def test_flatten(self):
dset_split = Dataset.from_dict(
{
"a": [{
"b": {
"c": ["text"]
}
}] * 10,
"foo": [1] * 10
},
features=Features({
"a": {
"b": Sequence({"c": Value("string")})
},
"foo": Value("int64")
}),
)
dset = DatasetDict({"train": dset_split, "test": dset_split})
dset = dset.flatten()
self.assertDictEqual(dset.column_names, {
"train": ["a.b.c", "foo"],
"test": ["a.b.c", "foo"]
})
self.assertListEqual(list(dset["train"].features.keys()),
["a.b.c", "foo"])
self.assertDictEqual(
dset["train"].features,
Features({
"a.b.c": Sequence(Value("string")),
"foo": Value("int64")
}))
del dset
def test_cast_array_to_features():
arr = pa.array([[0, 1]])
assert cast_array_to_feature(arr, Sequence(
Value("string"))).type == pa.list_(pa.string())
with pytest.raises(TypeError):
cast_array_to_feature(arr,
Sequence(Value("string")),
allow_number_to_str=False)
def test_dataset_with_image_feature_with_none():
data = {"image": [None]}
features = Features({"image": Image()})
dset = Dataset.from_dict(data, features=features)
item = dset[0]
assert item.keys() == {"image"}
assert item["image"] is None
batch = dset[:1]
assert len(batch) == 1
assert batch.keys() == {"image"}
assert isinstance(batch["image"], list) and all(item is None for item in batch["image"])
column = dset["image"]
assert len(column) == 1
assert isinstance(column, list) and all(item is None for item in column)
# nested tests
data = {"images": [[None]]}
features = Features({"images": Sequence(Image())})
dset = Dataset.from_dict(data, features=features)
item = dset[0]
assert item.keys() == {"images"}
assert all(i is None for i in item["images"])
data = {"nested": [{"image": None}]}
features = Features({"nested": {"image": Image()}})
dset = Dataset.from_dict(data, features=features)
item = dset[0]
assert item.keys() == {"nested"}
assert item["nested"].keys() == {"image"}
assert item["nested"]["image"] is None
def test_image_feature_type_to_arrow():
features = Features({"image": Image()})
assert features.arrow_schema == pa.schema({"image": Image().pa_type})
features = Features({"struct_containing_an_image": {"image": Image()}})
assert features.arrow_schema == pa.schema({"struct_containing_an_image": pa.struct({"image": Image().pa_type})})
features = Features({"sequence_of_images": Sequence(Image())})
assert features.arrow_schema == pa.schema({"sequence_of_images": pa.list_(Image().pa_type)})
def save_data(train_df, val_df):
train_f = Features({
'answers':
Sequence(feature={
'text': Value(dtype='string', id=None),
'answer_start': Value(dtype='int32', id=None)
},
length=-1,
id=None),
'context':
Value(dtype='string', id=None),
'id':
Value(dtype='string', id=None),
'question':
Value(dtype='string', id=None),
'question_type':
Value(dtype='int32', id=None)
})
train_datasets = DatasetDict({
'train':
Dataset.from_pandas(train_df, features=train_f),
'validation':
Dataset.from_pandas(val_df, features=train_f)
})
file = open("../../data/question_type.pkl", "wb")
pickle.dump(train_datasets, file)
file.close()
def get_etr_dataset(args):
etr_path = p.join(args.path.train_data_dir, "etr_qa_dataset.json")
if not p.exists(etr_path):
raise FileNotFoundError(
f"ETRI 데이터 셋 {etr_path}로 파일명 바꿔서 데이터 넣어주시길 바랍니다.")
with open(etr_path, "r") as f:
etr_dict = json.load(f)
# print(etr_dict["data"][0])
new_dataset = defaultdict(list)
cnt = 0
for datas in etr_dict["data"]:
title = datas["title"]
context = datas["paragraphs"][0]["context"]
for questions in datas["paragraphs"][0]["qas"]:
question = questions["question"]
answers = {
"answer_start": [questions["answers"][0]["answer_start"]],
"text": [questions["answers"][0]["text"]],
}
new_dataset["id"].append(f"etr-custom-{cnt}")
new_dataset["title"].append(title)
new_dataset["context"].append(context)
new_dataset["question"].append(question)
new_dataset["answers"].append(answers)
cnt += 1
f = Features({
"answers":
Sequence(
feature={
"text": Value(dtype="string", id=None),
"answer_start": Value(dtype="int32", id=None)
},
length=-1,
id=None,
),
"id":
Value(dtype="string", id=None),
"context":
Value(dtype="string", id=None),
"question":
Value(dtype="string", id=None),
"title":
Value(dtype="string", id=None),
})
df = pd.DataFrame(new_dataset)
etr_dataset = Dataset.from_pandas(df, features=f)
return etr_dataset
def main(
rag_example_args: "RagExampleArguments",
processing_args: "ProcessingArguments",
index_hnsw_args: "IndexHnswArguments",
):
######################################
logger.info("Step 1 - Create the dataset")
######################################
# The dataset needed for RAG must have three columns:
# - title (string): title of the document
# - text (string): text of a passage of the document
# - embeddings (array of dimension d): DPR representation of the passage
# Let's say you have documents in tab-separated csv files with columns "title" and "text"
assert os.path.isfile(rag_example_args.csv_path), "Please provide a valid path to a csv file"
# You can load a Dataset object this way
dataset = load_dataset(
"csv", data_files=[rag_example_args.csv_path], split="train", delimiter="\t", column_names=["title", "text"]
)
# More info about loading csv files in the documentation: https://huggingface.co/docs/datasets/loading_datasets.html?highlight=csv#csv-files
# Then split the documents into passages of 100 words
dataset = dataset.map(split_documents, batched=True, num_proc=processing_args.num_proc)
# And compute the embeddings
ctx_encoder = DPRContextEncoder.from_pretrained(rag_example_args.dpr_ctx_encoder_model_name).to(device=device)
ctx_tokenizer = DPRContextEncoderTokenizerFast.from_pretrained(rag_example_args.dpr_ctx_encoder_model_name)
new_features = Features(
{"text": Value("string"), "title": Value("string"), "embeddings": Sequence(Value("float32"))}
) # optional, save as float32 instead of float64 to save space
dataset = dataset.map(
partial(embed, ctx_encoder=ctx_encoder, ctx_tokenizer=ctx_tokenizer),
batched=True,
batch_size=processing_args.batch_size,
features=new_features,
)
# And finally save your dataset
passages_path = os.path.join(rag_example_args.output_dir, "my_knowledge_dataset")
dataset.save_to_disk(passages_path)
# from datasets import load_from_disk
# dataset = load_from_disk(passages_path) # to reload the dataset
######################################
logger.info("Step 2 - Index the dataset")
######################################
# Let's use the Faiss implementation of HNSW for fast approximate nearest neighbor search
index = faiss.IndexHNSWFlat(index_hnsw_args.d, index_hnsw_args.m, faiss.METRIC_INNER_PRODUCT)
dataset.add_faiss_index("embeddings", custom_index=index)
# And save the index
index_path = os.path.join(rag_example_args.output_dir, "my_knowledge_dataset_hnsw_index.faiss")
dataset.get_index("embeddings").save(index_path)
def make_negative_dataset(args,
bm25,
queries,
answers,
contexts,
name,
num=16):
total = []
scores, indices = bm25.get_relevant_doc_bulk(queries, topk=num * 2)
answers, indices = np.array(answers, dtype="object"), np.array(indices)
contexts = np.array(contexts, dtype="object")
for idx, query in enumerate(queries):
label = idx % num
answer = answers[idx]
context_list = contexts[indices[idx]]
check_in = np.argwhere(context_list == answer)
if check_in.shape[0] == 0:
context_list[label] = answer
context_list = context_list[:num]
else:
context_list[check_in[0][0]] = context_list[num]
context_list[label] = answer
context_list = context_list[:num]
if idx % 100 == 0:
print("query: ", query)
print("answer: ", answer)
print("negative:", context_list)
print("label:", label)
tmp = {
"query": query,
"negative_samples": context_list,
"label": label
}
total.append(tmp)
df = pd.DataFrame(total)
f = Features({
"query":
Value(dtype="string", id=None),
"negative_samples":
Sequence(feature=Value(dtype="string", id=None), length=-1, id=None),
"label":
Value(dtype="int32", id=None),
})
dataset = Dataset.from_pandas(df, features=f)
dataset.save_to_disk(os.path.join(args.path.train_data_dir, name))
def generate_faiss_index_dataset(data, ctx_encoder_name, args, device):
"""
Adapted from Huggingface example script at https://github.com/huggingface/transformers/blob/master/examples/research_projects/rag/use_own_knowledge_dataset.py
"""
import faiss
if isinstance(data, str):
dataset = load_dataset("csv",
data_files=data,
delimiter="\t",
column_names=["title", "text"])
else:
dataset = HFDataset.from_pandas(data)
dataset = dataset.map(
partial(split_documents,
split_text_n=args.split_text_n,
split_text_character=args.split_text_character),
batched=True,
num_proc=args.process_count,
)
ctx_encoder = DPRContextEncoder.from_pretrained(ctx_encoder_name).to(
device=device)
ctx_tokenizer = DPRContextEncoderTokenizerFast.from_pretrained(
ctx_encoder_name)
new_features = Features({
"text": Value("string"),
"title": Value("string"),
"embeddings": Sequence(Value("float32"))
}) # optional, save as float32 instead of float64 to save space
dataset = dataset.map(
partial(embed,
ctx_encoder=ctx_encoder,
ctx_tokenizer=ctx_tokenizer,
device=device),
batched=True,
batch_size=args.rag_embed_batch_size,
features=new_features,
)
if isinstance(data, str):
dataset = dataset["train"]
if args.save_knowledge_dataset:
output_dataset_directory = os.path.join(args.output_dir,
"knowledge_dataset")
os.makedirs(output_dataset_directory, exist_ok=True)
dataset.save_to_disk(output_dataset_directory)
index = faiss.IndexHNSWFlat(args.faiss_d, args.faiss_m,
faiss.METRIC_INNER_PRODUCT)
dataset.add_faiss_index("embeddings", custom_index=index)
return dataset
def embed_update(ctx_encoder, total_processes, device, process_num, shard_dir,
csv_path):
kb_dataset = load_dataset("csv",
data_files=[csv_path],
split="train",
delimiter="\t",
column_names=["title", "text"])
kb_dataset = kb_dataset.map(
split_documents, batched=True,
num_proc=1) # if you want you can load already splitted csv.
kb_list = [
kb_dataset.shard(total_processes, i, contiguous=True)
for i in range(total_processes)
]
data_shrad = kb_list[process_num]
arrow_folder = "data_" + str(process_num)
passages_path = os.path.join(shard_dir, arrow_folder)
context_tokenizer = DPRContextEncoderTokenizerFast.from_pretrained(
"facebook/dpr-ctx_encoder-multiset-base")
ctx_encoder = ctx_encoder.to(device=device)
def embed(documents: dict, ctx_encoder: DPRContextEncoder,
ctx_tokenizer: DPRContextEncoderTokenizerFast, device) -> dict:
"""Compute the DPR embeddings of document passages"""
input_ids = ctx_tokenizer(documents["title"],
documents["text"],
truncation=True,
padding="longest",
return_tensors="pt")["input_ids"]
embeddings = ctx_encoder(input_ids.to(device=device),
return_dict=True).pooler_output
return {"embeddings": embeddings.detach().cpu().numpy()}
new_features = Features({
"text": Value("string"),
"title": Value("string"),
"embeddings": Sequence(Value("float32"))
}) # optional, save as float32 instead of float64 to save space
dataset = data_shrad.map(
partial(embed,
ctx_encoder=ctx_encoder,
ctx_tokenizer=context_tokenizer,
device=device),
batched=True,
batch_size=16,
features=new_features,
)
dataset.save_to_disk(passages_path)
def run_sparse_retrieval(datasets, training_args):
#### retreival process ####
retriever = SparseRetrieval(tokenize_fn=tokenize,
data_path="./data",
context_path="wikipedia_documents.json"
# context_path="all_wikipedia_documents.json"
)
# sparse embedding retrieval
# retriever.get_sparse_embedding()
#df = retriever.retrieve(datasets['validation'])
# bm25 retrieval
# retriever.get_embedding_BM25()
# df = retriever.retrieve_BM25(query_or_dataset=datasets['validation'], topk=10)
# elastic search retrieval
# retriever.get_elastic_search()
df = retriever.retrieve_ES(query_or_dataset=datasets['validation'],
topk=10)
# faiss retrieval
# df = retriever.retrieve_faiss(dataset['validation'])
if training_args.do_predict: # test data 에 대해선 정답이 없으므로 id question context 로만 데이터셋이 구성됩니다.
f = Features({
'context': Value(dtype='string', id=None),
'id': Value(dtype='string', id=None),
'question': Value(dtype='string', id=None)
})
elif training_args.do_eval: # train data 에 대해선 정답이 존재하므로 id question context answer 로 데이터셋이 구성됩니다.
f = Features({
'answers':
Sequence(feature={
'text': Value(dtype='string', id=None),
'answer_start': Value(dtype='int32', id=None)
},
length=-1,
id=None),
'context':
Value(dtype='string', id=None),
'id':
Value(dtype='string', id=None),
'question':
Value(dtype='string', id=None)
})
datasets = DatasetDict({'validation': Dataset.from_pandas(df, features=f)})
return datasets
def run_sparse_retrieval(datasets, training_args, inf_args):
#### retreival process ####
if inf_args.retrieval == None:
retriever = SparseRetrieval_BM25PLUS(
tokenize_fn=tokenize,
data_path="./data",
context_path="wikipedia_documents.json")
elif inf_args.retrieval.lower() == "sparse":
retriever = SparseRetrieval(tokenize_fn=tokenize,
data_path="./data",
context_path="wikipedia_documents.json")
# elif inf_args.retrieval.lower() == "bm25" or inf_args.retrieval.lower() == "bm25":
# retriever = SparseRetrieval_BM25(tokenize_fn=tokenize,
# data_path="./data",
# context_path="wikipedia_documents.json")
retriever.get_sparse_embedding()
df = retriever.retrieve(datasets['validation'], inf_args.k)
# faiss retrieval
# test data 에 대해선 정답이 없으므로 id question context 로만 데이터셋이 구성됩니다.
if training_args.do_predict:
f = Features({
'contexts': Value(dtype='string', id=None),
'id': Value(dtype='string', id=None),
'question': Value(dtype='string', id=None)
})
# train data 에 대해선 정답이 존재하므로 id question context answer 로 데이터셋이 구성됩니다.
elif training_args.do_eval:
f = Features({
'answers':
Sequence(feature={
'text': Value(dtype='string', id=None),
'answer_start': Value(dtype='int32', id=None)
},
length=-1,
id=None),
'context':
Value(dtype='string', id=None),
'id':
Value(dtype='string', id=None),
'question':
Value(dtype='string', id=None)
})
datasets = DatasetDict({'validation': Dataset.from_pandas(df, features=f)})
return datasets
def read_dataset_from_csv(csv_path):
"""
read the prepared csv data as Dataset object
"""
df = pd.read_csv(csv_path,
converters={
'token': str,
'written': str,
'spoken': str
})
feature_tag = Sequence(
ClassLabel(num_classes=3, names=list(pd.factorize(df['tag'])[1])))
df['tag'] = df['tag'].apply(feature_tag.feature.str2int)
df_text = df.groupby(['sentence_id']).agg({'token': list, 'tag': list})
dataset = Dataset.from_pandas(df_text)
dataset.features["tag"] = feature_tag
return dataset
def load_dataset(self) -> None:
logger.debug('loading rag dataset: %s', self.name)
self.dataset = load_dataset('csv',
data_files=[self.csv_path],
split='train',
delimiter=',',
column_names=['title', 'text'])
self.dataset = self.dataset.map(
split_documents,
batched=False,
num_proc=6,
batch_size=100,
)
ctx_encoder = DPRContextEncoder.from_pretrained(
self.context_encoder).to(device=self.device)
ctx_tokenizer = DPRContextEncoderTokenizerFast.from_pretrained(
self.context_encoder)
new_features = Features({
'text': Value('string'),
'title': Value('string'),
'embeddings': Sequence(Value('float32'))
}) # optional, save as float32 instead of float64 to save space
self.dataset = self.dataset.map(
partial(embed,
ctx_encoder=ctx_encoder,
ctx_tokenizer=ctx_tokenizer,
device=self.device),
batched=True,
batch_size=16,
features=new_features,
)
self.dataset.save_to_disk(self.dataset_path)
index = faiss.IndexHNSWFlat(768, 128, faiss.METRIC_INNER_PRODUCT)
self.dataset.add_faiss_index('embeddings', custom_index=index)
self.dataset.get_index('embeddings').save(self.faiss_path)
def predict(self, input_path, output_path):
key = 'tmp'
input_df = pd.DataFrame()
if self.pretrained:
input_df['src_token'] = read_txt(input_path)
input_df['src_token'] = input_df['src_token'].str.lower()
input_df['token'] = input_df['src_token'].str.split()
input_df['tag'] = input_df['token'].apply(lambda x: ['O'] * len(x))
input_df['sentence_id'] = input_df.index
trainer = Trainer(model=self.model,
tokenizer=self.tokenizer,
data_collator=self.data_collator)
feature_tag = Sequence(
ClassLabel(num_classes=3, names=self.label_list))
input_df['tag'] = input_df['tag'].apply(
feature_tag.feature.str2int)
eval_dataset = Dataset.from_pandas(input_df)
eval_dataset.features["tag"] = feature_tag
# predict
tokenized_datasets = DatasetDict({
key: eval_dataset
}).map(self.tokenize_and_align_labels, batched=True)
_, true_predictions = self.predict_dataset(trainer,
tokenized_datasets[key])
result = save_classifier_result(eval_dataset, true_predictions,
output_path)
return result
else:
input_df['token'] = read_txt(input_path)
input_df['sentence_id'] = input_df.index
input_df['tag'] = 'B'
input_df.to_csv(output_path, index=False)
print("Result saved to ", output_path)
return input_df
def main():
# See all possible arguments in src/transformers/training_args.py
# or by passing the --help flag to this script.
# We now keep distinct sets of args, for a cleaner separation of concerns.
parser = HfArgumentParser(
(ModelArguments, DataTrainingArguments, TrainingArguments))
if len(sys.argv) == 2 and sys.argv[1].endswith(".json"):
# If we pass only one argument to the script and it's the path to a json file,
# let's parse it to get our arguments.
model_args, data_args, training_args = parser.parse_json_file(
json_file=os.path.abspath(sys.argv[1]))
else:
model_args, data_args, training_args = parser.parse_args_into_dataclasses(
)
if (os.path.exists(training_args.output_dir)
and os.listdir(training_args.output_dir) and training_args.do_train
and not training_args.overwrite_output_dir):
raise ValueError(
f"Output directory ({training_args.output_dir}) already exists and is not empty."
"Use --overwrite_output_dir to overcome.")
# Setup logging
logging.basicConfig(
format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
datefmt="%m/%d/%Y %H:%M:%S",
level=logging.INFO
if is_main_process(training_args.local_rank) else logging.WARN,
)
# Log on each process the small summary:
logger.warning(
f"Process rank: {training_args.local_rank}, device: {training_args.device}, n_gpu: {training_args.n_gpu}"
+
f"distributed training: {bool(training_args.local_rank != -1)}, 16-bits training: {training_args.fp16}"
)
# Set the verbosity to info of the Transformers logger (on main process only):
if is_main_process(training_args.local_rank):
transformers.utils.logging.set_verbosity_info()
transformers.utils.logging.enable_default_handler()
transformers.utils.logging.enable_explicit_format()
logger.info("Training/evaluation parameters %s", training_args)
# Set seed before initializing model.
set_seed(training_args.seed)
# Get the datasets: you can either provide your own CSV/JSON/TXT training and evaluation files (see below)
# or just provide the name of one of the public datasets available on the hub at https://huggingface.co/datasets/
# (the dataset will be downloaded automatically from the datasets Hub).
#
# For CSV/JSON files, this script will use the column called 'text' or the first column if no column called
# 'text' is found. You can easily tweak this behavior (see below).
#
# In distributed training, the load_dataset function guarantee that only one local process can concurrently
# download the dataset.
if data_args.dataset_name is not None:
# Downloading and loading a dataset from the hub.
datasets = load_dataset(data_args.dataset_name,
data_args.dataset_config_name)
else:
data_files = {}
if data_args.train_file is not None:
data_files["train"] = data_args.train_file
if data_args.validation_file is not None:
data_files["validation"] = data_args.validation_file
if data_args.test_file is not None:
data_files["test"] = data_args.test_file
table = csv.read_csv("./data/train.csv",
parse_options=ParseOptions(delimiter="\t"))
class_label_ = table.column("label").unique()
class_label = ClassLabel(num_classes=len(class_label_),
names=class_label_.tolist())
train = main_ner.process_data(data_args.train_file, class_label)
test = main_ner.process_data(data_args.test_file, class_label)
val = main_ner.process_data(data_args.validation_file, class_label)
# table = csv.read_csv(data_args.train_file)
extension = data_args.train_file.split(".")[-1]
datasets = load_dataset(extension,
data_files=data_files,
delimiter="\t",
quoting=csv_lib.QUOTE_NONE)
train_dataset = datasets["train"]
test_dataset = datasets["test"]
val_dataset = datasets["validation"]
table = train_dataset.data
label = table.column("label")
class_label_ = label.unique()
class_label = Sequence(feature=ClassLabel(
num_classes=len(class_label_), names=class_label_.tolist()))
train_dataset.features['ner_tags'] = class_label
# train_ner_list: ChunkedArray = class_label.feature.str2int(train_dataset.data.column('label').to_numpy())
# train_ner_array = pa.array(train_ner_list)
# train_data = train_dataset.data.append_column("ner_tags", train_ner_array)
train_dataset._data = train
test_dataset.features['ner_tags'] = class_label
test_dataset._data = test
val_dataset.features['ner_tags'] = class_label
# val_ner_list: ChunkedArray = class_label.feature.str2int(val_dataset.data.column('label').to_numpy())
# val_ner_array = pa.array(val_ner_list)
# val_data = val_dataset.data.append_column("ner_tags", val_ner_array)
val_dataset._data = val
# See more about loading any type of standard or custom dataset (from files, python dict, pandas DataFrame, etc) at
# https://huggingface.co/docs/datasets/loading_datasets.html.
if training_args.do_train:
column_names = datasets["train"].column_names
features = datasets["train"].features
else:
column_names = datasets["validation"].column_names
features = datasets["validation"].features
text_column_name = "tokens" if "tokens" in column_names else column_names[0]
label_column_name = (f"{data_args.task_name}_tags"
if f"{data_args.task_name}_tags" in column_names else
column_names[1])
# In the event the labels are not a `Sequence[ClassLabel]`, we will need to go through the dataset to get the
# unique labels.
def get_label_list(labels):
unique_labels = set()
for label in labels:
unique_labels = unique_labels | set(label)
label_list = list(unique_labels)
label_list.sort()
return label_list
seq: Sequence = features[label_column_name]
# label_list = ["O", "B-GENE", "I-GENE"]
# label_to_id = {i: i for i in range(len(label_list))}
if isinstance(seq.feature, ClassLabel):
label_list = features[label_column_name].feature.names
# No need to convert the labels since they are already ints.
label_to_id = {i: i for i in range(len(label_list))}
else:
label_list = get_label_list(datasets["train"][label_column_name])
label_to_id = {l: i for i, l in enumerate(label_list)}
num_labels = len(label_list)
# Load pretrained model and tokenizer
#
# Distributed training:
# The .from_pretrained methods guarantee that only one local process can concurrently
# download model & vocab.
config = AutoConfig.from_pretrained(
model_args.config_name
if model_args.config_name else model_args.model_name_or_path,
num_labels=num_labels,
finetuning_task=data_args.task_name,
cache_dir=model_args.cache_dir,
revision=model_args.model_revision,
use_auth_token=True if model_args.use_auth_token else None,
)
tokenizer = AutoTokenizer.from_pretrained(
model_args.tokenizer_name
if model_args.tokenizer_name else model_args.model_name_or_path,
cache_dir=model_args.cache_dir,
use_fast=True,
revision=model_args.model_revision,
use_auth_token=True if model_args.use_auth_token else None,
)
model = AutoModelForTokenClassification.from_pretrained(
model_args.model_name_or_path,
from_tf=bool(".ckpt" in model_args.model_name_or_path),
config=config,
cache_dir=model_args.cache_dir,
revision=model_args.model_revision,
use_auth_token=True if model_args.use_auth_token else None,
)
# Tokenizer check: this script requires a fast tokenizer.
if not isinstance(tokenizer, PreTrainedTokenizerFast):
raise ValueError(
"This example script only works for models that have a fast tokenizer. Checkout the big table of models "
"at https://huggingface.co/transformers/index.html#bigtable to find the model types that meet this "
"requirement")
# Preprocessing the dataset
# Padding strategy
padding = "max_length" if data_args.pad_to_max_length else False
# Tokenize all texts and align the labels with them.
def tokenize_and_align_labels(examples):
tokenized_inputs = tokenizer(
examples[text_column_name],
padding=padding,
truncation=True,
# We use this argument because the texts in our dataset are lists of words (with a label for each word).
is_split_into_words=True,
)
labels = []
if len(examples) == 3:
for i, label in enumerate(examples[label_column_name]):
word_ids = tokenized_inputs.word_ids(batch_index=i)
previous_word_idx = None
label_ids = []
for word_idx in word_ids:
# Special tokens have a word id that is None. We set the label to -100 so they are automatically
# ignored in the loss function.
if word_idx is None:
label_ids.append(-100)
# We set the label for the first token of each word.
elif word_idx != previous_word_idx:
label_ids.append(label_to_id[label[word_idx]])
# For the other tokens in a word, we set the label to either the current label or -100, depending on
# the label_all_tokens flag.
else:
label_ids.append(label_to_id[label[word_idx]] if
data_args.label_all_tokens else -100)
previous_word_idx = word_idx
labels.append(label_ids)
tokenized_inputs["labels"] = labels
return tokenized_inputs
else:
print("asdasdsa")
tokenized_datasets = datasets.map(
tokenize_and_align_labels,
batched=True,
num_proc=data_args.preprocessing_num_workers,
load_from_cache_file=not data_args.overwrite_cache,
)
# Data collator
data_collator = DataCollatorForTokenClassification(tokenizer)
# Metrics
metric = load_metric("seqeval")
def compute_metrics(p):
predictions, labels = p
predictions = np.argmax(predictions, axis=2)
# Remove ignored index (special tokens)
true_predictions = [[
label_list[p] for (p, l) in zip(prediction, label) if l != -100
] for prediction, label in zip(predictions, labels)]
true_labels = [[
label_list[l] for (p, l) in zip(prediction, label) if l != -100
] for prediction, label in zip(predictions, labels)]
results = metric.compute(predictions=true_predictions,
references=true_labels)
if data_args.return_entity_level_metrics:
# Unpack nested dictionaries
final_results = {}
for key, value in results.items():
if isinstance(value, dict):
for n, v in value.items():
final_results[f"{key}_{n}"] = v
else:
final_results[key] = value
return final_results
else:
return {
"precision": results["overall_precision"],
"recall": results["overall_recall"],
"f1": results["overall_f1"],
"accuracy": results["overall_accuracy"],
}
# Initialize our Trainer
trainer = Trainer(
model=model,
args=training_args,
train_dataset=tokenized_datasets["train"]
if training_args.do_train else None,
eval_dataset=tokenized_datasets["validation"]
if training_args.do_eval else None,
tokenizer=tokenizer,
data_collator=data_collator,
compute_metrics=compute_metrics,
)
# Training
if training_args.do_train:
train_result = trainer.train(
model_path=model_args.model_name_or_path if os.path.
isdir(model_args.model_name_or_path) else None)
trainer.save_model() # Saves the tokenizer too for easy upload
output_train_file = os.path.join(training_args.output_dir,
"train_results.txt")
if trainer.is_world_process_zero():
with open(output_train_file, "w") as writer:
logger.info("***** Train results *****")
for key, value in sorted(train_result.metrics.items()):
logger.info(f" {key} = {value}")
writer.write(f"{key} = {value}\n")
# Need to save the state, since Trainer.save_model saves only the tokenizer with the model
trainer.state.save_to_json(
os.path.join(training_args.output_dir, "trainer_state.json"))
# Evaluation
results = {}
if training_args.do_eval:
logger.info("*** Evaluate ***")
results = trainer.evaluate()
output_eval_file = os.path.join(training_args.output_dir,
"eval_results_ner.txt")
if trainer.is_world_process_zero():
with open(output_eval_file, "w") as writer:
logger.info("***** Eval results *****")
for key, value in results.items():
logger.info(f" {key} = {value}")
writer.write(f"{key} = {value}\n")
# Predict
if training_args.do_predict:
logger.info("*** Predict ***")
test_dataset = tokenized_datasets["test"]
predictions, labels, metrics = trainer.predict(test_dataset)
predictions = np.argmax(predictions, axis=2)
# Remove ignored index (special tokens)
true_predictions = [[
label_list[p] for (p, l) in zip(prediction, label) if l != -100
] for prediction, label in zip(predictions, labels)]
output_test_results_file = os.path.join(training_args.output_dir,
"test_results.txt")
if trainer.is_world_process_zero():
with open(output_test_results_file, "w") as writer:
for key, value in sorted(metrics.items()):
logger.info(f" {key} = {value}")
writer.write(f"{key} = {value}\n")
# Save predictions
output_test_predictions_file = os.path.join(training_args.output_dir,
"test_predictions.txt")
if trainer.is_world_process_zero():
with open(output_test_predictions_file, "w") as writer:
for prediction in true_predictions:
writer.write(" ".join(prediction) + "\n")
return results
# Padding of token_boxes up the bounding boxes to the sequence length.
input_ids = tokenizer(' '.join(words), truncation=True)["input_ids"]
padding_length = max_seq_length - len(input_ids)
token_boxes += [pad_token_box] * padding_length
encoding['bbox'] = token_boxes
assert len(encoding['input_ids']) == max_seq_length
assert len(encoding['attention_mask']) == max_seq_length
assert len(encoding['token_type_ids']) == max_seq_length
assert len(encoding['bbox']) == max_seq_length
return encoding
# we need to define the features ourselves as the bbox of LayoutLM are an extra feature
features = Features({
'input_ids': Sequence(feature=Value(dtype='int64')),
'bbox': Array2D(dtype="int64", shape=(512, 4)),
'attention_mask': Sequence(Value(dtype='int64')),
'token_type_ids': Sequence(Value(dtype='int64')),
'image_path': Value(dtype='string'),
'words': Sequence(feature=Value(dtype='string')),
})
classes = ["bill", "invoice", "others", "Purchase_Order", "remittance"]
# Model Loading
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
@st.cache(allow_output_mutation=True)
def load_model():
url = "https://vast-ml-models.s3-ap-southeast-2.amazonaws.com/Document-Classification-5-labels-final.bin"
def make_custom_dataset(dataset_path):
if not (os.path.isdir("../data/train_dataset")
or os.path.isdir("../data/wikipedia_documents.json")):
raise Exception("Set the original data path to '../data'")
train_f = Features({
'answers':
Sequence(feature={
'text': Value(dtype='string', id=None),
'answer_start': Value(dtype='int32', id=None)
},
length=-1,
id=None),
'context':
Value(dtype='string', id=None),
'id':
Value(dtype='string', id=None),
'question':
Value(dtype='string', id=None)
})
if not os.path.isfile("../data/preprocess_wiki.json"):
with open("../data/wikipedia_documents.json", "r") as f:
wiki = json.load(f)
new_wiki = dict()
for ids in range(len(wiki)):
new_wiki[str(ids)] = run_preprocess_to(wiki[str(ids)])
with open('../data/preprocess_wiki.json', 'w',
encoding='utf-8') as make_file:
json.dump(new_wiki, make_file, indent="\t", ensure_ascii=False)
if not os.path.isfile("/opt/ml/input/data/preprocess_train.pkl"):
train_dataset = load_from_disk("../data/train_dataset")['train']
val_dataset = load_from_disk("../data/train_dataset")['validation']
new_train_data, new_val_data = [], []
for data in train_dataset:
new_data = run_preprocess(data)
new_train_data.append(new_data)
for data in val_dataset:
new_data = run_preprocess(data)
new_val_data.append(new_data)
train_df = pd.DataFrame(new_train_data)
val_df = pd.DataFrame(new_val_data)
dataset = DatasetDict({
'train':
Dataset.from_pandas(train_df, features=train_f),
'validation':
Dataset.from_pandas(val_df, features=train_f)
})
save_pickle(dataset_path, dataset)
if 'preprocess' in dataset_path:
return dataset
if 'squad' in dataset_path:
train_data = get_pickle("../data/preprocess_train.pkl")["train"]
val_data = get_pickle("../data/preprocess_train.pkl")["validation"]
korquad_data = load_dataset("squad_kor_v1")["train"]
df_train_data = pd.DataFrame(train_data)
df_val_data = pd.DataFrame(val_data)
df_korquad_data = pd.DataFrame(
korquad_data, columns=['answers', 'context', 'id', 'question'])
df_total_train = pd.concat([df_train_data, df_korquad_data])
dataset = DatasetDict({
'train':
Dataset.from_pandas(df_total_train, features=train_f),
'validation':
Dataset.from_pandas(df_val_data, features=train_f)
})
save_pickle("../data/korquad_train.pkl", dataset)
return train_dataset
if 'concat' in dataset_path:
base_dataset = get_pickle("../data/preprocess_train.pkl")
train_dataset, val_dataset = base_dataset["train"], base_dataset[
"validation"]
train_data = [{
"id": train_dataset[i]["id"],
"question": train_dataset[i]["question"],
"answers": train_dataset[i]["answers"],
"context": train_dataset[i]["context"]
} for i in range(len(train_dataset))]
val_data = [{
"id": val_dataset[i]["id"],
"question": val_dataset[i]["question"],
"answers": val_dataset[i]["answers"],
"context": val_dataset[i]["context"]
} for i in range(len(val_dataset))]
config = {'host': 'localhost', 'port': 9200}
es = Elasticsearch([config])
k = 5 # k : how many contexts to concatenate
for idx, train in enumerate(train_data):
res = search_es(es, "wiki-index", question["question"], k)
context_list = [(hit['_source']['document_text'], hit['_score'])
for hit in res['hits']['hits']]
contexts = train["context"]
count = 0
for context in context_list:
# if same context already exists, don't concatenate
if train["context"] == context[0]:
continue
contexts += " " + context[0]
count += 1
if count == (k - 1):
break
train_data[idx]["context"] = contexts
for idx, val in enumerate(val_data):
res = search_es(es, "wiki-index", question["question"], k)
context_list = [(hit['_source']['document_text'], hit['_score'])
for hit in res['hits']['hits']]
contexts = val["context"]
count = 0
for context in context_list:
if val["context"] == context[0]:
continue
contexts += " " + context[0]
count += 1
if count == (k - 1):
break
val_data[idx]["context"] = contexts
train_df = pd.DataFrame(train_data)
val_df = pd.DataFrame(val_data)
dataset = DatasetDict({
'train':
Dataset.from_pandas(train_df, features=train_f),
'validation':
Dataset.from_pandas(val_df, features=train_f)
})
save_pickle(dataset_path, dataset)
return dataset
if "split_wiki_400" in dataset_path:
with open("/opt/ml/input/data/preprocess_wiki.json", "r") as f:
wiki = json.load(f)
new_wiki = dict()
for i in tqdm(range(len(wiki))):
if len(wiki[str(i)]["text"]) < 800:
new_wiki[str(i)] = wiki[str(i)]
continue
data_list, count = passage_split_400(wiki[str(i)]["text"])
for j in range(count):
new_wiki[str(i) + f"_{j}"] = {
"text": data_list[j],
"corpus_source": wiki[str(i)]["corpus_source"],
"url": wiki[str(i)]["url"],
"domain": wiki[str(i)]["domain"],
"title": wiki[str(i)]["title"],
"author": wiki[str(i)]["author"],
"html": wiki[str(i)]["html"],
"document_id": wiki[str(i)]["document_id"]
}
save_data("../data/wiki-index-split-400.json", new_wiki)
if "split_wiki" in dataset_path and dataset_path != "split_wiki_400":
with open("/opt/ml/input/data/preprocess_wiki.json", "r") as f:
wiki = json.load(f)
limit = 0
if "800" in dataset_path:
limit = 800
if "1000" in dataset_path:
limit = 1000
new_wiki = dict()
for i in tqdm(range(len(wiki))):
if len(wiki[str(i)]["text"]) < limit:
new_wiki[str(i)] = wiki[str(i)]
continue
data_1, data_2 = passage_split(wiki[str(i)]["text"])
new_wiki[str(i) + f"_1"] = {
"text": data_1,
"corpus_source": wiki[str(i)]["corpus_source"],
"url": wiki[str(i)]["url"],
"domain": wiki[str(i)]["domain"],
"title": wiki[str(i)]["title"],
"author": wiki[str(i)]["author"],
"html": wiki[str(i)]["html"],
"document_id": wiki[str(i)]["document_id"]
}
new_wiki[str(i) + f"_2"] = {
"text": data_2,
"corpus_source": wiki[str(i)]["corpus_source"],
"url": wiki[str(i)]["url"],
"domain": wiki[str(i)]["domain"],
"title": wiki[str(i)]["title"],
"author": wiki[str(i)]["author"],
"html": wiki[str(i)]["html"],
"document_id": wiki[str(i)]["document_id"]
}
save_data(f"../data/split_wiki_{limit}.json")
def test_cast_array_to_features_nested():
arr = pa.array([[{"foo": [0]}]])
assert cast_array_to_feature(arr, [{
"foo": Sequence(Value("string"))
}]).type == pa.list_(pa.struct({"foo": pa.list_(pa.string())}))
None: 'violet',
'pn': 'yellow',
'h': 'red',
'wh': 'purple',
'fg': 'brown',
'fn': 'grey',
'tb': 'beige'
}
id2label = {v: k for k, v in label2id.items()}
LABELS = [label2id[L] for L in LABELS]
from datasets import Features, Sequence, ClassLabel, Value, Array2D, Array3D
FEATURES = Features({
'image':
Array3D(dtype="int64", shape=(3, 224, 224)),
'input_ids':
Sequence(feature=Value(dtype='int64')),
'attention_mask':
Sequence(Value(dtype='int64')),
'token_type_ids':
Sequence(Value(dtype='int64')),
'bbox':
Array2D(dtype="int64", shape=(512, 4)),
'labels':
Sequence(ClassLabel(names=LABELS + [max(LABELS) + 1]))
})
NUM_LABELS = len(LABELS)
PROCESSOR_PICKLE = f"processor_module{NUM_LABELS}.pickle"
MODEL_PICKLE = f"model_module{NUM_LABELS}.pickle"
EPOCHS_LAYOUT = 84
PDF_UPLOAD_DIR = hidden_folder + "/pdf_upload/"
ELMO_DIFFERENCE_MODEL_PATH = hidden_folder + "elmo_difference_models"
def main(
rag_example_args: "RagExampleArguments",
processing_args: "ProcessingArguments",
index_hnsw_args: "IndexHnswArguments",
):
######################################
logger.info("Step 1 - Create the dataset")
######################################
# The dataset needed for RAG must have three columns:
# - title (string): title of the document
# - text (string): text of a passage of the document
# - embeddings (array of dimension d): DPR representation of the passage
# Let's say you have documents in tab-separated csv files with columns "title" and "text"
assert os.path.isfile(
rag_example_args.csv_path), "Please provide a valid path to a csv file"
# You can load a Dataset object this way
dataset = load_dataset("csv",
data_files=[rag_example_args.csv_path],
split="train",
delimiter="\t",
column_names=["title", "text"])
# More info about loading csv files in the documentation: https://huggingface.co/docs/datasets/loading_datasets.html?highlight=csv#csv-files
# Then split the documents into passages of n words (changing the param in split_text to what you want n to be)
dataset = dataset.map(split_documents,
batched=True,
num_proc=processing_args.num_proc)
# And compute the embeddings
if use_generated_model:
model_path = 'ragfinetune_4_4_false_50_true/checkpoint2/' # SET PATH TO CHECKPOINT
config = RagConfig.from_pretrained(model_path)
config.n_docs = 4
config.n_docs_splits = 4
retriever = RagRetriever.from_pretrained(model_path, config=config)
checkpoint_model = RagSequenceForGeneration.from_pretrained(
model_path, config=config, retriever=retriever).cuda()
ctx_encoder = checkpoint_model.generator.get_encoder()
ctx_tokenizer = checkpoint_model.retriever.generator_tokenizer
else:
ctx_encoder = DPRContextEncoder.from_pretrained(
rag_example_args.dpr_ctx_encoder_model_name).to(device=device)
ctx_tokenizer = DPRContextEncoderTokenizerFast.from_pretrained(
rag_example_args.dpr_ctx_encoder_model_name)
new_features = Features({
"text": Value("string"),
"title": Value("string"),
"embeddings": Sequence(Value("float32"))
}) # optional, save as float32 instead of float64 to save space
dataset = dataset.map(
partial(embed, ctx_encoder=ctx_encoder, ctx_tokenizer=ctx_tokenizer),
batched=True,
batch_size=processing_args.batch_size,
features=new_features,
)
# And finally save your dataset
passages_path = os.path.join(rag_example_args.output_dir,
"my_knowledge_dataset")
dataset.save_to_disk(passages_path)
# from datasets import load_from_disk
# dataset = load_from_disk(passages_path) # to reload the dataset
######################################
logger.info("Step 2 - Index the dataset")
######################################
# Let's use the Faiss implementation of HNSW for fast approximate nearest neighbor search
index = faiss.IndexHNSWFlat(index_hnsw_args.d, index_hnsw_args.m,
faiss.METRIC_INNER_PRODUCT)
dataset.add_faiss_index("embeddings", custom_index=index)
# And save the index
index_path = os.path.join(rag_example_args.output_dir,
"my_knowledge_dataset_hnsw_index.faiss")
dataset.get_index("embeddings").save(index_path)
# dataset.load_faiss_index("embeddings", index_path) # to reload the index
######################################
logger.info("Step 3 - Load RAG")
######################################
# Easy way to load the model
retriever = RagRetriever.from_pretrained(rag_example_args.rag_model_name,
index_name="custom",
indexed_dataset=dataset)
model = RagSequenceForGeneration.from_pretrained(
rag_example_args.rag_model_name, retriever=retriever)
tokenizer = RagTokenizer.from_pretrained(rag_example_args.rag_model_name)
# For distributed fine-tuning you'll need to provide the paths instead, as the dataset and the index are loaded separately.
# retriever = RagRetriever.from_pretrained(rag_model_name, index_name="custom", passages_path=passages_path, index_path=index_path)
######################################
logger.info("Step 4 - Have fun")
######################################
question = rag_example_args.question or "What does Moses' rod turn into ?"
input_ids = tokenizer.question_encoder(question,
return_tensors="pt")["input_ids"]
generated = model.generate(input_ids)
generated_string = tokenizer.batch_decode(generated,
skip_special_tokens=True)[0]
logger.info("Q: " + question)
logger.info("A: " + generated_string)
def retrieve(self, query_or_dataset, topk=1):
assert self.p_embedding is not None, "get_embedding()을 먼저 수행한 후에 retrieve()를 작동시켜 주세요. "
total = []
# 중복을 걸러내기 위해 40 + topk (확인된 최대 중복 개수 40 + topk개)으로 최소값을 설정하고, topk의 alpha 배수로 뽑습니다.
alpha = 2
doc_scores, doc_indices = self.get_relevant_doc_bulk(
query_or_dataset["question"], topk=max(40 + topk, alpha * topk)
)
for idx, example in enumerate(tqdm(query_or_dataset, desc="Retrieval: ")):
doc_scores_topk = [doc_scores[idx][0]]
doc_indices_topk = [doc_indices[idx][0]]
pointer = 1
while len(doc_indices_topk) != topk:
is_non_duplicate = True
new_text_idx = doc_indices[idx][pointer]
new_text = self.contexts[new_text_idx]
for d_id in doc_indices_topk:
if fuzz.ratio(self.contexts[d_id], new_text) > 65:
is_non_duplicate = False
break
if is_non_duplicate:
doc_scores_topk.append(doc_scores[idx][pointer])
doc_indices_topk.append(new_text_idx)
pointer += 1
if pointer == max(40 + topk, alpha * topk):
break
assert len(doc_indices_topk) == topk, "중복 없는 topk 추출을 위해 alpha 값을 증가시켜 주세요."
for doc_id in range(topk):
doc_idx = doc_indices_topk[doc_id]
tmp = {
"question": example["question"],
"id": example["id"],
"context_id": self.context_ids[doc_idx], # retrieved id
"context": self.contexts[doc_idx], # retrieved document
}
if "context" in example.keys() and "answers" in example.keys():
tmp["original_context"] = example["context"] # original document
tmp["answers"] = example["answers"] # original answer
total.append(tmp)
df = pd.DataFrame(total)
if self.args.train.do_predict is True:
f = Features(
{
"context": Value(dtype="string", id=None),
"id": Value(dtype="string", id=None),
"question": Value(dtype="string", id=None),
"context_id": Value(dtype="int32", id=None),
}
)
else:
f = Features(
{
"answers": Sequence(
feature={"text": Value(dtype="string", id=None), "answer_start": Value(dtype="int32", id=None)},
length=-1,
id=None,
),
"context": Value(dtype="string", id=None),
"id": Value(dtype="string", id=None),
"question": Value(dtype="string", id=None),
"original_context": Value(dtype="string", id=None),
"context_id": Value(dtype="int32", id=None),
}
)
datasets = DatasetDict({"validation": Dataset.from_pandas(df, features=f)})
return datasets
import os.path as p
from collections import defaultdict
import pandas as pd
from datasets import load_dataset
from datasets import concatenate_datasets
from datasets import Sequence, Value, Features, Dataset, DatasetDict
from utils.tools import get_args
f = Features({
"answers":
Sequence(
feature={
"text": Value(dtype="string", id=None),
"answer_start": Value(dtype="int32", id=None)
},
length=-1,
id=None,
),
"id":
Value(dtype="string", id=None),
"context":
Value(dtype="string", id=None),
"question":
Value(dtype="string", id=None),
"title":
Value(dtype="string", id=None),
})
def remove_multiple_indexes(rlist, indexes):