:
return hashlib.md5('__'.join(t).encode()).hexdigest()
def md5_hash_kwargs(**kwargs) -> str:
# We ignore special hf args that start with _ like '__cached__setup_devices'.
safe_kwargs = {k: str(v) for k,v in kwargs.items() if not k.startswith('_')}
s = json.dumps(safe_kwargs, sort_keys=True)
return hashlib.md5(s.encode()).hexdigest()
def download_url(url: str, save_path: str, chunk_size: int = 1024):
"""Download url with progress bar using tqdm
https://stackoverflow.com/questions/15644964/python-progress-bar-and-downloads
Args:
url (str): downloadable url
save_path (str): local path to save the downloaded file
chunk_size (int, optional): chunking of files. Defaults to 1024.
"""
r = requests.get(url, stream=True)
total = int(r.headers.get('Content-Length', 0))
with open(save_path, 'wb') as fd, tqdm.tqdm(
desc=save_path,
total=total,
unit='iB',
unit_scale=True,
unit_divisor=chunk_size,
) as bar:
for data in r.iter_content(chunk_size=chunk_size):
size = fd.write(data)
bar.update(size)
def unzip(zip_file: str, out_dir: str):
print("unzipping =>", zip_file)
zip_ = zipfile.ZipFile(zip_file, "r")
zip_.extractall(path=out_dir)
zip_.close()
def download_url_and_unzip(url: str, out_dir: str, chunk_size: int = 1024) -> str:
os.makedirs(out_dir, exist_ok=True)
dataset = url.split("/")[-1]
zip_file = os.path.join(out_dir, dataset)
if not os.path.isfile(zip_file):
logging.info("Downloading {} ...".format(dataset))
download_url(url, zip_file, chunk_size)
if not os.path.isdir(zip_file.replace(".zip", "")):
logging.info("Unzipping {} ...".format(dataset))
unzip(zip_file, out_dir)
return os.path.join(out_dir, dataset.replace(".zip", ""))
def tqdm_if_main_worker(iterable: Iterable, **kwargs) -> Iterable:
if get_rank() == 0:
return tqdm.tqdm(iterable, **kwargs)
else:
return iterable
class ContextualModelConfig(transformers.configuration_utils.PretrainedConfig):
"""We create a dummy configuration class that will just set properties
based on whatever kwargs we pass in.
When this class is initialized (see experiments.py) we pass in the
union of all data, model, and training args, all of which should
get saved to the config json.
"""
def __init__(self, **kwargs):
for key, value in kwargs.items():
try:
json.dumps(value)
setattr(self, key, value)
except TypeError:
# value was not JSON-serializable, skip
continue
super().__init__()
def independent_crop(
input_ids: torch.Tensor, pad_token_id: int,
l1: int = 256, l2: int = 256) -> Tuple[torch.Tensor, torch.Tensor]:
"""Returns two independent crops from input_ids.
Assumes input_ids has a beginning and end token, like
[101, ..., 102, 0, 0, 0].
Args:
input_ids: tensor of IDs
pad_token_id: ID of pad tokens in input_ids
l1: length of span 1, cropped
l2: length of span 2, cropped
Returns:
span1: first crop (of length l1)
span2: second crop (of length l2)
"""
# Count tokens until pad.
if (input_ids == pad_token_id).sum() == 0:
N = len(input_ids)
else:
N = (input_ids == pad_token_id).int().argmax().item()
####
###
##
## Contriever: We use the random cropping data
## augmentation, with documents of 256 tokens and span
## sizes sampled between 5% and 50% of the document
## length
##
###
#####
####### LaPraDor: The maximum lengths set for queries and
####### documents are 64 and 350...
#####
# TODO is this divide-by-two a good idea? (Don't want s1=s2 ever..)
nl1 = min(N//2, l1)
nl2 = min(N//2, l2)
s1_start = random.randint(1, N-nl1)
s2_start = random.randint(1, N-nl2)
s1_idxs = itertools.chain(
[0], range(s1_start, s1_start+nl1), [N-1]
)
s1 = input_ids[torch.tensor(list(s1_idxs))]
s2_idxs = itertools.chain(
[0], range(s2_start, s2_start+nl2), [N-1]
)
s2 = input_ids[torch.tensor(list(s2_idxs))]
return (s1, s2)
def load_dataset_tables(
files: Iterable[str], num_workers: int = 16
) -> Iterable[datasets.table.MemoryMappedTable]:
import concurrent
from multiprocessing import Pool
# num_workers = min(num_workers, len(files))
num_workers = min(32, len(files))
use_threads = True
if use_threads:
pool_cls = concurrent.futures.ThreadPoolExecutor
pool_kwargs = {"max_workers": num_workers}
else:
pool_cls = Pool
pool_kwargs = {"processes": num_workers}
with pool_cls(**pool_kwargs) as pool:
if len(files) > 10:
files = tqdm_if_main_worker(
files,
desc=f"Loading {len(files)} files with {num_workers} workers",
total=len(files),
colour="#ffbd88"
)
result = list(
pool.map(datasets.table.MemoryMappedTable.from_file, files)
)
return result
def datasets_fast_load_from_disk(cache_path: str) -> datasets.Dataset:
logging.info(f"fast_load_from_disk called with path:", cache_path)
dataset_info_path = os.path.join(cache_path, "dataset_info.json")
with open(dataset_info_path, encoding="utf-8") as dataset_info_file:
dataset_info = datasets.DatasetInfo.from_dict(json.load(dataset_info_file))
dataset_state_path = os.path.join(cache_path, "state.json")
with open(dataset_state_path, encoding="utf-8") as state_file:
state = json.load(state_file)
files = glob.glob(os.path.join(cache_path, "data-*.arrow"))
files = sorted(files)
num_workers = get_num_proc()
ds_tables = load_dataset_tables(
files=files,
num_workers=num_workers
)
arrow_table = datasets.table.concat_tables(ds_tables)
split = state["_split"]
split = datasets.splits.Split(split) if split is not None else split
# print("returning dataset")
return datasets.Dataset(
arrow_table=arrow_table,
info=dataset_info,
split=split,
fingerprint=state["_fingerprint"],
)
def tokenize_dataset(
dataset: datasets.Dataset,
tokenizer: transformers.PreTrainedTokenizer,
max_length: int,
text_key: str,
padding_strategy: str
) -> datasets.Dataset:
def tokenize_text(ex: Dict) -> Dict:
tt = tokenizer(
ex[text_key],
max_length=max_length,
truncation=True,
padding=padding_strategy,
)
for k,v in tt.items():
ex[f"{text_key}_{k}"] = v
ex["length"] = [len(tt) for tt in ex[f"{text_key}_input_ids"]]
return ex
# generate unique hash for tokenizer
vocab = tokenizer.vocab
vocab_words = tuple(sorted(vocab.keys(), key=lambda word: vocab[word]))
vocab_hash = md5_hash(vocab_words)
data_fingerprint = '__'.join((
dataset._fingerprint, str(vocab_hash), str(max_length),
text_key, padding_strategy
))
data_fingerprint = md5_hash(data_fingerprint)
dataset = dataset.map(
tokenize_text,
new_fingerprint=data_fingerprint,
batched=True,
load_from_cache_file=True,
)
return dataset
class TensorRunningAverages:
_store_sum: Dict[str, torch.Tensor]
_store_total: Dict[str, torch.Tensor]
def __init__(self):
self._store_sum = {}
self._store_total = {}
def __iter__(self) -> Iterable[str]:
return iter(self._store_sum.keys())
def update(self, key: str, val: Union[int, float, torch.Tensor]) -> None:
if key not in self._store_sum:
self.clear(key)
if isinstance(val, torch.Tensor):
val = val.item() # tensor -> num
self._store_sum[key] += val
self._store_total[key] += 1
def get(self, key: str) -> float:
total = max(self._store_total.get(key).item(), 1.0)
return (self._store_sum[key] / float(total)).item() or 0.0
def clear(self, key: str) -> None:
self._store_sum[key] = torch.tensor(0.0, dtype=torch.float32)
self._store_total[key] = torch.tensor(0, dtype=torch.int32)
def clear_all(self) -> None:
for key in self._store_sum:
self.clear(key)
def get_and_clear_all(self) -> Dict[str, float]:
metrics = {}
for key in self:
metrics[key] = self.get(key)
self.clear(key)
return metrics
def load_embedder_and_tokenizer(name: str) -> Tuple[
transformers.PreTrainedModel,
transformers.PreTrainedTokenizer
]:
if name.startswith("nomic") or (name == "bert-base-uncased"):
from cde.lib.nomic_bert import NomicBertModel
if name.endswith("--from-scratch"):
name = name.replace("--from-scratch", "")
config = transformers.AutoConfig.from_pretrained(name, trust_remote_code=True)
model = NomicBertModel._from_config(config)
else:
model = NomicBertModel.from_pretrained(
name, add_pooling_layer=False
)
tokenizer = transformers.AutoTokenizer.from_pretrained(name)
elif name in ["gtr-base", "gtr_base"]:
model = transformers.AutoModel.from_pretrained(
"sentence-transformers/gtr-t5-base"
).encoder
tokenizer = transformers.AutoTokenizer.from_pretrained(
"sentence-transformers/gtr-t5-base"
)
elif name == "pile-t5-base-encoder":
model = transformers.AutoModel.from_pretrained(
"EleutherAI/pile-t5-base"
).encoder
tokenizer = transformers.AutoTokenizer.from_pretrained(
"EleutherAI/pile-t5-base"
)
tokenizer.pad_token = tokenizer.eos_token
elif name == "pile-t5-base-decoder":
model = transformers.AutoModel.from_pretrained(
"EleutherAI/pile-t5-base"
).decoder
tokenizer = transformers.AutoTokenizer.from_pretrained(
"EleutherAI/pile-t5-base"
)
tokenizer.pad_token = tokenizer.eos_token
elif name.startswith("gpt2") or name.startswith("meta-llama") or ("Llama" in name):
model = transformers.AutoModelForCausalLM.from_pretrained(
name,
# torch_dtype=torch.bfloat16,
attn_implementation="flash_attention_2" if torch.cuda.is_available() else "sdpa",
low_cpu_mem_usage=True,
# device_map="auto",
)
model.padding_side = "right"
tokenizer = transformers.AutoTokenizer.from_pretrained(name)
tokenizer.pad_token = tokenizer.eos_token
tokenizer.add_eos_token = True
elif "Modern" in name:
print("special loading for ModernBERT!")
# [1] needed for faster training
# model = transformers.AutoModel.from_pretrained(name, trust_remote_code=True, reference_compile=True)
# [2] needed for non-breaking inference
model = transformers.AutoModel.from_pretrained(name, trust_remote_code=True, reference_compile=False)
tokenizer = transformers.AutoTokenizer.from_pretrained(name)
else:
model = transformers.AutoModel.from_pretrained(name, trust_remote_code=True)
tokenizer = transformers.AutoTokenizer.from_pretrained(name)
return model, tokenizer
def inputs_for_key(inputs: Dict[str, torch.Tensor], key: str):
key += "_"
return {k.replace(key, ""): v for k,v in inputs.items() if k.startswith(key)}
def count_cpus() -> int:
try:
return len(os.sched_getaffinity(0))
except AttributeError:
return multiprocessing.cpu_count()
def shuffle_batches(g: torch.Generator, list_of_tensors: List[torch.Tensor]) -> List[int]:
all_indices = []
for batch_tensor in tqdm_if_main_worker(list_of_tensors, colour="green", desc="Sampler shuffling per-batch"):
rand_perm = torch.randperm(len(batch_tensor), generator=g)
batch_list = batch_tensor[rand_perm].tolist()
all_indices.extend(batch_list)
return all_indices
# def shuffle_batches_multiproc(g: torch.Generator, list_of_tensors: List[torch.Tensor], num_processes: int = 8) -> List[int]:
# all_indices = []
# print(f"Shuffling {len(list_of_tensors)} tensors with {num_processes} workers.")
# pbar = tqdm_if_main_worker(list_of_tensors, colour="orange", desc=f"Sampler shuffling per-batch (nproc={num_processes})")
# pool = multiprocessing.Pool(processes=num_processes)
# chunk_size = len(list_of_tensors) // num_processes
# chunks = [list_of_tensors[i:i + chunk_size] for i in range(0, len(list_of_tensors), chunk_size)]
# worker_func = functools.partial(shuffle_batches, g=g)
# results = pool.map(worker_func, chunks)
# all_indices = []
# for result in results:
# all_indices.extend(result)
# pbar.update()
# return all_indices
def exit_if_running_or_finished_wandb(
project_name: str,
exp_group: str, exp_name: str
) -> None:
print("Checking if experiment is already running...")
import wandb
api = wandb.Api()
running_runs = api.runs(
path="cde-0",
filters={
"display_name": exp_name,
"state": {"$regex": "Running|Finished"},
"config.exp_group": exp_group,
}
)
print("Found", len(running_runs), f"runs with name {exp_name} and group {exp_group} in {project_name}.")
if len(running_runs) > 0:
print("Exiting because experiment is already running or completed.")
sys.exit(0)
HN_FILTER_TOKENIZER_MAP = {
"nomic": "nomic-ai/nomic-embed-text-v1",
"stella": "dunzhang/stella_en_400M_v5",
"sbert": "sentence-transformers/all-MiniLM-L6-v2",
"sentence_t5": "sentence-transformers/sentence-t5-base",
"gte": "Alibaba-NLP/gte-large-en-v1.5",
}
def load_hn_filter_tokenizer(tokenizer_name: str) -> Optional[transformers.PreTrainedTokenizer]:
if tokenizer_name in HN_FILTER_TOKENIZER_MAP:
return transformers.AutoTokenizer.from_pretrained(HN_FILTER_TOKENIZER_MAP[tokenizer_name])
else:
return None

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[
{
"idx": 0,
"name": "0",
"path": "",
"type": "sentence_transformers_impl.Transformer",
"kwargs": ["dataset_embeddings"]
}
]

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{}

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from __future__ import annotations
import json
import logging
import os
from typing import Any, Optional
import torch
from torch import nn
from transformers import AutoConfig, AutoModel, AutoTokenizer
logger = logging.getLogger(__name__)
class Transformer(nn.Module):
"""Hugging Face AutoModel to generate token embeddings.
Loads the correct class, e.g. BERT / RoBERTa etc.
Args:
model_name_or_path: Hugging Face models name
(https://huggingface.co/models)
max_seq_length: Truncate any inputs longer than max_seq_length
model_args: Keyword arguments passed to the Hugging Face
Transformers model
tokenizer_args: Keyword arguments passed to the Hugging Face
Transformers tokenizer
config_args: Keyword arguments passed to the Hugging Face
Transformers config
cache_dir: Cache dir for Hugging Face Transformers to store/load
models
do_lower_case: If true, lowercases the input (independent if the
model is cased or not)
tokenizer_name_or_path: Name or path of the tokenizer. When
None, then model_name_or_path is used
backend: Backend used for model inference. Can be `torch`, `onnx`,
or `openvino`. Default is `torch`.
"""
save_in_root: bool = True
def __init__(
self,
model_name_or_path: str,
model_args: dict[str, Any] | None = None,
tokenizer_args: dict[str, Any] | None = None,
config_args: dict[str, Any] | None = None,
cache_dir: str | None = None,
**kwargs,
) -> None:
super().__init__()
if model_args is None:
model_args = {}
if tokenizer_args is None:
tokenizer_args = {}
if config_args is None:
config_args = {}
if not model_args.get("trust_remote_code", False):
raise ValueError(
"You need to set `trust_remote_code=True` to load this model."
)
self.config = AutoConfig.from_pretrained(model_name_or_path, **config_args, cache_dir=cache_dir)
self.auto_model = AutoModel.from_pretrained(model_name_or_path, config=self.config, cache_dir=cache_dir, **model_args)
self.tokenizer = AutoTokenizer.from_pretrained(
"answerdotai/ModernBERT-base",
cache_dir=cache_dir,
**tokenizer_args,
)
def __repr__(self) -> str:
return f"Transformer({self.get_config_dict()}) with Transformer model: {self.auto_model.__class__.__name__} "
def forward(self, features: dict[str, torch.Tensor], dataset_embeddings: Optional[torch.Tensor] = None, **kwargs) -> dict[str, torch.Tensor]:
"""Returns token_embeddings, cls_token"""
# If we don't have embeddings, then run the 1st stage model.
# If we do, then run the 2nd stage model.
if dataset_embeddings is None:
sentence_embedding = self.auto_model.first_stage_model(
input_ids=features["input_ids"],
attention_mask=features["attention_mask"],
)
else:
sentence_embedding = self.auto_model.second_stage_model(
input_ids=features["input_ids"],
attention_mask=features["attention_mask"],
dataset_embeddings=dataset_embeddings,
)
features["sentence_embedding"] = sentence_embedding
return features
def get_word_embedding_dimension(self) -> int:
return self.auto_model.config.hidden_size
def tokenize(
self, texts: list[str] | list[dict] | list[tuple[str, str]], padding: str | bool = True
) -> dict[str, torch.Tensor]:
"""Tokenizes a text and maps tokens to token-ids"""
output = {}
if isinstance(texts[0], str):
to_tokenize = [texts]
elif isinstance(texts[0], dict):
to_tokenize = []
output["text_keys"] = []
for lookup in texts:
text_key, text = next(iter(lookup.items()))
to_tokenize.append(text)
output["text_keys"].append(text_key)
to_tokenize = [to_tokenize]
else:
batch1, batch2 = [], []
for text_tuple in texts:
batch1.append(text_tuple[0])
batch2.append(text_tuple[1])
to_tokenize = [batch1, batch2]
max_seq_length = self.config.max_seq_length
output.update(
self.tokenizer(
*to_tokenize,
padding=padding,
truncation="longest_first",
return_tensors="pt",
max_length=max_seq_length,
)
)
return output
def get_config_dict(self) -> dict[str, Any]:
return {}
def save(self, output_path: str, safe_serialization: bool = True) -> None:
self.auto_model.save_pretrained(output_path, safe_serialization=safe_serialization)
self.tokenizer.save_pretrained(output_path)
with open(os.path.join(output_path, "sentence_bert_config.json"), "w") as fOut:
json.dump(self.get_config_dict(), fOut, indent=2)
@classmethod
def load(cls, input_path: str) -> Transformer:
sbert_config_path = os.path.join(input_path, "sentence_bert_config.json")
if not os.path.exists(sbert_config_path):
return cls(model_name_or_path=input_path)
with open(sbert_config_path) as fIn:
config = json.load(fIn)
# Don't allow configs to set trust_remote_code
if "model_args" in config and "trust_remote_code" in config["model_args"]:
config["model_args"].pop("trust_remote_code")
if "tokenizer_args" in config and "trust_remote_code" in config["tokenizer_args"]:
config["tokenizer_args"].pop("trust_remote_code")
if "config_args" in config and "trust_remote_code" in config["config_args"]:
config["config_args"].pop("trust_remote_code")
return cls(model_name_or_path=input_path, **config)