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Browse files- app.py +566 -0
- int_to_doc_id.pkl +3 -0
- requirements.txt +12 -0
app.py
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| 1 |
+
from qdrant_client import QdrantClient
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| 2 |
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from qdrant_client.models import VectorParams, Distance
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| 3 |
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from sentence_transformers import SentenceTransformer, CrossEncoder
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| 4 |
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from datasets import load_dataset
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| 5 |
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import numpy as np
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import pandas as pd
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import time
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| 8 |
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from tqdm import tqdm
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| 9 |
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import os, pickle
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| 10 |
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import gradio as gr
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| 11 |
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from gradio_client import Client
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from math import log2
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# =====================
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| 15 |
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# PARAMETERS
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# =====================
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retrieval_n = 50
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num_queries = 10
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docs_n = 100000
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| 20 |
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batch_size = 1000
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| 21 |
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embedding_models = ["all-MiniLM-L6-v2"]
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| 22 |
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rerank_models = [
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| 23 |
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"cross-encoder/ms-marco-MiniLM-L-6-v2",
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| 24 |
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"cross-encoder/ms-marco-TinyBERT-L-6",
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| 25 |
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#"cross-encoder/nli-deberta-v3-base-biomed", # biomedical NLI fine-tune
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| 26 |
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#"ncbi/MedCPT-Cross-Encoder-msmarco" # biomedical passage reranker
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| 27 |
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]
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| 28 |
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collection_name = "trec_covid"
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| 30 |
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qdrant_url = os.getenv("QDRANT_URL", "http://localhost:6333")k_values = [1, 3, 5, 10, 20]
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| 31 |
+
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| 32 |
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# =====================
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# LOAD DATA
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| 34 |
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# =====================
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print("Loading datasets...")
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| 36 |
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corpus = load_dataset("BeIR/trec-covid", "corpus")
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| 37 |
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queries = load_dataset("BeIR/trec-covid", "queries")
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| 38 |
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qrels = load_dataset("BeIR/trec-covid-qrels", split='test')
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| 39 |
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| 40 |
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print(f"Preparing corpus dict from first {docs_n} docs...")
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| 41 |
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corpus_docs = corpus['corpus'][:docs_n]
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| 42 |
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corpus_dict= {}
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| 43 |
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for i in tqdm(range(len(corpus_docs['_id'])), desc="Corpus dict build"):
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| 44 |
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corpus_dict[corpus_docs['_id'][i]] = corpus_docs['text'][i]
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| 45 |
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doc_ids_set = set(corpus_dict.keys())
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| 46 |
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| 47 |
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print("Building qrels dictionary...")
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| 48 |
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qrels_dict = {}
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| 49 |
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for row in tqdm(qrels, desc="Processing qrels"):
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| 50 |
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qid = int(row['query-id'])
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| 51 |
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if qid not in qrels_dict:
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| 52 |
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qrels_dict[qid] = {}
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| 53 |
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if row['corpus-id'] in doc_ids_set:
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| 54 |
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qrels_dict[qid][row['corpus-id']] = int(row['score'])
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| 55 |
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| 56 |
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filtered_qids = [qid for qid in qrels_dict.keys() if len(qrels_dict[qid]) > 0][:num_queries]
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| 57 |
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| 58 |
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print(f"Filtering and loading {len(filtered_qids)} queries...")
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| 59 |
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queries_list = []
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| 60 |
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for qid in tqdm(filtered_qids, desc="Loading queries"):
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| 61 |
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filtered_query = queries['queries'].filter(lambda x: x['_id'] == str(qid))
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| 62 |
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if len(filtered_query) > 0:
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| 63 |
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queries_list.append((qid, filtered_query[0]['text']))
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| 64 |
+
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| 65 |
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avg_relevant_docs = np.mean([len([doc for doc, score in rel.items() if score >= 2]) for rel in qrels_dict.values()])
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| 66 |
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print(f"Average relevant docs per query: {avg_relevant_docs:.2f}")
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| 68 |
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| 69 |
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# =====================
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| 70 |
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# METRICS FUNCTIONS
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| 71 |
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# =====================
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| 72 |
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def recall_at_k(relevant, retrieved, k):
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| 73 |
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relevant_set = set(relevant.keys())
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| 74 |
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retrieved_k = set(retrieved[:k])
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| 75 |
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return len(relevant_set.intersection(retrieved_k)) / len(relevant_set) if relevant_set else 0
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| 76 |
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| 77 |
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def precision_at_k(relevant, retrieved, k, rel_threshold=1):
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| 78 |
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relevant_set = set(doc for doc, score in relevant.items() if score >= rel_threshold)
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| 79 |
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retrieved_k = retrieved[:k]
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| 80 |
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return sum(1 for doc in retrieved_k if doc in relevant_set) / k
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| 81 |
+
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| 82 |
+
def dcg_at_k(rels, k):
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| 83 |
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return sum((2**rel - 1) / np.log2(idx + 2) for idx, rel in enumerate(rels[:k]))
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| 84 |
+
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| 85 |
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def ndcg_at_k(relevant_scores, retrieved_ids, k):
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| 86 |
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retrieved_rels = [relevant_scores.get(doc_id, 0) for doc_id in retrieved_ids[:k]]
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| 87 |
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ideal_rels = sorted(relevant_scores.values(), reverse=True)[:k]
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| 88 |
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ideal_dcg = dcg_at_k(ideal_rels, k)
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| 89 |
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actual_dcg = dcg_at_k(retrieved_rels, k)
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| 90 |
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return actual_dcg / ideal_dcg if ideal_dcg > 0 else 0
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| 91 |
+
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| 92 |
+
def average_precision(relevant, retrieved, rel_threshold=1):
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| 93 |
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relevant_set = set(doc for doc, score in relevant.items() if score >= rel_threshold)
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| 94 |
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hits = 0
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sum_prec = 0.0
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| 96 |
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for i, doc_id in enumerate(retrieved):
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| 97 |
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if doc_id in relevant_set:
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| 98 |
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hits += 1
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| 99 |
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sum_prec += hits / (i + 1)
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| 100 |
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return sum_prec / len(relevant_set) if relevant_set else 0
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| 101 |
+
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| 102 |
+
def reciprocal_rank(relevant, retrieved, rel_threshold=1):
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| 103 |
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relevant_set = set(doc for doc, score in relevant.items() if score >= rel_threshold)
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| 104 |
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for i, doc_id in enumerate(retrieved):
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| 105 |
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if doc_id in relevant_set:
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| 106 |
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return 1 / (i + 1)
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| 107 |
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return 0
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| 108 |
+
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| 109 |
+
def success_at_k(relevant, retrieved, k, rel_threshold=1):
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| 110 |
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relevant_set = set(doc for doc, score in relevant.items() if score >= rel_threshold)
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| 111 |
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return int(any(doc in relevant_set for doc in retrieved[:k]))
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| 112 |
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| 113 |
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# =====================
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| 114 |
+
# METRICS EVALUATION FUNCTION
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| 115 |
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# =====================
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| 116 |
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def evaluate_metrics(results_data, qrels_dict, k_values):
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| 117 |
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rows = []
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| 118 |
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for model_name, data in results_data.items():
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| 119 |
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recalls = {k: [] for k in k_values}
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| 120 |
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precisions = {k: [] for k in k_values}
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| 121 |
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ndcgs = {k: [] for k in k_values}
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| 122 |
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success = {k: [] for k in k_values}
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| 123 |
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maps = []
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| 124 |
+
mrrs = []
|
| 125 |
+
retrieval_times = data.get("retrieval_times", [])
|
| 126 |
+
rerank_times = data.get("rerank_times", [])
|
| 127 |
+
|
| 128 |
+
print(f"Evaluating metrics for {model_name} ...")
|
| 129 |
+
for i, (qid, retrieved, rerank_scores) in enumerate(tqdm(zip(data["qids"], data["retrieved"], data["rerank_scores"]), total=len(data["qids"]), desc=f"Metrics {model_name}")):
|
| 130 |
+
relevant = qrels_dict.get(qid, {})
|
| 131 |
+
if rerank_scores:
|
| 132 |
+
sorted_docs = [doc for doc, score in sorted(zip(retrieved, rerank_scores), key=lambda x: x[1], reverse=True)]
|
| 133 |
+
else:
|
| 134 |
+
sorted_docs = retrieved
|
| 135 |
+
|
| 136 |
+
for k in k_values:
|
| 137 |
+
recalls[k].append(recall_at_k(relevant, sorted_docs, k))
|
| 138 |
+
precisions[k].append(precision_at_k(relevant, sorted_docs, k))
|
| 139 |
+
ndcgs[k].append(ndcg_at_k(relevant, sorted_docs, k))
|
| 140 |
+
success[k].append(success_at_k(relevant, sorted_docs, k))
|
| 141 |
+
|
| 142 |
+
maps.append(average_precision(relevant, sorted_docs))
|
| 143 |
+
mrrs.append(reciprocal_rank(relevant, sorted_docs))
|
| 144 |
+
|
| 145 |
+
avg_retrieval_time = np.mean(retrieval_times) if retrieval_times else 0
|
| 146 |
+
avg_rerank_time = np.mean(rerank_times) if rerank_times else 0
|
| 147 |
+
|
| 148 |
+
row = {"Model": model_name}
|
| 149 |
+
for k in k_values:
|
| 150 |
+
row[f"Recall@{k}"] = round(np.mean(recalls[k]), 4)
|
| 151 |
+
row[f"Precision@{k}"] = round(np.mean(precisions[k]), 4)
|
| 152 |
+
row[f"NDCG@{k}"] = round(np.mean(ndcgs[k]), 4)
|
| 153 |
+
row[f"Success@{k}"] = round(np.mean(success[k]), 4)
|
| 154 |
+
row["MAP"] = round(np.mean(maps), 4)
|
| 155 |
+
row["MRR"] = round(np.mean(mrrs), 4)
|
| 156 |
+
row["AvgRetrievalTime(s)"] = round(avg_retrieval_time, 4)
|
| 157 |
+
row["AvgRerankTime(s)"] = round(avg_rerank_time, 4)
|
| 158 |
+
rows.append(row)
|
| 159 |
+
return pd.DataFrame(rows)
|
| 160 |
+
|
| 161 |
+
# =====================
|
| 162 |
+
# Encoding + Upload
|
| 163 |
+
# =====================
|
| 164 |
+
|
| 165 |
+
def encode_and_upload():
|
| 166 |
+
client = QdrantClient(url=qdrant_url, api_key=os.getenv("eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJhY2Nlc3MiOiJtIn0.4a-XqSJIvuhW6_IO8kKpRir9k6NfWH7yY3NcZciHx-4"))
|
| 167 |
+
|
| 168 |
+
for embedding_model in embedding_models:
|
| 169 |
+
print(f"Encoding corpus with embedding model {embedding_model} ...")
|
| 170 |
+
embedder = SentenceTransformer(embedding_model)
|
| 171 |
+
|
| 172 |
+
corpus_ids = list(doc_ids_set)
|
| 173 |
+
corpus_texts = [corpus_dict[doc_id] for doc_id in tqdm(corpus_ids, desc="Encoding corpus texts")]
|
| 174 |
+
|
| 175 |
+
# Normalize embeddings for cosine similarity
|
| 176 |
+
vectors = embedder.encode(corpus_texts, normalize_embeddings=True).tolist()
|
| 177 |
+
|
| 178 |
+
global doc_id_to_int, int_to_doc_id
|
| 179 |
+
doc_id_to_int = {doc_id: i for i, doc_id in enumerate(corpus_ids)}
|
| 180 |
+
int_to_doc_id = {i: doc_id for doc_id, i in doc_id_to_int.items()}
|
| 181 |
+
|
| 182 |
+
# Create collection only if it doesn't exist
|
| 183 |
+
if not client.collection_exists(collection_name):
|
| 184 |
+
print(f"Creating collection '{collection_name}' ...")
|
| 185 |
+
client.create_collection(
|
| 186 |
+
collection_name=collection_name,
|
| 187 |
+
vectors_config=VectorParams(size=len(vectors[0]), distance=Distance.COSINE)
|
| 188 |
+
)
|
| 189 |
+
else:
|
| 190 |
+
print(f"Collection '{collection_name}' already exists. Skipping creation.")
|
| 191 |
+
|
| 192 |
+
# Check already uploaded points
|
| 193 |
+
existing_ids = set()
|
| 194 |
+
scroll_res, _ = client.scroll(collection_name=collection_name, with_payload=False, limit=100000)
|
| 195 |
+
existing_ids = {point.id for point in scroll_res}
|
| 196 |
+
print(f"Already stored {len(existing_ids)} points in '{collection_name}'.")
|
| 197 |
+
|
| 198 |
+
# Prepare points for only missing IDs
|
| 199 |
+
new_points = []
|
| 200 |
+
for doc_id, vec in zip(corpus_ids, vectors):
|
| 201 |
+
pid = doc_id_to_int[doc_id]
|
| 202 |
+
if pid not in existing_ids:
|
| 203 |
+
new_points.append({"id": pid, "vector": vec, "payload": {"text": corpus_dict[doc_id]}})
|
| 204 |
+
|
| 205 |
+
print(f"Uploading {len(new_points)} new points to collection '{collection_name}' ...")
|
| 206 |
+
for i in tqdm(range(0, len(new_points), batch_size), desc="Upserting points in batches"):
|
| 207 |
+
batch = new_points[i:i + batch_size]
|
| 208 |
+
client.upsert(collection_name=collection_name, points=batch)
|
| 209 |
+
|
| 210 |
+
# Preview first 5 stored docs
|
| 211 |
+
preview, _ = client.scroll(collection_name=collection_name, limit=5, with_payload=True)
|
| 212 |
+
print("\nPreview of stored points:")
|
| 213 |
+
for point in preview:
|
| 214 |
+
print(f"ID: {point.id} | Text: {point.payload['text'][:80]}...")
|
| 215 |
+
|
| 216 |
+
return embedder
|
| 217 |
+
|
| 218 |
+
# =====================
|
| 219 |
+
# Baseline Retrieval (No rerank)
|
| 220 |
+
# =====================
|
| 221 |
+
def run_retrieval(embedder):
|
| 222 |
+
client = QdrantClient(url=qdrant_url, api_key=os.getenv("QDRANT_API_KEY"))
|
| 223 |
+
retrieval_times = []
|
| 224 |
+
retrieved_docs_list = []
|
| 225 |
+
rerank_scores_list = []
|
| 226 |
+
qids = []
|
| 227 |
+
|
| 228 |
+
print("Running baseline retrieval ...")
|
| 229 |
+
for qid, qtext in tqdm(queries_list, desc="Baseline retrieval queries"):
|
| 230 |
+
q_vec = embedder.encode([qtext], normalize_embeddings=True)[0]
|
| 231 |
+
|
| 232 |
+
start_time = time.time()
|
| 233 |
+
search_result = client.query_points(
|
| 234 |
+
collection_name=collection_name,
|
| 235 |
+
query=q_vec,
|
| 236 |
+
limit=retrieval_n,
|
| 237 |
+
with_payload=True
|
| 238 |
+
)
|
| 239 |
+
retrieval_time = time.time() - start_time
|
| 240 |
+
retrieval_times.append(retrieval_time)
|
| 241 |
+
|
| 242 |
+
retrieved_ids_int = [hit.id for hit in search_result.points]
|
| 243 |
+
retrieved_ids = [int_to_doc_id[i] for i in retrieved_ids_int]
|
| 244 |
+
|
| 245 |
+
qids.append(qid)
|
| 246 |
+
retrieved_docs_list.append(retrieved_ids)
|
| 247 |
+
rerank_scores_list.append([])
|
| 248 |
+
|
| 249 |
+
results = {
|
| 250 |
+
"qids": qids,
|
| 251 |
+
"retrieved": retrieved_docs_list,
|
| 252 |
+
"rerank_scores": rerank_scores_list,
|
| 253 |
+
"retrieval_times": retrieval_times,
|
| 254 |
+
"rerank_times": []
|
| 255 |
+
}
|
| 256 |
+
return results
|
| 257 |
+
|
| 258 |
+
# =====================
|
| 259 |
+
# Retrieval + Rerank
|
| 260 |
+
# =====================
|
| 261 |
+
def run_rerank(embedder):
|
| 262 |
+
client = QdrantClient(url=qdrant_url, api_key=os.getenv("QDRANT_API_KEY"))
|
| 263 |
+
results_data = {}
|
| 264 |
+
|
| 265 |
+
for rerank_model in rerank_models:
|
| 266 |
+
print(f"Running retrieval + reranking with model {rerank_model} ...")
|
| 267 |
+
reranker = CrossEncoder(rerank_model, trust_remote_code=True)
|
| 268 |
+
retrieval_times = []
|
| 269 |
+
rerank_times = []
|
| 270 |
+
retrieved_docs_list = []
|
| 271 |
+
rerank_scores_list = []
|
| 272 |
+
qids = []
|
| 273 |
+
|
| 274 |
+
for qid, qtext in tqdm(queries_list, desc=f"Retrieval + rerank with {rerank_model}"):
|
| 275 |
+
q_vec = embedder.encode([qtext], normalize_embeddings=True)[0]
|
| 276 |
+
|
| 277 |
+
start_retrieval = time.time()
|
| 278 |
+
search_result = client.query_points(
|
| 279 |
+
collection_name=collection_name,
|
| 280 |
+
query=q_vec,
|
| 281 |
+
limit=retrieval_n,
|
| 282 |
+
with_payload=True
|
| 283 |
+
)
|
| 284 |
+
retrieval_time = time.time() - start_retrieval
|
| 285 |
+
retrieval_times.append(retrieval_time)
|
| 286 |
+
|
| 287 |
+
retrieved_ids_int = [hit.id for hit in search_result.points]
|
| 288 |
+
retrieved_ids = [int_to_doc_id[i] for i in retrieved_ids_int]
|
| 289 |
+
retrieved_texts = [hit.payload['text'] for hit in search_result.points]
|
| 290 |
+
|
| 291 |
+
start_rerank = time.time()
|
| 292 |
+
pairs = [(qtext, txt) for txt in retrieved_texts]
|
| 293 |
+
rerank_scores = reranker.predict(pairs)
|
| 294 |
+
rerank_time = time.time() - start_rerank
|
| 295 |
+
rerank_times.append(rerank_time)
|
| 296 |
+
|
| 297 |
+
qids.append(qid)
|
| 298 |
+
retrieved_docs_list.append(retrieved_ids)
|
| 299 |
+
rerank_scores_list.append(list(rerank_scores))
|
| 300 |
+
|
| 301 |
+
results_data[rerank_model] = {
|
| 302 |
+
"qids": qids,
|
| 303 |
+
"retrieved": retrieved_docs_list,
|
| 304 |
+
"rerank_scores": rerank_scores_list,
|
| 305 |
+
"retrieval_times": retrieval_times,
|
| 306 |
+
"rerank_times": rerank_times
|
| 307 |
+
}
|
| 308 |
+
|
| 309 |
+
return results_data
|
| 310 |
+
|
| 311 |
+
|
| 312 |
+
# =====================
|
| 313 |
+
# MAIN RUN
|
| 314 |
+
# =====================
|
| 315 |
+
if __name__ == "__main__":
|
| 316 |
+
#embedder = encode_and_upload()
|
| 317 |
+
|
| 318 |
+
#baseline_results = run_retrieval(embedder)
|
| 319 |
+
rerank_results = run_rerank(embedder)
|
| 320 |
+
|
| 321 |
+
#all_results = {"Qdrant Baseline": baseline_results}
|
| 322 |
+
all_results.update(rerank_results)
|
| 323 |
+
|
| 324 |
+
df_metrics = evaluate_metrics(all_results, qrels_dict, k_values)
|
| 325 |
+
|
| 326 |
+
|
| 327 |
+
# Prepare column groups
|
| 328 |
+
recall_cols = ["Model"] + [f"Recall@{k}" for k in k_values] + [f"Precision@{k}" for k in k_values]
|
| 329 |
+
ndcg_success_cols = ["Model"] + [f"NDCG@{k}" for k in k_values] + [f"Success@{k}" for k in k_values]
|
| 330 |
+
summary_cols = ["Model", "MAP", "MRR", "AvgRetrievalTime(s)", "AvgRerankTime(s)"]
|
| 331 |
+
|
| 332 |
+
print("\n--- Recall and Precision ---")
|
| 333 |
+
print(df_metrics[recall_cols].to_string(index=False))
|
| 334 |
+
|
| 335 |
+
print("\n--- NDCG and Success ---")
|
| 336 |
+
print(df_metrics[ndcg_success_cols].to_string(index=False))
|
| 337 |
+
|
| 338 |
+
print("\n--- Summary Metrics and Timing ---")
|
| 339 |
+
print(df_metrics[summary_cols].to_string(index=False))
|
| 340 |
+
|
| 341 |
+
|
| 342 |
+
avg_relevant_docs = np.mean([len([doc for doc, score in rel.items() if score >= 1]) for rel in qrels_dict.values()])
|
| 343 |
+
print(f"Average relevant docs per query: {avg_relevant_docs:.2f}")
|
| 344 |
+
|
| 345 |
+
|
| 346 |
+
# --------------------
|
| 347 |
+
# CONFIG
|
| 348 |
+
# --------------------
|
| 349 |
+
QDRANT_URL = os.getenv("https://5cd56757-1989-4ce6-b7b6-97f6e13f9e89.us-east4-0.gcp.cloud.qdrant.io:6333", "http://localhost:6333")COLLECTION_NAME = "trec_covid"
|
| 350 |
+
EMBEDDING_MODEL = "all-MiniLM-L6-v2"
|
| 351 |
+
MAPPING_FILE = "int_to_doc_id.pkl"
|
| 352 |
+
# --------------------
|
| 353 |
+
# DATA
|
| 354 |
+
# --------------------
|
| 355 |
+
corpus = load_dataset("BeIR/trec-covid", "corpus")
|
| 356 |
+
queries = load_dataset("BeIR/trec-covid", "queries")
|
| 357 |
+
qrels = load_dataset("BeIR/trec-covid-qrels", split="test")
|
| 358 |
+
|
| 359 |
+
qrels_dict = {}
|
| 360 |
+
for row in qrels:
|
| 361 |
+
qid = int(row["query-id"])
|
| 362 |
+
qrels_dict.setdefault(qid, {})[row["corpus-id"]] = int(row["score"])
|
| 363 |
+
|
| 364 |
+
qds = queries["queries"]
|
| 365 |
+
max_dd = min(200, len(qds))
|
| 366 |
+
_qids = qds["_id"][:max_dd]
|
| 367 |
+
_texts = qds["text"][:max_dd]
|
| 368 |
+
trec_queries = [(f"{_qids[i]}: {_texts[i][:80]}", int(_qids[i]), _texts[i]) for i in range(max_dd)]
|
| 369 |
+
label2qt = {lab: (qid, txt) for (lab, qid, txt) in trec_queries}
|
| 370 |
+
|
| 371 |
+
# --------------------
|
| 372 |
+
# ID MAP
|
| 373 |
+
# --------------------
|
| 374 |
+
if not os.path.exists(MAPPING_FILE):
|
| 375 |
+
raise FileNotFoundError(f"Missing {MAPPING_FILE}. Save it during indexing.")
|
| 376 |
+
with open(MAPPING_FILE, "rb") as f:
|
| 377 |
+
int_to_doc_id = pickle.load(f)
|
| 378 |
+
INDEXED_DOC_IDS = set(int_to_doc_id.values())
|
| 379 |
+
|
| 380 |
+
# --------------------
|
| 381 |
+
# Lazy singletons
|
| 382 |
+
# --------------------
|
| 383 |
+
_client = None
|
| 384 |
+
_embedder = None
|
| 385 |
+
_rerankers = {}
|
| 386 |
+
def get_client():
|
| 387 |
+
global _client
|
| 388 |
+
if _client is None:
|
| 389 |
+
_client = QdrantClient(url=QDRANT_URL, api_key=os.getenv("QDRANT_API_KEY"))
|
| 390 |
+
return _client
|
| 391 |
+
|
| 392 |
+
def get_embedder():
|
| 393 |
+
global _embedder
|
| 394 |
+
if _embedder is None:
|
| 395 |
+
_embedder = SentenceTransformer(EMBEDDING_MODEL)
|
| 396 |
+
return _embedder
|
| 397 |
+
|
| 398 |
+
def get_reranker(model_name):
|
| 399 |
+
if model_name not in _rerankers:
|
| 400 |
+
_rerankers[model_name] = CrossEncoder(model_name, trust_remote_code=True)
|
| 401 |
+
return _rerankers[model_name]
|
| 402 |
+
|
| 403 |
+
# --------------------
|
| 404 |
+
# Metrics
|
| 405 |
+
# --------------------
|
| 406 |
+
def recall_at_k(relevant_ids_set, retrieved_ids, k):
|
| 407 |
+
if not relevant_ids_set:
|
| 408 |
+
return None
|
| 409 |
+
return len(relevant_ids_set.intersection(retrieved_ids[:k])) / len(relevant_ids_set)
|
| 410 |
+
|
| 411 |
+
def precision_at_k(relevant_ids_set, retrieved_ids, k):
|
| 412 |
+
if k == 0:
|
| 413 |
+
return None
|
| 414 |
+
return len(relevant_ids_set.intersection(retrieved_ids[:k])) / k
|
| 415 |
+
|
| 416 |
+
def hit_at_k(relevant_ids_set, retrieved_ids, k):
|
| 417 |
+
return int(len(relevant_ids_set.intersection(retrieved_ids[:k])) > 0)
|
| 418 |
+
|
| 419 |
+
def ndcg_at_k(relevant_ids_scores, retrieved_ids, k):
|
| 420 |
+
dcg = 0.0
|
| 421 |
+
idcg = 0.0
|
| 422 |
+
for i, doc_id in enumerate(retrieved_ids[:k]):
|
| 423 |
+
rel = relevant_ids_scores.get(doc_id, 0)
|
| 424 |
+
if rel > 0:
|
| 425 |
+
dcg += (2**rel - 1) / log2(i+2)
|
| 426 |
+
sorted_rels = sorted(relevant_ids_scores.values(), reverse=True)[:k]
|
| 427 |
+
for i, rel in enumerate(sorted_rels):
|
| 428 |
+
if rel > 0:
|
| 429 |
+
idcg += (2**rel - 1) / log2(i+2)
|
| 430 |
+
return dcg / idcg if idcg > 0 else None
|
| 431 |
+
|
| 432 |
+
def evaluate_model(relevant_in_collection, relevant_scores_in_collection, doc_order, k):
|
| 433 |
+
return {
|
| 434 |
+
"Recall@k": round(recall_at_k(relevant_in_collection, doc_order, k), 4),
|
| 435 |
+
"Precision@k": round(precision_at_k(relevant_in_collection, doc_order, k), 4),
|
| 436 |
+
"Hit@k": hit_at_k(relevant_in_collection, doc_order, k),
|
| 437 |
+
"NDCG@k": None if ndcg_at_k(relevant_scores_in_collection, doc_order, k) is None else round(ndcg_at_k(relevant_scores_in_collection, doc_order, k), 4),
|
| 438 |
+
}
|
| 439 |
+
|
| 440 |
+
# --------------------
|
| 441 |
+
# Core
|
| 442 |
+
# --------------------
|
| 443 |
+
def run_demo(
|
| 444 |
+
query_text, retrieval_n, top_k, use_trec, trec_label, rel_threshold,
|
| 445 |
+
use_baseline, *selected_rerankers
|
| 446 |
+
):
|
| 447 |
+
client = get_client()
|
| 448 |
+
embedder = get_embedder()
|
| 449 |
+
|
| 450 |
+
qid = None
|
| 451 |
+
if use_trec and trec_label:
|
| 452 |
+
qid, query_text = label2qt[trec_label]
|
| 453 |
+
|
| 454 |
+
if not query_text or not query_text.strip():
|
| 455 |
+
return pd.DataFrame(), {"Note": "Empty query."}
|
| 456 |
+
|
| 457 |
+
q_vec = embedder.encode([query_text], normalize_embeddings=True)[0]
|
| 458 |
+
res = client.query_points(
|
| 459 |
+
collection_name=COLLECTION_NAME,
|
| 460 |
+
query=q_vec,
|
| 461 |
+
limit=int(retrieval_n),
|
| 462 |
+
with_payload=True
|
| 463 |
+
)
|
| 464 |
+
points = getattr(res, "points", res)
|
| 465 |
+
|
| 466 |
+
cand_docs, cand_texts, cand_qdrant_scores = [], [], []
|
| 467 |
+
for p in points:
|
| 468 |
+
payload = getattr(p, "payload", {}) or {}
|
| 469 |
+
pid = int(getattr(p, "id"))
|
| 470 |
+
doc_id = payload.get("doc_id", int_to_doc_id.get(pid, str(pid)))
|
| 471 |
+
cand_docs.append(doc_id)
|
| 472 |
+
cand_texts.append(payload.get("text", ""))
|
| 473 |
+
cand_qdrant_scores.append(getattr(p, "score", None))
|
| 474 |
+
|
| 475 |
+
cols = {
|
| 476 |
+
"rank": list(range(1, int(top_k)+1)),
|
| 477 |
+
"doc_id": [],
|
| 478 |
+
"score_qdrant": [],
|
| 479 |
+
"text_snippet": [],
|
| 480 |
+
}
|
| 481 |
+
reranker_scores = {}
|
| 482 |
+
|
| 483 |
+
for model_name, is_selected in zip(rerank_models, selected_rerankers):
|
| 484 |
+
if is_selected:
|
| 485 |
+
rr = get_reranker(model_name)
|
| 486 |
+
reranker_scores[model_name] = rr.predict([(query_text, t) for t in cand_texts])
|
| 487 |
+
|
| 488 |
+
for i in range(min(int(top_k), len(cand_docs))):
|
| 489 |
+
cols["doc_id"].append(cand_docs[i])
|
| 490 |
+
cols["score_qdrant"].append(cand_qdrant_scores[i])
|
| 491 |
+
txt = cand_texts[i]
|
| 492 |
+
cols["text_snippet"].append(txt[:300] + ("…" if len(txt) > 300 else ""))
|
| 493 |
+
for model_name in reranker_scores:
|
| 494 |
+
col_key = f"score_{model_name.split('/')[-1]}"
|
| 495 |
+
if col_key not in cols:
|
| 496 |
+
cols[col_key] = []
|
| 497 |
+
cols[col_key].append(float(reranker_scores[model_name][i]))
|
| 498 |
+
|
| 499 |
+
df = pd.DataFrame(cols)
|
| 500 |
+
|
| 501 |
+
metrics = {}
|
| 502 |
+
if qid is not None:
|
| 503 |
+
rels = qrels_dict.get(qid, {})
|
| 504 |
+
relevant_all = {d for d, s in rels.items() if s >= rel_threshold}
|
| 505 |
+
relevant_in_collection = relevant_all & INDEXED_DOC_IDS
|
| 506 |
+
relevant_scores_in_collection = {d: s for d, s in rels.items() if d in INDEXED_DOC_IDS}
|
| 507 |
+
ceiling_recall = round(len(relevant_in_collection) / len(relevant_all), 4) if relevant_all else None
|
| 508 |
+
|
| 509 |
+
if use_baseline:
|
| 510 |
+
metrics["Qdrant"] = evaluate_model(relevant_in_collection, relevant_scores_in_collection, cand_docs, int(top_k))
|
| 511 |
+
|
| 512 |
+
for model_name, is_selected in zip(rerank_models, selected_rerankers):
|
| 513 |
+
if is_selected:
|
| 514 |
+
order = sorted(range(len(cand_docs)), key=lambda i: reranker_scores[model_name][i], reverse=True)
|
| 515 |
+
top_docs = [cand_docs[i] for i in order[:int(top_k)]]
|
| 516 |
+
metrics[model_name] = evaluate_model(relevant_in_collection, relevant_scores_in_collection, top_docs, int(top_k))
|
| 517 |
+
|
| 518 |
+
metrics["QueryID"] = int(qid)
|
| 519 |
+
metrics["Relevant>=threshold (all)"] = len(relevant_all)
|
| 520 |
+
metrics["Relevant in collection"] = len(relevant_in_collection)
|
| 521 |
+
metrics["Recall Ceiling (collection)"] = ceiling_recall
|
| 522 |
+
|
| 523 |
+
return df, metrics
|
| 524 |
+
|
| 525 |
+
# --------------------
|
| 526 |
+
# UI
|
| 527 |
+
# --------------------
|
| 528 |
+
with gr.Blocks(title="Qdrant Retrieval Demo") as demo:
|
| 529 |
+
gr.Markdown("### Qdrant Retrieval Demo (TREC-COVID) + Multiple Metrics")
|
| 530 |
+
|
| 531 |
+
with gr.Row():
|
| 532 |
+
query_text = gr.Textbox(label="Query (free text)", placeholder="e.g., ACE2 inhibitors and COVID-19", lines=2)
|
| 533 |
+
with gr.Row():
|
| 534 |
+
retrieval_n = gr.Slider(10, 2000, value=50, step=10, label="retrieval_n (candidates from Qdrant)")
|
| 535 |
+
top_k = gr.Slider(1, 500, value=10, step=1, label="top_k (metrics cutoff)")
|
| 536 |
+
with gr.Row():
|
| 537 |
+
use_trec = gr.Checkbox(label="Use a TREC-COVID query", value=True)
|
| 538 |
+
trec_choice = gr.Dropdown(choices=[lab for (lab, _, _) in trec_queries],
|
| 539 |
+
value=trec_queries[0][0] if trec_queries else None,
|
| 540 |
+
label="Pick TREC-COVID query")
|
| 541 |
+
rel_threshold = gr.Radio(choices=[1, 2], value=1, label="Relevance threshold")
|
| 542 |
+
|
| 543 |
+
gr.Markdown("**Models to evaluate:**")
|
| 544 |
+
with gr.Row():
|
| 545 |
+
use_baseline = gr.Checkbox(label="Qdrant baseline", value=True)
|
| 546 |
+
ce_checkboxes = [gr.Checkbox(label=model_name, value=False) for model_name in rerank_models]
|
| 547 |
+
|
| 548 |
+
run_btn = gr.Button("Search")
|
| 549 |
+
out_df = gr.Dataframe(label="Retrieved Docs + Scores", wrap=True)
|
| 550 |
+
out_metrics = gr.JSON(label="Metrics (per selected model + ceiling recall)")
|
| 551 |
+
|
| 552 |
+
run_btn.click(
|
| 553 |
+
fn=run_demo,
|
| 554 |
+
inputs=[query_text, retrieval_n, top_k, use_trec, trec_choice, rel_threshold,
|
| 555 |
+
use_baseline, *ce_checkboxes],
|
| 556 |
+
outputs=[out_df, out_metrics]
|
| 557 |
+
)
|
| 558 |
+
# demo.launch(...) # disabled for Spaces; see __main__ block below
|
| 559 |
+
|
| 560 |
+
|
| 561 |
+
if __name__ == "__main__":
|
| 562 |
+
try:
|
| 563 |
+
demo # Gradio Blocks defined in the notebook
|
| 564 |
+
except NameError:
|
| 565 |
+
raise RuntimeError("Could not find `demo`. Ensure your notebook defines `demo = gr.Blocks(...)`.")
|
| 566 |
+
demo.launch(server_name="0.0.0.0", server_port=int(os.getenv("PORT", 7860)))
|
int_to_doc_id.pkl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2646d9e29946c295f2f697dfe63232cf5a8540cc24c2a98a4c1fcbf0d6b4a870
|
| 3 |
+
size 1469086
|
requirements.txt
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
gradio
|
| 2 |
+
fastapi
|
| 3 |
+
uvicorn
|
| 4 |
+
qdrant-client
|
| 5 |
+
sentence-transformers
|
| 6 |
+
transformers
|
| 7 |
+
datasets
|
| 8 |
+
pandas
|
| 9 |
+
numpy
|
| 10 |
+
scikit-learn
|
| 11 |
+
torch
|
| 12 |
+
accelerate
|