dewey_en_beta / scripts /evaluate /run_evaluate_loco.py

Upload run_evaluate_loco.py

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import json
import random

import pandas as pd
import torch
import os

os.environ["HF_ENDPOINT"] = "https://hf-mirror.com"
from sentence_transformers import SentenceTransformer
import tqdm
import numpy as np
import faiss
from sklearn.metrics import ndcg_score
from os.path import join
from sklearn.preprocessing import normalize
from transformers import AutoTokenizer, AutoModel

faiss.omp_set_num_threads(16)


def find_topk_by_vecs(source_vecs: np.ndarray, target_vecs: np.ndarray, topk: int):
    if topk > len(target_vecs):
        topk = len(target_vecs)
    faiss_index = faiss.IndexFlatIP(target_vecs.shape[1])
    faiss_index.add(target_vecs)

    res_distance, res_index = faiss_index.search(source_vecs, topk)
    return res_index, res_distance


def get_loco_path_info(q_dir, d_dir):
    names = []
    for name in sorted(os.listdir(q_dir)):
        if name.endswith(".jsonl"):
            names.append(name)
    for name in os.listdir(d_dir):
        if name.endswith(".jsonl"):
            assert name in names
    infos = []
    for name in names:
        infos.append(["LOCO-V1", name, join(q_dir, name), join(d_dir, name)])
    infos.sort(key=lambda x: x[1])
    return infos


def get_loco_data(q_path, d_path):
    passage_list, query2passage_list = [], {}

    original_doc_id2doc = {}

    with open(d_path, "r", encoding="utf8") as fr:
        for line in fr:
            item = json.loads(line)
            if item["passage"].strip():
                original_doc_id2doc[item["pid"]] = item["passage"].strip()
                passage_list.append(item["passage"].strip())

    with open(q_path, "r", encoding="utf8") as fr:
        for line in fr:
            item = json.loads(line)
            if item["query"].strip():
                query2passage_list[item["query"].strip()] = [
                    original_doc_id2doc[answer_pid]
                    for answer_pid in item["answer_pids"]
                    if answer_pid in original_doc_id2doc
                ]
    query2passage_list = {k: list(set(v)) for k, v in query2passage_list.items() if list(set(v))}
    passage_list = list(set(passage_list))
    passage2id = {passage: idx for idx, passage in enumerate(passage_list)}
    query2id_list = {k: list(set([passage2id[i] for i in v])) for k, v in query2passage_list.items()}
    query_list = list(query2id_list.keys())
    return query_list, passage_list, query2id_list


def get_ndcg_score(query_list, passage_list, query2passage_id_list, topk=10, error_data_save_path: str = None):
    chunk_id2passage_id = {}
    q_vecs = model.encode(
        sentences=query_list,
        batch_size=batch_size,
        chunk_size=chunk_size,
        chunk_overlap=chunk_overlap,
        max_seq_length=max_seq_length,
        is_q=True,
    )
    p_vecs = model.encode(
        sentences=passage_list,
        batch_size=batch_size,
        chunk_size=chunk_size,
        chunk_overlap=chunk_overlap,
        max_seq_length=max_seq_length,
        is_q=False,
    )
    # according query2id_list get labels_list
    query_id_list = [query2passage_id_list[query] for query in query_list]
    max_doc = max((len(id_list) for id_list in query_id_list))

    labels = np.array([(id_list * max_doc)[:max_doc] for id_list in query_id_list])
    if isinstance(p_vecs, list):
        for idx, vec in enumerate(p_vecs):
            if multi_vec_strategy == "full_text":
                p_vecs[idx] = normalize(np.mean(vec[1:2, :], axis=0, keepdims=True), axis=1)
            elif multi_vec_strategy == "full_text+chunks":
                n_chunk = (vec.shape[0] - 2) // 2
                if n_chunk > 0:
                    p_vecs[idx] = np.vstack(
                        (
                            normalize(np.mean(vec[:2, :], axis=0, keepdims=True), axis=1),
                            vec[2:2 + n_chunk, :],
                        )
                    )
                else:
                    p_vecs[idx] = normalize(np.mean(vec[:2, :], axis=0, keepdims=True), axis=1)
        p_vecs = np.vstack(p_vecs)

    if isinstance(q_vecs, list):
        for idx, vec in enumerate(q_vecs):
            q_vecs[idx] = normalize(np.mean(vec[0:2, :], axis=0, keepdims=True), axis=1)
        q_vecs = np.vstack(q_vecs)
    print("q_vecs.shape and dtype", q_vecs.shape, q_vecs.dtype)
    print("p_vecs.shape and dtype", p_vecs.shape, p_vecs.dtype)
    # search topk
    # we calculate ndcg@10
    topk_index, topk_scores = find_topk_by_vecs(q_vecs, p_vecs, topk * 100)
    # print("topk_index", topk_index.shape, topk_index)
    # print("topk_scores", topk_scores.shape, topk_scores)
    ### we may use multi vectors, so we should modify topk_index and topk_scores
    if chunk_id2passage_id:
        new_topk_index, new_topk_scores = [], []
        # print("chunk_id2passage_id")
        for chunk_ids, chunk_scores in tqdm.tqdm(zip(topk_index, topk_scores),
                                                 desc="modify topk_index and topk_scores", disable=True):
            # processed by row
            row_ids, row_scores, passage_id_set = [], [], set()
            for idx, chunk_id in enumerate(chunk_ids):
                passage_id = chunk_id2passage_id[chunk_id]
                if passage_id not in passage_id_set:
                    passage_id_set.add(passage_id)
                    row_ids.append(passage_id)
                    row_scores.append(chunk_scores[idx])
            new_topk_index.append(row_ids[:topk])
            new_topk_scores.append(row_scores[:topk])
        topk_index = np.array(new_topk_index)
        # print("topk_index", topk_index)
        topk_scores = np.array(new_topk_scores)
    topk_index, topk_scores = topk_index[:, :topk], topk_scores[:, :topk]
    is_match = (topk_index == labels[:, :1])
    for idx in range(1, max_doc):
        # the or operator means that only one positive doc in pred topk, we think it is recalled
        is_match = is_match | (topk_index == labels[:, idx:idx + 1])

    # compute recall at topk
    print("is_match.shape", is_match.shape)
    # recall_at_k = is_match.sum(axis=1).astype(bool).mean()
    ndcg = ndcg_score(is_match.astype(dtype=np.float32), topk_scores)

    if error_data_save_path:
        in_top_k = is_match.sum(axis=1).astype(bool)
        err_data = []
        for idx, pred_res in enumerate(in_top_k):
            if not pred_res:
                query = query_list[idx]
                label_doc = passage_list[query2passage_id_list[query][0]]
                pred_doc = passage_list[topk_index[idx][0]]
                err_data.append([query, label_doc, pred_doc])
        pd.DataFrame(err_data, columns=["Query", "Label", "Pred"]).to_excel(error_data_save_path, index=False)
    return float(ndcg)


class ModelWrapper:
    def __init__(self, model_dir, model_type, max_seq_length):
        assert model_type in ["dewey", "sentence_transformer"]
        self.model_type = model_type
        self.tokenizer = AutoTokenizer.from_pretrained(model_dir)
        if model_type == "dewey":
            self.model = AutoModel.from_pretrained(
                model_dir,
                attn_implementation="flash_attention_2",
                trust_remote_code=True,
            ).cuda().bfloat16().eval()
            self.model.tokenizer = self.tokenizer
        else:
            self.model = SentenceTransformer(
                model_dir,
                trust_remote_code=True,
                device="cpu",
                model_kwargs={
                    "torch_dtype": torch.bfloat16,  # fp16
                    "attn_implementation": "flash_attention_2"
                },
            )
            self.model.max_seq_length = max_seq_length
            if "NV-Embed-v2" in model_dir:
                self.model.tokenizer.padding_side = "right"
            self.pool = self.model.start_multi_process_pool()

    def encode(
            self,
            sentences,
            batch_size,
            chunk_size,
            chunk_overlap,
            max_seq_length,
            is_q,
    ):
        if self.model_type == "dewey":
            if is_q:
                prompt = "<|START_INSTRUCTION|>Answer the question<|END_INSTRUCTION|>"
            else:
                prompt = "<|START_INSTRUCTION|>Candidate document<|END_INSTRUCTION|>"
            return self.model.encode(
                sentences=sentences,
                batch_size=batch_size,
                use_cuda=True,
                show_progress_bar=True,
                chunk_size=chunk_size,
                chunk_overlap=chunk_overlap,
                convert_to_tensor=False,
                max_seq_length=max_seq_length,
                normalize_embeddings=True,
                prompt=prompt,
                fast_chunk=True,
            )[0]
        self.model.max_seq_length = max_seq_length
        prompt = None
        if is_q and (
                "Linq-Embed-Mistral" in model_dir or "e5-mistral-7b-instruct" in model_dir or "SFR-Embedding-Mistral" in model_dir):
            prompt = PROMPT_E5
        if is_q and ("NV-Embed-v2" in model_dir):
            prompt = PROMPT_NV
        if "chunk_alignment" in model_dir or "dewey" in model_dir:
            if is_q:
                prompt = "<|START_INSTRUCTION|>Answer the question<|END_INSTRUCTION|>"
            else:
                prompt = "<|START_INSTRUCTION|>Candidate document<|END_INSTRUCTION|>"
        vecs = self.model.encode_multi_process(
            add_eos(sentences) if "NV-Embed-v2" in model_dir else sentences,
            pool=self.pool,
            show_progress_bar=True,
            batch_size=batch_size,
            normalize_embeddings=True,
            prompt=prompt
        )
        return vecs


def add_eos(input_examples):
    input_examples = [input_example + model.tokenizer.eos_token for input_example in input_examples]
    return input_examples


PROMPT_BGE = "Represent this sentence for searching relevant passages:"
PROMPT_E5 = "Instruct: Given a web search query, retrieve relevant passages that answer the query.\nQuery: "
PROMPT_NV = "Instruct: Given a question, retrieve passages that answer the question\nQuery: "
if __name__ == "__main__":
    chunk_size = -1
    chunk_overlap = 32
    batch_size = 2
    max_seq_length = 8 * 1024
    multi_vec_strategy = "full_text"  # full_text; full_text+chunks
    err_data_save_path = None
    topk = 10

    model_dir = "infgrad/dewey_en_beta"
    # model_dir = "/home/zd/public_models/Linq-Embed-Mistral/"
    # model_dir = "/home/zd/public_models/SFR-Embedding-Mistral"
    # model_dir = "/home/zd/public_models/e5-mistral-7b-instruct"
    # model_dir = "/home/zd/public_models/bge-m3"
    # model_dir = "/home/zd/public_models/gte-modernbert-base"
    # model_dir = "/home/zd/public_models/NV-Embed-v2"

    # sentence_transformer dewey
    model_type = "sentence_transformer"
    ## get data info
    # TODO Please download LOCOV1 data first!
    data_info = get_loco_path_info(
        "/home/zd/public_data/LoCoV1-Queries/documents/",
        "/home/zd/public_data/LoCoV1-Documents/documents/",
    )

    # load model
    model = ModelWrapper(model_dir=model_dir, model_type=model_type, max_seq_length=max_seq_length)
    # model = zd()
    ndcg_score_list = []
    for item in data_info:
        print("\n\n\n\n" + "=" * 20)
        print(f"evaluate {item[:2]}...")
        query_list, passage_list, query2passage_id_list = get_loco_data(*item[2:])
        print("number of all queries", len(query_list))
        print("number of all passages", len(passage_list))
        ndcg = get_ndcg_score(query_list, passage_list, query2passage_id_list, topk=topk,
                              error_data_save_path=err_data_save_path)
        print(f"{ndcg}")
        ndcg_score_list.append(ndcg)

    for i in data_info:
        print(i[0])
    print("\n\n\n")
    for i in data_info:
        print(i[1].replace(".jsonl", ""))
    print("\n\n\n")

    print(os.path.basename(model_dir))
    for i in ndcg_score_list:
        print(i)

	import json
	import random

	import pandas as pd
	import torch
	import os

	os.environ["HF_ENDPOINT"] = "https://hf-mirror.com"
	from sentence_transformers import SentenceTransformer
	import tqdm
	import numpy as np
	import faiss
	from sklearn.metrics import ndcg_score
	from os.path import join
	from sklearn.preprocessing import normalize
	from transformers import AutoTokenizer, AutoModel

	faiss.omp_set_num_threads(16)


	def find_topk_by_vecs(source_vecs: np.ndarray, target_vecs: np.ndarray, topk: int):
	if topk > len(target_vecs):
	topk = len(target_vecs)
	faiss_index = faiss.IndexFlatIP(target_vecs.shape[1])
	faiss_index.add(target_vecs)

	res_distance, res_index = faiss_index.search(source_vecs, topk)
	return res_index, res_distance


	def get_loco_path_info(q_dir, d_dir):
	names = []
	for name in sorted(os.listdir(q_dir)):
	if name.endswith(".jsonl"):
	names.append(name)
	for name in os.listdir(d_dir):
	if name.endswith(".jsonl"):
	assert name in names
	infos = []
	for name in names:
	infos.append(["LOCO-V1", name, join(q_dir, name), join(d_dir, name)])
	infos.sort(key=lambda x: x[1])
	return infos


	def get_loco_data(q_path, d_path):
	passage_list, query2passage_list = [], {}

	original_doc_id2doc = {}

	with open(d_path, "r", encoding="utf8") as fr:
	for line in fr:
	item = json.loads(line)
	if item["passage"].strip():
	original_doc_id2doc[item["pid"]] = item["passage"].strip()
	passage_list.append(item["passage"].strip())

	with open(q_path, "r", encoding="utf8") as fr:
	for line in fr:
	item = json.loads(line)
	if item["query"].strip():
	query2passage_list[item["query"].strip()] = [
	original_doc_id2doc[answer_pid]
	for answer_pid in item["answer_pids"]
	if answer_pid in original_doc_id2doc
	]
	query2passage_list = {k: list(set(v)) for k, v in query2passage_list.items() if list(set(v))}
	passage_list = list(set(passage_list))
	passage2id = {passage: idx for idx, passage in enumerate(passage_list)}
	query2id_list = {k: list(set([passage2id[i] for i in v])) for k, v in query2passage_list.items()}
	query_list = list(query2id_list.keys())
	return query_list, passage_list, query2id_list


	def get_ndcg_score(query_list, passage_list, query2passage_id_list, topk=10, error_data_save_path: str = None):
	chunk_id2passage_id = {}
	q_vecs = model.encode(
	sentences=query_list,
	batch_size=batch_size,
	chunk_size=chunk_size,
	chunk_overlap=chunk_overlap,
	max_seq_length=max_seq_length,
	is_q=True,
	)
	p_vecs = model.encode(
	sentences=passage_list,
	batch_size=batch_size,
	chunk_size=chunk_size,
	chunk_overlap=chunk_overlap,
	max_seq_length=max_seq_length,
	is_q=False,
	)
	# according query2id_list get labels_list
	query_id_list = [query2passage_id_list[query] for query in query_list]
	max_doc = max((len(id_list) for id_list in query_id_list))

	labels = np.array([(id_list * max_doc)[:max_doc] for id_list in query_id_list])
	if isinstance(p_vecs, list):
	for idx, vec in enumerate(p_vecs):
	if multi_vec_strategy == "full_text":
	p_vecs[idx] = normalize(np.mean(vec[1:2, :], axis=0, keepdims=True), axis=1)
	elif multi_vec_strategy == "full_text+chunks":
	n_chunk = (vec.shape[0] - 2) // 2
	if n_chunk > 0:
	p_vecs[idx] = np.vstack(
	(
	normalize(np.mean(vec[:2, :], axis=0, keepdims=True), axis=1),
	vec[2:2 + n_chunk, :],
	)
	)
	else:
	p_vecs[idx] = normalize(np.mean(vec[:2, :], axis=0, keepdims=True), axis=1)
	p_vecs = np.vstack(p_vecs)

	if isinstance(q_vecs, list):
	for idx, vec in enumerate(q_vecs):
	q_vecs[idx] = normalize(np.mean(vec[0:2, :], axis=0, keepdims=True), axis=1)
	q_vecs = np.vstack(q_vecs)
	print("q_vecs.shape and dtype", q_vecs.shape, q_vecs.dtype)
	print("p_vecs.shape and dtype", p_vecs.shape, p_vecs.dtype)
	# search topk
	# we calculate ndcg@10
	topk_index, topk_scores = find_topk_by_vecs(q_vecs, p_vecs, topk * 100)
	# print("topk_index", topk_index.shape, topk_index)
	# print("topk_scores", topk_scores.shape, topk_scores)
	### we may use multi vectors, so we should modify topk_index and topk_scores
	if chunk_id2passage_id:
	new_topk_index, new_topk_scores = [], []
	# print("chunk_id2passage_id")
	for chunk_ids, chunk_scores in tqdm.tqdm(zip(topk_index, topk_scores),
	desc="modify topk_index and topk_scores", disable=True):
	# processed by row
	row_ids, row_scores, passage_id_set = [], [], set()
	for idx, chunk_id in enumerate(chunk_ids):
	passage_id = chunk_id2passage_id[chunk_id]
	if passage_id not in passage_id_set:
	passage_id_set.add(passage_id)
	row_ids.append(passage_id)
	row_scores.append(chunk_scores[idx])
	new_topk_index.append(row_ids[:topk])
	new_topk_scores.append(row_scores[:topk])
	topk_index = np.array(new_topk_index)
	# print("topk_index", topk_index)
	topk_scores = np.array(new_topk_scores)
	topk_index, topk_scores = topk_index[:, :topk], topk_scores[:, :topk]
	is_match = (topk_index == labels[:, :1])
	for idx in range(1, max_doc):
	# the or operator means that only one positive doc in pred topk, we think it is recalled
	is_match = is_match \| (topk_index == labels[:, idx:idx + 1])

	# compute recall at topk
	print("is_match.shape", is_match.shape)
	# recall_at_k = is_match.sum(axis=1).astype(bool).mean()
	ndcg = ndcg_score(is_match.astype(dtype=np.float32), topk_scores)

	if error_data_save_path:
	in_top_k = is_match.sum(axis=1).astype(bool)
	err_data = []
	for idx, pred_res in enumerate(in_top_k):
	if not pred_res:
	query = query_list[idx]
	label_doc = passage_list[query2passage_id_list[query][0]]
	pred_doc = passage_list[topk_index[idx][0]]
	err_data.append([query, label_doc, pred_doc])
	pd.DataFrame(err_data, columns=["Query", "Label", "Pred"]).to_excel(error_data_save_path, index=False)
	return float(ndcg)


	class ModelWrapper:
	def __init__(self, model_dir, model_type, max_seq_length):
	assert model_type in ["dewey", "sentence_transformer"]
	self.model_type = model_type
	self.tokenizer = AutoTokenizer.from_pretrained(model_dir)
	if model_type == "dewey":
	self.model = AutoModel.from_pretrained(
	model_dir,
	attn_implementation="flash_attention_2",
	trust_remote_code=True,
	).cuda().bfloat16().eval()
	self.model.tokenizer = self.tokenizer
	else:
	self.model = SentenceTransformer(
	model_dir,
	trust_remote_code=True,
	device="cpu",
	model_kwargs={
	"torch_dtype": torch.bfloat16, # fp16
	"attn_implementation": "flash_attention_2"
	},
	)
	self.model.max_seq_length = max_seq_length
	if "NV-Embed-v2" in model_dir:
	self.model.tokenizer.padding_side = "right"
	self.pool = self.model.start_multi_process_pool()

	def encode(
	self,
	sentences,
	batch_size,
	chunk_size,
	chunk_overlap,
	max_seq_length,
	is_q,
	):
	if self.model_type == "dewey":
	if is_q:
	prompt = "<\|START_INSTRUCTION\|>Answer the question<\|END_INSTRUCTION\|>"
	else:
	prompt = "<\|START_INSTRUCTION\|>Candidate document<\|END_INSTRUCTION\|>"
	return self.model.encode(
	sentences=sentences,
	batch_size=batch_size,
	use_cuda=True,
	show_progress_bar=True,
	chunk_size=chunk_size,
	chunk_overlap=chunk_overlap,
	convert_to_tensor=False,
	max_seq_length=max_seq_length,
	normalize_embeddings=True,
	prompt=prompt,
	fast_chunk=True,
	)[0]
	self.model.max_seq_length = max_seq_length
	prompt = None
	if is_q and (
	"Linq-Embed-Mistral" in model_dir or "e5-mistral-7b-instruct" in model_dir or "SFR-Embedding-Mistral" in model_dir):
	prompt = PROMPT_E5
	if is_q and ("NV-Embed-v2" in model_dir):
	prompt = PROMPT_NV
	if "chunk_alignment" in model_dir or "dewey" in model_dir:
	if is_q:
	prompt = "<\|START_INSTRUCTION\|>Answer the question<\|END_INSTRUCTION\|>"
	else:
	prompt = "<\|START_INSTRUCTION\|>Candidate document<\|END_INSTRUCTION\|>"
	vecs = self.model.encode_multi_process(
	add_eos(sentences) if "NV-Embed-v2" in model_dir else sentences,
	pool=self.pool,
	show_progress_bar=True,
	batch_size=batch_size,
	normalize_embeddings=True,
	prompt=prompt
	)
	return vecs


	def add_eos(input_examples):
	input_examples = [input_example + model.tokenizer.eos_token for input_example in input_examples]
	return input_examples


	PROMPT_BGE = "Represent this sentence for searching relevant passages:"
	PROMPT_E5 = "Instruct: Given a web search query, retrieve relevant passages that answer the query.\nQuery: "
	PROMPT_NV = "Instruct: Given a question, retrieve passages that answer the question\nQuery: "
	if __name__ == "__main__":
	chunk_size = -1
	chunk_overlap = 32
	batch_size = 2
	max_seq_length = 8 * 1024
	multi_vec_strategy = "full_text" # full_text; full_text+chunks
	err_data_save_path = None
	topk = 10

	model_dir = "infgrad/dewey_en_beta"
	# model_dir = "/home/zd/public_models/Linq-Embed-Mistral/"
	# model_dir = "/home/zd/public_models/SFR-Embedding-Mistral"
	# model_dir = "/home/zd/public_models/e5-mistral-7b-instruct"
	# model_dir = "/home/zd/public_models/bge-m3"
	# model_dir = "/home/zd/public_models/gte-modernbert-base"
	# model_dir = "/home/zd/public_models/NV-Embed-v2"

	# sentence_transformer dewey
	model_type = "sentence_transformer"
	## get data info
	# TODO Please download LOCOV1 data first!
	data_info = get_loco_path_info(
	"/home/zd/public_data/LoCoV1-Queries/documents/",
	"/home/zd/public_data/LoCoV1-Documents/documents/",
	)

	# load model
	model = ModelWrapper(model_dir=model_dir, model_type=model_type, max_seq_length=max_seq_length)
	# model = zd()
	ndcg_score_list = []
	for item in data_info:
	print("\n\n\n\n" + "=" * 20)
	print(f"evaluate {item[:2]}...")
	query_list, passage_list, query2passage_id_list = get_loco_data(*item[2:])
	print("number of all queries", len(query_list))
	print("number of all passages", len(passage_list))
	ndcg = get_ndcg_score(query_list, passage_list, query2passage_id_list, topk=topk,
	error_data_save_path=err_data_save_path)
	print(f"{ndcg}")
	ndcg_score_list.append(ndcg)

	for i in data_info:
	print(i[0])
	print("\n\n\n")
	for i in data_info:
	print(i[1].replace(".jsonl", ""))
	print("\n\n\n")

	print(os.path.basename(model_dir))
	for i in ndcg_score_list:
	print(i)