Spaces:
Running on Zero
Running on Zero
Commit ·
725c26b
1
Parent(s): 77d5515
Deploy ResearchGPT application
Browse files- .gitattributes +1 -0
- app.py +1050 -0
- artifacts/chunks.json +0 -0
- artifacts/index_config.json +9 -0
- artifacts/research_index.faiss +3 -0
- artifacts/retrieval_texts.json +0 -0
- requirements.txt +7 -0
.gitattributes
CHANGED
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@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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+
*.faiss filter=lfs diff=lfs merge=lfs -text
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app.py
ADDED
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@@ -0,0 +1,1050 @@
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|
| 1 |
+
from __future__ import annotations
|
| 2 |
+
|
| 3 |
+
import json
|
| 4 |
+
import os
|
| 5 |
+
import re
|
| 6 |
+
from dataclasses import dataclass
|
| 7 |
+
from pathlib import Path
|
| 8 |
+
from typing import Any
|
| 9 |
+
|
| 10 |
+
import faiss
|
| 11 |
+
import gradio as gr
|
| 12 |
+
import numpy as np
|
| 13 |
+
from google import genai
|
| 14 |
+
from rank_bm25 import BM25Okapi
|
| 15 |
+
from sentence_transformers import CrossEncoder, SentenceTransformer
|
| 16 |
+
|
| 17 |
+
|
| 18 |
+
# =============================================================================
|
| 19 |
+
# Configuration
|
| 20 |
+
# =============================================================================
|
| 21 |
+
|
| 22 |
+
BASE_DIR = Path(__file__).resolve().parent
|
| 23 |
+
ARTIFACT_DIR = BASE_DIR / "artifacts"
|
| 24 |
+
|
| 25 |
+
INDEX_PATH = ARTIFACT_DIR / "research_index.faiss"
|
| 26 |
+
CHUNKS_PATH = ARTIFACT_DIR / "chunks.json"
|
| 27 |
+
RETRIEVAL_TEXTS_PATH = ARTIFACT_DIR / "retrieval_texts.json"
|
| 28 |
+
CONFIG_PATH = ARTIFACT_DIR / "index_config.json"
|
| 29 |
+
|
| 30 |
+
GEMINI_MODEL = os.getenv("GEMINI_MODEL", "gemini-2.5-flash")
|
| 31 |
+
|
| 32 |
+
TOP_K = 8
|
| 33 |
+
FAISS_K = 50
|
| 34 |
+
BM25_K = 20
|
| 35 |
+
MAX_HISTORY_MESSAGES = 6
|
| 36 |
+
|
| 37 |
+
QUERY_EXPANSIONS = {
|
| 38 |
+
"gan": "generative adversarial network",
|
| 39 |
+
"gans": "generative adversarial networks",
|
| 40 |
+
"cnn": "convolutional neural network",
|
| 41 |
+
"llm": "large language model",
|
| 42 |
+
"llms": "large language models",
|
| 43 |
+
"lora": "low-rank adaptation",
|
| 44 |
+
"grpo": "group relative policy optimization",
|
| 45 |
+
"rnn": "recurrent neural network",
|
| 46 |
+
"lstm": "long short-term memory",
|
| 47 |
+
}
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
# =============================================================================
|
| 51 |
+
# Data structure
|
| 52 |
+
# =============================================================================
|
| 53 |
+
|
| 54 |
+
@dataclass
|
| 55 |
+
class Chunk:
|
| 56 |
+
text: str
|
| 57 |
+
source: str
|
| 58 |
+
file_type: str
|
| 59 |
+
chunk_id: str
|
| 60 |
+
|
| 61 |
+
page: int | None = None
|
| 62 |
+
document_type: str | None = None
|
| 63 |
+
page_header: str | None = None
|
| 64 |
+
|
| 65 |
+
repository: str | None = None
|
| 66 |
+
relative_path: str | None = None
|
| 67 |
+
section: str | None = None
|
| 68 |
+
|
| 69 |
+
|
| 70 |
+
# =============================================================================
|
| 71 |
+
# Load saved artifacts
|
| 72 |
+
# =============================================================================
|
| 73 |
+
|
| 74 |
+
def require_file(path: Path) -> None:
|
| 75 |
+
if not path.exists():
|
| 76 |
+
raise FileNotFoundError(
|
| 77 |
+
f"Required artifact is missing: {path}\n"
|
| 78 |
+
"Run the notebook artifact-saving section first."
|
| 79 |
+
)
|
| 80 |
+
|
| 81 |
+
|
| 82 |
+
for required_path in (
|
| 83 |
+
INDEX_PATH,
|
| 84 |
+
CHUNKS_PATH,
|
| 85 |
+
RETRIEVAL_TEXTS_PATH,
|
| 86 |
+
CONFIG_PATH,
|
| 87 |
+
):
|
| 88 |
+
require_file(required_path)
|
| 89 |
+
|
| 90 |
+
|
| 91 |
+
with CONFIG_PATH.open("r", encoding="utf-8") as file:
|
| 92 |
+
index_config = json.load(file)
|
| 93 |
+
|
| 94 |
+
EMBEDDING_MODEL_NAME = index_config["embedding_model"]
|
| 95 |
+
RERANKER_MODEL_NAME = index_config["reranker_model"]
|
| 96 |
+
QUERY_INSTRUCTION = index_config["query_instruction"]
|
| 97 |
+
|
| 98 |
+
index = faiss.read_index(str(INDEX_PATH))
|
| 99 |
+
|
| 100 |
+
with CHUNKS_PATH.open("r", encoding="utf-8") as file:
|
| 101 |
+
chunks = [
|
| 102 |
+
Chunk(**item)
|
| 103 |
+
for item in json.load(file)
|
| 104 |
+
]
|
| 105 |
+
|
| 106 |
+
with RETRIEVAL_TEXTS_PATH.open("r", encoding="utf-8") as file:
|
| 107 |
+
retrieval_texts: list[str] = json.load(file)
|
| 108 |
+
|
| 109 |
+
|
| 110 |
+
if index.ntotal != len(chunks):
|
| 111 |
+
raise ValueError(
|
| 112 |
+
f"FAISS contains {index.ntotal} vectors, "
|
| 113 |
+
f"but chunks.json contains {len(chunks)} chunks."
|
| 114 |
+
)
|
| 115 |
+
|
| 116 |
+
if len(chunks) != len(retrieval_texts):
|
| 117 |
+
raise ValueError(
|
| 118 |
+
"chunks.json and retrieval_texts.json contain "
|
| 119 |
+
"different numbers of records."
|
| 120 |
+
)
|
| 121 |
+
|
| 122 |
+
if index.d != index_config["embedding_dimension"]:
|
| 123 |
+
raise ValueError(
|
| 124 |
+
"The FAISS embedding dimension does not match index_config.json."
|
| 125 |
+
)
|
| 126 |
+
|
| 127 |
+
|
| 128 |
+
# Load retrieval models once when the app starts.
|
| 129 |
+
embedding_model = SentenceTransformer(
|
| 130 |
+
EMBEDDING_MODEL_NAME
|
| 131 |
+
)
|
| 132 |
+
|
| 133 |
+
reranker = CrossEncoder(
|
| 134 |
+
RERANKER_MODEL_NAME
|
| 135 |
+
)
|
| 136 |
+
|
| 137 |
+
|
| 138 |
+
def tokenize_for_bm25(text: str) -> list[str]:
|
| 139 |
+
"""
|
| 140 |
+
Tokenize text while preserving technical terms and filenames.
|
| 141 |
+
"""
|
| 142 |
+
|
| 143 |
+
return re.findall(
|
| 144 |
+
r"\b[a-zA-Z0-9][a-zA-Z0-9_.+-]*\b",
|
| 145 |
+
text.lower(),
|
| 146 |
+
)
|
| 147 |
+
|
| 148 |
+
|
| 149 |
+
bm25 = BM25Okapi(
|
| 150 |
+
[
|
| 151 |
+
tokenize_for_bm25(text)
|
| 152 |
+
for text in retrieval_texts
|
| 153 |
+
]
|
| 154 |
+
)
|
| 155 |
+
|
| 156 |
+
|
| 157 |
+
# =============================================================================
|
| 158 |
+
# Query processing
|
| 159 |
+
# =============================================================================
|
| 160 |
+
|
| 161 |
+
def expand_query(query: str) -> str:
|
| 162 |
+
"""
|
| 163 |
+
Append full forms of common technical abbreviations.
|
| 164 |
+
"""
|
| 165 |
+
|
| 166 |
+
words = re.findall(
|
| 167 |
+
r"\b[\w-]+\b",
|
| 168 |
+
query.lower(),
|
| 169 |
+
)
|
| 170 |
+
|
| 171 |
+
expansions = [
|
| 172 |
+
QUERY_EXPANSIONS[word]
|
| 173 |
+
for word in words
|
| 174 |
+
if word in QUERY_EXPANSIONS
|
| 175 |
+
]
|
| 176 |
+
|
| 177 |
+
if not expansions:
|
| 178 |
+
return query
|
| 179 |
+
|
| 180 |
+
unique_expansions = list(
|
| 181 |
+
dict.fromkeys(expansions)
|
| 182 |
+
)
|
| 183 |
+
|
| 184 |
+
return query + " " + " ".join(unique_expansions)
|
| 185 |
+
|
| 186 |
+
|
| 187 |
+
def encode_query(query: str) -> np.ndarray:
|
| 188 |
+
"""
|
| 189 |
+
Encode a query for semantic retrieval using the same
|
| 190 |
+
instruction used when building the index.
|
| 191 |
+
"""
|
| 192 |
+
|
| 193 |
+
instructed_query = (
|
| 194 |
+
QUERY_INSTRUCTION
|
| 195 |
+
+ query.strip()
|
| 196 |
+
)
|
| 197 |
+
|
| 198 |
+
query_embedding = embedding_model.encode(
|
| 199 |
+
[instructed_query],
|
| 200 |
+
normalize_embeddings=True,
|
| 201 |
+
)
|
| 202 |
+
|
| 203 |
+
return np.asarray(
|
| 204 |
+
query_embedding,
|
| 205 |
+
dtype="float32",
|
| 206 |
+
)
|
| 207 |
+
|
| 208 |
+
|
| 209 |
+
# =============================================================================
|
| 210 |
+
# FAISS and BM25 retrieval
|
| 211 |
+
# =============================================================================
|
| 212 |
+
|
| 213 |
+
def retrieve_faiss_candidates(
|
| 214 |
+
query: str,
|
| 215 |
+
top_k: int = FAISS_K,
|
| 216 |
+
) -> list[dict[str, Any]]:
|
| 217 |
+
"""
|
| 218 |
+
Retrieve semantic candidates from FAISS.
|
| 219 |
+
"""
|
| 220 |
+
|
| 221 |
+
if top_k <= 0:
|
| 222 |
+
raise ValueError("top_k must be positive")
|
| 223 |
+
|
| 224 |
+
search_k = min(
|
| 225 |
+
top_k,
|
| 226 |
+
index.ntotal,
|
| 227 |
+
)
|
| 228 |
+
|
| 229 |
+
scores, indices = index.search(
|
| 230 |
+
encode_query(query),
|
| 231 |
+
search_k,
|
| 232 |
+
)
|
| 233 |
+
|
| 234 |
+
results = []
|
| 235 |
+
|
| 236 |
+
for rank, (score, chunk_index) in enumerate(
|
| 237 |
+
zip(scores[0], indices[0]),
|
| 238 |
+
start=1,
|
| 239 |
+
):
|
| 240 |
+
if chunk_index < 0:
|
| 241 |
+
continue
|
| 242 |
+
|
| 243 |
+
results.append(
|
| 244 |
+
{
|
| 245 |
+
"chunk_index": int(chunk_index),
|
| 246 |
+
"faiss_score": float(score),
|
| 247 |
+
"faiss_rank": rank,
|
| 248 |
+
}
|
| 249 |
+
)
|
| 250 |
+
|
| 251 |
+
return results
|
| 252 |
+
|
| 253 |
+
|
| 254 |
+
def retrieve_bm25_candidates(
|
| 255 |
+
query: str,
|
| 256 |
+
top_k: int = BM25_K,
|
| 257 |
+
) -> list[dict[str, Any]]:
|
| 258 |
+
"""
|
| 259 |
+
Retrieve keyword candidates from BM25.
|
| 260 |
+
"""
|
| 261 |
+
|
| 262 |
+
if top_k <= 0:
|
| 263 |
+
raise ValueError("top_k must be positive")
|
| 264 |
+
|
| 265 |
+
query_tokens = tokenize_for_bm25(query)
|
| 266 |
+
|
| 267 |
+
if not query_tokens:
|
| 268 |
+
return []
|
| 269 |
+
|
| 270 |
+
scores = bm25.get_scores(query_tokens)
|
| 271 |
+
|
| 272 |
+
top_indices = np.argsort(
|
| 273 |
+
scores
|
| 274 |
+
)[::-1][:top_k]
|
| 275 |
+
|
| 276 |
+
results = []
|
| 277 |
+
|
| 278 |
+
for rank, chunk_index in enumerate(
|
| 279 |
+
top_indices,
|
| 280 |
+
start=1,
|
| 281 |
+
):
|
| 282 |
+
score = float(scores[chunk_index])
|
| 283 |
+
|
| 284 |
+
if score <= 0:
|
| 285 |
+
continue
|
| 286 |
+
|
| 287 |
+
results.append(
|
| 288 |
+
{
|
| 289 |
+
"chunk_index": int(chunk_index),
|
| 290 |
+
"bm25_score": score,
|
| 291 |
+
"bm25_rank": rank,
|
| 292 |
+
}
|
| 293 |
+
)
|
| 294 |
+
|
| 295 |
+
return results
|
| 296 |
+
|
| 297 |
+
|
| 298 |
+
def merge_candidates(
|
| 299 |
+
faiss_results: list[dict[str, Any]],
|
| 300 |
+
bm25_results: list[dict[str, Any]],
|
| 301 |
+
) -> list[dict[str, Any]]:
|
| 302 |
+
"""
|
| 303 |
+
Merge FAISS and BM25 candidates by chunk index.
|
| 304 |
+
"""
|
| 305 |
+
|
| 306 |
+
merged: dict[int, dict[str, Any]] = {}
|
| 307 |
+
|
| 308 |
+
for result in faiss_results:
|
| 309 |
+
chunk_index = result["chunk_index"]
|
| 310 |
+
|
| 311 |
+
merged[chunk_index] = {
|
| 312 |
+
"chunk_index": chunk_index,
|
| 313 |
+
"faiss_score": result["faiss_score"],
|
| 314 |
+
"faiss_rank": result["faiss_rank"],
|
| 315 |
+
"bm25_score": None,
|
| 316 |
+
"bm25_rank": None,
|
| 317 |
+
"retrieved_by": {"faiss"},
|
| 318 |
+
}
|
| 319 |
+
|
| 320 |
+
for result in bm25_results:
|
| 321 |
+
chunk_index = result["chunk_index"]
|
| 322 |
+
|
| 323 |
+
if chunk_index not in merged:
|
| 324 |
+
merged[chunk_index] = {
|
| 325 |
+
"chunk_index": chunk_index,
|
| 326 |
+
"faiss_score": None,
|
| 327 |
+
"faiss_rank": None,
|
| 328 |
+
"bm25_score": result["bm25_score"],
|
| 329 |
+
"bm25_rank": result["bm25_rank"],
|
| 330 |
+
"retrieved_by": {"bm25"},
|
| 331 |
+
}
|
| 332 |
+
else:
|
| 333 |
+
merged[chunk_index]["bm25_score"] = (
|
| 334 |
+
result["bm25_score"]
|
| 335 |
+
)
|
| 336 |
+
merged[chunk_index]["bm25_rank"] = (
|
| 337 |
+
result["bm25_rank"]
|
| 338 |
+
)
|
| 339 |
+
merged[chunk_index]["retrieved_by"].add(
|
| 340 |
+
"bm25"
|
| 341 |
+
)
|
| 342 |
+
|
| 343 |
+
merged_results = list(
|
| 344 |
+
merged.values()
|
| 345 |
+
)
|
| 346 |
+
|
| 347 |
+
for result in merged_results:
|
| 348 |
+
result["retrieved_by"] = sorted(
|
| 349 |
+
result["retrieved_by"]
|
| 350 |
+
)
|
| 351 |
+
|
| 352 |
+
return merged_results
|
| 353 |
+
|
| 354 |
+
|
| 355 |
+
def retrieve_hybrid_candidates(
|
| 356 |
+
query: str,
|
| 357 |
+
faiss_k: int = FAISS_K,
|
| 358 |
+
bm25_k: int = BM25_K,
|
| 359 |
+
) -> list[dict[str, Any]]:
|
| 360 |
+
"""
|
| 361 |
+
Retrieve and combine FAISS and BM25 candidates.
|
| 362 |
+
"""
|
| 363 |
+
|
| 364 |
+
faiss_results = retrieve_faiss_candidates(
|
| 365 |
+
query=query,
|
| 366 |
+
top_k=faiss_k,
|
| 367 |
+
)
|
| 368 |
+
|
| 369 |
+
bm25_results = retrieve_bm25_candidates(
|
| 370 |
+
query=query,
|
| 371 |
+
top_k=bm25_k,
|
| 372 |
+
)
|
| 373 |
+
|
| 374 |
+
return merge_candidates(
|
| 375 |
+
faiss_results=faiss_results,
|
| 376 |
+
bm25_results=bm25_results,
|
| 377 |
+
)
|
| 378 |
+
|
| 379 |
+
|
| 380 |
+
def enrich_candidates(
|
| 381 |
+
candidates: list[dict[str, Any]],
|
| 382 |
+
) -> list[dict[str, Any]]:
|
| 383 |
+
"""
|
| 384 |
+
Attach chunk text and metadata to retrieval candidates.
|
| 385 |
+
"""
|
| 386 |
+
|
| 387 |
+
enriched_results = []
|
| 388 |
+
|
| 389 |
+
for candidate in candidates:
|
| 390 |
+
chunk_index = candidate["chunk_index"]
|
| 391 |
+
chunk = chunks[chunk_index]
|
| 392 |
+
|
| 393 |
+
enriched_results.append(
|
| 394 |
+
{
|
| 395 |
+
**candidate,
|
| 396 |
+
"text": chunk.text,
|
| 397 |
+
"retrieval_text": retrieval_texts[
|
| 398 |
+
chunk_index
|
| 399 |
+
],
|
| 400 |
+
"source": chunk.source,
|
| 401 |
+
"file_type": chunk.file_type,
|
| 402 |
+
"page": chunk.page,
|
| 403 |
+
"document_type": chunk.document_type,
|
| 404 |
+
"page_header": chunk.page_header,
|
| 405 |
+
"repository": chunk.repository,
|
| 406 |
+
"relative_path": chunk.relative_path,
|
| 407 |
+
"section": chunk.section,
|
| 408 |
+
"chunk_id": chunk.chunk_id,
|
| 409 |
+
}
|
| 410 |
+
)
|
| 411 |
+
|
| 412 |
+
return enriched_results
|
| 413 |
+
|
| 414 |
+
|
| 415 |
+
def rerank_candidates(
|
| 416 |
+
query: str,
|
| 417 |
+
candidates: list[dict[str, Any]],
|
| 418 |
+
top_k: int = TOP_K,
|
| 419 |
+
) -> list[dict[str, Any]]:
|
| 420 |
+
"""
|
| 421 |
+
Rerank hybrid candidates using the cross-encoder.
|
| 422 |
+
"""
|
| 423 |
+
|
| 424 |
+
if top_k <= 0:
|
| 425 |
+
raise ValueError("top_k must be positive")
|
| 426 |
+
|
| 427 |
+
if not candidates:
|
| 428 |
+
return []
|
| 429 |
+
|
| 430 |
+
query_chunk_pairs = [
|
| 431 |
+
[
|
| 432 |
+
query,
|
| 433 |
+
candidate["retrieval_text"],
|
| 434 |
+
]
|
| 435 |
+
for candidate in candidates
|
| 436 |
+
]
|
| 437 |
+
|
| 438 |
+
reranker_scores = reranker.predict(
|
| 439 |
+
query_chunk_pairs,
|
| 440 |
+
show_progress_bar=False,
|
| 441 |
+
)
|
| 442 |
+
|
| 443 |
+
reranked_results = []
|
| 444 |
+
|
| 445 |
+
for candidate, score in zip(
|
| 446 |
+
candidates,
|
| 447 |
+
reranker_scores,
|
| 448 |
+
):
|
| 449 |
+
result = candidate.copy()
|
| 450 |
+
result["reranker_score"] = float(score)
|
| 451 |
+
reranked_results.append(result)
|
| 452 |
+
|
| 453 |
+
reranked_results.sort(
|
| 454 |
+
key=lambda result: result[
|
| 455 |
+
"reranker_score"
|
| 456 |
+
],
|
| 457 |
+
reverse=True,
|
| 458 |
+
)
|
| 459 |
+
|
| 460 |
+
return reranked_results[:top_k]
|
| 461 |
+
|
| 462 |
+
|
| 463 |
+
def retrieve_with_reranking(
|
| 464 |
+
query: str,
|
| 465 |
+
top_k: int = TOP_K,
|
| 466 |
+
faiss_k: int = FAISS_K,
|
| 467 |
+
bm25_k: int = BM25_K,
|
| 468 |
+
) -> list[dict[str, Any]]:
|
| 469 |
+
"""
|
| 470 |
+
Run query expansion, hybrid retrieval, and reranking.
|
| 471 |
+
"""
|
| 472 |
+
|
| 473 |
+
search_query = expand_query(query)
|
| 474 |
+
|
| 475 |
+
hybrid_candidates = retrieve_hybrid_candidates(
|
| 476 |
+
query=search_query,
|
| 477 |
+
faiss_k=faiss_k,
|
| 478 |
+
bm25_k=bm25_k,
|
| 479 |
+
)
|
| 480 |
+
|
| 481 |
+
enriched_candidates = enrich_candidates(
|
| 482 |
+
hybrid_candidates
|
| 483 |
+
)
|
| 484 |
+
|
| 485 |
+
return rerank_candidates(
|
| 486 |
+
query=query,
|
| 487 |
+
candidates=enriched_candidates,
|
| 488 |
+
top_k=top_k,
|
| 489 |
+
)
|
| 490 |
+
|
| 491 |
+
|
| 492 |
+
# =============================================================================
|
| 493 |
+
# Source formatting and context construction
|
| 494 |
+
# =============================================================================
|
| 495 |
+
|
| 496 |
+
def format_source_location(
|
| 497 |
+
result: dict[str, Any],
|
| 498 |
+
) -> str:
|
| 499 |
+
"""
|
| 500 |
+
Format source metadata for the LLM context.
|
| 501 |
+
"""
|
| 502 |
+
|
| 503 |
+
if result.get("repository"):
|
| 504 |
+
location = (
|
| 505 |
+
f"GitHub repository: "
|
| 506 |
+
f"{result['repository']}"
|
| 507 |
+
)
|
| 508 |
+
|
| 509 |
+
if result.get("relative_path"):
|
| 510 |
+
location += (
|
| 511 |
+
f", file: "
|
| 512 |
+
f"{result['relative_path']}"
|
| 513 |
+
)
|
| 514 |
+
|
| 515 |
+
if result.get("section"):
|
| 516 |
+
location += (
|
| 517 |
+
f", section: "
|
| 518 |
+
f"{result['section']}"
|
| 519 |
+
)
|
| 520 |
+
|
| 521 |
+
return location
|
| 522 |
+
|
| 523 |
+
location = result.get(
|
| 524 |
+
"source",
|
| 525 |
+
"Unknown source",
|
| 526 |
+
)
|
| 527 |
+
|
| 528 |
+
if result.get("page") is not None:
|
| 529 |
+
location += (
|
| 530 |
+
f", page {result['page']}"
|
| 531 |
+
)
|
| 532 |
+
|
| 533 |
+
if result.get("document_type"):
|
| 534 |
+
location += (
|
| 535 |
+
f", {result['document_type']}"
|
| 536 |
+
)
|
| 537 |
+
|
| 538 |
+
return location
|
| 539 |
+
|
| 540 |
+
|
| 541 |
+
def build_context(
|
| 542 |
+
results: list[dict[str, Any]],
|
| 543 |
+
) -> str:
|
| 544 |
+
"""
|
| 545 |
+
Build numbered source blocks for answer generation.
|
| 546 |
+
"""
|
| 547 |
+
|
| 548 |
+
context_parts = []
|
| 549 |
+
|
| 550 |
+
for source_number, result in enumerate(
|
| 551 |
+
results,
|
| 552 |
+
start=1,
|
| 553 |
+
):
|
| 554 |
+
location = format_source_location(
|
| 555 |
+
result
|
| 556 |
+
)
|
| 557 |
+
|
| 558 |
+
context_parts.append(
|
| 559 |
+
f"[Source {source_number}: "
|
| 560 |
+
f"{location}]\n"
|
| 561 |
+
f"{result['text']}"
|
| 562 |
+
)
|
| 563 |
+
|
| 564 |
+
return "\n\n".join(context_parts)
|
| 565 |
+
|
| 566 |
+
|
| 567 |
+
def format_source(
|
| 568 |
+
source: dict[str, Any],
|
| 569 |
+
) -> str:
|
| 570 |
+
"""
|
| 571 |
+
Create a readable public source label.
|
| 572 |
+
"""
|
| 573 |
+
|
| 574 |
+
if source.get("repository"):
|
| 575 |
+
location = (
|
| 576 |
+
f"GitHub: "
|
| 577 |
+
f"{source['repository']}"
|
| 578 |
+
)
|
| 579 |
+
|
| 580 |
+
if source.get("relative_path"):
|
| 581 |
+
location += (
|
| 582 |
+
f" / "
|
| 583 |
+
f"{source['relative_path']}"
|
| 584 |
+
)
|
| 585 |
+
|
| 586 |
+
if source.get("section"):
|
| 587 |
+
location += (
|
| 588 |
+
f" — "
|
| 589 |
+
f"{source['section']}"
|
| 590 |
+
)
|
| 591 |
+
|
| 592 |
+
return location
|
| 593 |
+
|
| 594 |
+
location = source.get(
|
| 595 |
+
"source",
|
| 596 |
+
"Unknown source",
|
| 597 |
+
)
|
| 598 |
+
|
| 599 |
+
if source.get("page") is not None:
|
| 600 |
+
location += (
|
| 601 |
+
f", page {source['page']}"
|
| 602 |
+
)
|
| 603 |
+
|
| 604 |
+
return location
|
| 605 |
+
|
| 606 |
+
|
| 607 |
+
def format_sources(
|
| 608 |
+
sources: list[dict[str, Any]],
|
| 609 |
+
) -> str:
|
| 610 |
+
"""
|
| 611 |
+
Format unique sources as Markdown.
|
| 612 |
+
"""
|
| 613 |
+
|
| 614 |
+
if not sources:
|
| 615 |
+
return ""
|
| 616 |
+
|
| 617 |
+
lines = ["### Sources"]
|
| 618 |
+
seen_locations = set()
|
| 619 |
+
|
| 620 |
+
for source in sources:
|
| 621 |
+
location = format_source(source)
|
| 622 |
+
|
| 623 |
+
if location in seen_locations:
|
| 624 |
+
continue
|
| 625 |
+
|
| 626 |
+
seen_locations.add(location)
|
| 627 |
+
lines.append(f"- {location}")
|
| 628 |
+
|
| 629 |
+
return "\n".join(lines)
|
| 630 |
+
|
| 631 |
+
|
| 632 |
+
# =============================================================================
|
| 633 |
+
# Conversation history
|
| 634 |
+
# =============================================================================
|
| 635 |
+
|
| 636 |
+
def remove_source_section(
|
| 637 |
+
text: str,
|
| 638 |
+
) -> str:
|
| 639 |
+
"""
|
| 640 |
+
Remove the displayed source list from a previous response.
|
| 641 |
+
"""
|
| 642 |
+
|
| 643 |
+
if not text:
|
| 644 |
+
return ""
|
| 645 |
+
|
| 646 |
+
marker = "\n\n---\n\n### Sources"
|
| 647 |
+
|
| 648 |
+
return text.split(
|
| 649 |
+
marker,
|
| 650 |
+
1,
|
| 651 |
+
)[0].strip()
|
| 652 |
+
|
| 653 |
+
|
| 654 |
+
def format_chat_history(
|
| 655 |
+
history,
|
| 656 |
+
max_messages: int = MAX_HISTORY_MESSAGES,
|
| 657 |
+
) -> str:
|
| 658 |
+
"""
|
| 659 |
+
Convert recent Gradio history into readable text.
|
| 660 |
+
|
| 661 |
+
Supports newer message dictionaries and older tuple-style history.
|
| 662 |
+
"""
|
| 663 |
+
|
| 664 |
+
if not history:
|
| 665 |
+
return ""
|
| 666 |
+
|
| 667 |
+
lines = []
|
| 668 |
+
|
| 669 |
+
for item in history[-max_messages:]:
|
| 670 |
+
|
| 671 |
+
if isinstance(item, dict):
|
| 672 |
+
role = str(
|
| 673 |
+
item.get("role", "")
|
| 674 |
+
).strip().lower()
|
| 675 |
+
|
| 676 |
+
content = item.get(
|
| 677 |
+
"content",
|
| 678 |
+
"",
|
| 679 |
+
)
|
| 680 |
+
|
| 681 |
+
if not isinstance(content, str):
|
| 682 |
+
continue
|
| 683 |
+
|
| 684 |
+
content = content.strip()
|
| 685 |
+
|
| 686 |
+
if role == "assistant":
|
| 687 |
+
content = remove_source_section(
|
| 688 |
+
content
|
| 689 |
+
)
|
| 690 |
+
|
| 691 |
+
if (
|
| 692 |
+
content
|
| 693 |
+
and role in {"user", "assistant"}
|
| 694 |
+
):
|
| 695 |
+
lines.append(
|
| 696 |
+
f"{role.capitalize()}: "
|
| 697 |
+
f"{content}"
|
| 698 |
+
)
|
| 699 |
+
|
| 700 |
+
elif (
|
| 701 |
+
isinstance(item, (list, tuple))
|
| 702 |
+
and len(item) == 2
|
| 703 |
+
):
|
| 704 |
+
user_message, assistant_message = item
|
| 705 |
+
|
| 706 |
+
if (
|
| 707 |
+
isinstance(user_message, str)
|
| 708 |
+
and user_message.strip()
|
| 709 |
+
):
|
| 710 |
+
lines.append(
|
| 711 |
+
f"User: "
|
| 712 |
+
f"{user_message.strip()}"
|
| 713 |
+
)
|
| 714 |
+
|
| 715 |
+
if isinstance(
|
| 716 |
+
assistant_message,
|
| 717 |
+
str,
|
| 718 |
+
):
|
| 719 |
+
assistant_message = (
|
| 720 |
+
remove_source_section(
|
| 721 |
+
assistant_message
|
| 722 |
+
)
|
| 723 |
+
)
|
| 724 |
+
|
| 725 |
+
if assistant_message:
|
| 726 |
+
lines.append(
|
| 727 |
+
f"Assistant: "
|
| 728 |
+
f"{assistant_message}"
|
| 729 |
+
)
|
| 730 |
+
|
| 731 |
+
return "\n".join(lines)
|
| 732 |
+
|
| 733 |
+
|
| 734 |
+
# =============================================================================
|
| 735 |
+
# Gemini generation
|
| 736 |
+
# =============================================================================
|
| 737 |
+
|
| 738 |
+
if not os.getenv("GEMINI_API_KEY"):
|
| 739 |
+
raise RuntimeError(
|
| 740 |
+
"GEMINI_API_KEY is not configured. Add it as a private Secret "
|
| 741 |
+
"in the Hugging Face Space settings."
|
| 742 |
+
)
|
| 743 |
+
|
| 744 |
+
gemini_client = genai.Client()
|
| 745 |
+
|
| 746 |
+
|
| 747 |
+
def generate_answer(
|
| 748 |
+
prompt: str,
|
| 749 |
+
model_name: str = GEMINI_MODEL,
|
| 750 |
+
) -> str:
|
| 751 |
+
"""
|
| 752 |
+
Generate a response using the Gemini API.
|
| 753 |
+
"""
|
| 754 |
+
|
| 755 |
+
interaction = gemini_client.interactions.create(
|
| 756 |
+
model=model_name,
|
| 757 |
+
input=prompt,
|
| 758 |
+
)
|
| 759 |
+
|
| 760 |
+
answer = interaction.output_text
|
| 761 |
+
|
| 762 |
+
if not answer:
|
| 763 |
+
raise RuntimeError(
|
| 764 |
+
"Gemini returned an empty response."
|
| 765 |
+
)
|
| 766 |
+
|
| 767 |
+
return answer.strip()
|
| 768 |
+
|
| 769 |
+
|
| 770 |
+
def rewrite_question_with_history(
|
| 771 |
+
question: str,
|
| 772 |
+
history,
|
| 773 |
+
model_name: str = GEMINI_MODEL,
|
| 774 |
+
) -> str:
|
| 775 |
+
"""
|
| 776 |
+
Rewrite a follow-up question as a standalone retrieval query.
|
| 777 |
+
"""
|
| 778 |
+
|
| 779 |
+
history_text = format_chat_history(history)
|
| 780 |
+
|
| 781 |
+
if not history_text:
|
| 782 |
+
return question
|
| 783 |
+
|
| 784 |
+
prompt = f"""
|
| 785 |
+
Rewrite the latest question as a standalone search query.
|
| 786 |
+
|
| 787 |
+
Use the conversation only to resolve references such as:
|
| 788 |
+
he, his, it, that project, that paper, or the thesis.
|
| 789 |
+
|
| 790 |
+
Do not answer the question.
|
| 791 |
+
Do not add unsupported facts.
|
| 792 |
+
Return only the rewritten query.
|
| 793 |
+
|
| 794 |
+
Conversation:
|
| 795 |
+
{history_text}
|
| 796 |
+
|
| 797 |
+
Latest question:
|
| 798 |
+
{question}
|
| 799 |
+
|
| 800 |
+
Standalone query:
|
| 801 |
+
""".strip()
|
| 802 |
+
|
| 803 |
+
try:
|
| 804 |
+
rewritten = generate_answer(
|
| 805 |
+
prompt=prompt,
|
| 806 |
+
model_name=model_name,
|
| 807 |
+
).strip()
|
| 808 |
+
|
| 809 |
+
return rewritten or question
|
| 810 |
+
|
| 811 |
+
except Exception:
|
| 812 |
+
return question
|
| 813 |
+
|
| 814 |
+
|
| 815 |
+
def build_prompt(
|
| 816 |
+
question: str,
|
| 817 |
+
results: list[dict[str, Any]],
|
| 818 |
+
history=None,
|
| 819 |
+
) -> str:
|
| 820 |
+
"""
|
| 821 |
+
Build the grounded answer-generation prompt.
|
| 822 |
+
"""
|
| 823 |
+
|
| 824 |
+
context = build_context(results)
|
| 825 |
+
history_text = format_chat_history(history)
|
| 826 |
+
|
| 827 |
+
if not history_text:
|
| 828 |
+
history_text = "No previous conversation."
|
| 829 |
+
|
| 830 |
+
return f"""
|
| 831 |
+
You are ResearchGPT, a research and portfolio assistant for Milad Saeedi.
|
| 832 |
+
|
| 833 |
+
Use only the retrieved context as factual evidence.
|
| 834 |
+
|
| 835 |
+
Citation requirements:
|
| 836 |
+
1. Every paragraph containing a factual claim must include at least one citation.
|
| 837 |
+
2. Use citations exactly in this format: [Source 1], [Source 2], etc.
|
| 838 |
+
3. Place citations immediately after the sentence or claim they support.
|
| 839 |
+
4. Use only source numbers that appear in the retrieved context.
|
| 840 |
+
5. Do not create a separate source list; the application adds it automatically.
|
| 841 |
+
6. Do not omit citations in summaries, lists, or conclusions.
|
| 842 |
+
|
| 843 |
+
Additional instructions:
|
| 844 |
+
1. Answer the latest question directly.
|
| 845 |
+
2. Use conversation history only to resolve follow-up references.
|
| 846 |
+
3. Do not treat conversation history as factual evidence.
|
| 847 |
+
4. Do not invent publications, methods, results, skills, projects, or experience.
|
| 848 |
+
5. If the retrieved context is insufficient, say so clearly.
|
| 849 |
+
6. Avoid unsupported praise or subjective claims.
|
| 850 |
+
7. Contact information may be provided only when explicitly requested.
|
| 851 |
+
8. Synthesize the evidence instead of copying long passages.
|
| 852 |
+
|
| 853 |
+
Recent conversation:
|
| 854 |
+
{history_text}
|
| 855 |
+
|
| 856 |
+
Retrieved context:
|
| 857 |
+
{context}
|
| 858 |
+
|
| 859 |
+
Latest question:
|
| 860 |
+
{question}
|
| 861 |
+
|
| 862 |
+
Write a grounded answer with inline citations:
|
| 863 |
+
""".strip()
|
| 864 |
+
|
| 865 |
+
|
| 866 |
+
def has_inline_citations(answer: str) -> bool:
|
| 867 |
+
"""
|
| 868 |
+
Check whether an answer contains at least one [Source N] citation.
|
| 869 |
+
"""
|
| 870 |
+
|
| 871 |
+
return bool(
|
| 872 |
+
re.search(r"\[Source\s+\d+\]", answer)
|
| 873 |
+
)
|
| 874 |
+
|
| 875 |
+
|
| 876 |
+
def answer_question(
|
| 877 |
+
question: str,
|
| 878 |
+
history=None,
|
| 879 |
+
top_k: int = TOP_K,
|
| 880 |
+
faiss_k: int = FAISS_K,
|
| 881 |
+
bm25_k: int = BM25_K,
|
| 882 |
+
model_name: str = GEMINI_MODEL,
|
| 883 |
+
) -> tuple[str, list[dict[str, Any]]]:
|
| 884 |
+
"""
|
| 885 |
+
Retrieve evidence and generate a grounded answer.
|
| 886 |
+
"""
|
| 887 |
+
|
| 888 |
+
question = question.strip()
|
| 889 |
+
|
| 890 |
+
if not question:
|
| 891 |
+
return "Please enter a question.", []
|
| 892 |
+
|
| 893 |
+
retrieval_query = rewrite_question_with_history(
|
| 894 |
+
question=question,
|
| 895 |
+
history=history,
|
| 896 |
+
model_name=model_name,
|
| 897 |
+
)
|
| 898 |
+
|
| 899 |
+
results = retrieve_with_reranking(
|
| 900 |
+
query=retrieval_query,
|
| 901 |
+
top_k=top_k,
|
| 902 |
+
faiss_k=faiss_k,
|
| 903 |
+
bm25_k=bm25_k,
|
| 904 |
+
)
|
| 905 |
+
|
| 906 |
+
if not results:
|
| 907 |
+
return (
|
| 908 |
+
"I could not find relevant information in the knowledge base.",
|
| 909 |
+
[],
|
| 910 |
+
)
|
| 911 |
+
|
| 912 |
+
answer = generate_answer(
|
| 913 |
+
prompt=build_prompt(
|
| 914 |
+
question=question,
|
| 915 |
+
results=results,
|
| 916 |
+
history=history,
|
| 917 |
+
),
|
| 918 |
+
model_name=model_name,
|
| 919 |
+
)
|
| 920 |
+
|
| 921 |
+
# Retry once if Gemini omitted the required inline citations.
|
| 922 |
+
if not has_inline_citations(answer):
|
| 923 |
+
retry_prompt = f"""
|
| 924 |
+
Revise the answer below by adding accurate inline citations.
|
| 925 |
+
|
| 926 |
+
Requirements:
|
| 927 |
+
- Every factual paragraph must contain at least one citation.
|
| 928 |
+
- Use only [Source 1] through [Source {len(results)}].
|
| 929 |
+
- Use the retrieved context to determine which citation supports each claim.
|
| 930 |
+
- Do not invent facts.
|
| 931 |
+
- Do not add a separate source list.
|
| 932 |
+
- Return only the revised answer.
|
| 933 |
+
|
| 934 |
+
Retrieved context:
|
| 935 |
+
{build_context(results)}
|
| 936 |
+
|
| 937 |
+
Original answer:
|
| 938 |
+
{answer}
|
| 939 |
+
""".strip()
|
| 940 |
+
|
| 941 |
+
answer = generate_answer(
|
| 942 |
+
prompt=retry_prompt,
|
| 943 |
+
model_name=model_name,
|
| 944 |
+
)
|
| 945 |
+
|
| 946 |
+
return answer, results
|
| 947 |
+
|
| 948 |
+
|
| 949 |
+
# =============================================================================
|
| 950 |
+
# Gradio application
|
| 951 |
+
# =============================================================================
|
| 952 |
+
|
| 953 |
+
def research_chat(
|
| 954 |
+
message: str,
|
| 955 |
+
history,
|
| 956 |
+
) -> str:
|
| 957 |
+
"""
|
| 958 |
+
Answer one Gradio message using the RAG pipeline.
|
| 959 |
+
"""
|
| 960 |
+
|
| 961 |
+
message = message.strip()
|
| 962 |
+
|
| 963 |
+
if not message:
|
| 964 |
+
return "Please enter a question."
|
| 965 |
+
|
| 966 |
+
try:
|
| 967 |
+
answer, sources = answer_question(
|
| 968 |
+
question=message,
|
| 969 |
+
history=history,
|
| 970 |
+
top_k=TOP_K,
|
| 971 |
+
faiss_k=FAISS_K,
|
| 972 |
+
bm25_k=BM25_K,
|
| 973 |
+
model_name=GEMINI_MODEL,
|
| 974 |
+
)
|
| 975 |
+
|
| 976 |
+
response = answer
|
| 977 |
+
|
| 978 |
+
sources_markdown = format_sources(
|
| 979 |
+
sources
|
| 980 |
+
)
|
| 981 |
+
|
| 982 |
+
if sources_markdown:
|
| 983 |
+
response += (
|
| 984 |
+
f"\n\n---\n\n"
|
| 985 |
+
f"{sources_markdown}"
|
| 986 |
+
)
|
| 987 |
+
|
| 988 |
+
return response
|
| 989 |
+
|
| 990 |
+
except Exception as error:
|
| 991 |
+
return (
|
| 992 |
+
"I could not process this question because "
|
| 993 |
+
"an error occurred.\n\n"
|
| 994 |
+
f"`{type(error).__name__}: {error}`"
|
| 995 |
+
)
|
| 996 |
+
|
| 997 |
+
|
| 998 |
+
with gr.Blocks(
|
| 999 |
+
title="ResearchGPT — Milad Saeedi",
|
| 1000 |
+
) as demo:
|
| 1001 |
+
|
| 1002 |
+
gr.Markdown(
|
| 1003 |
+
"""
|
| 1004 |
+
# ResearchGPT — Milad Saeedi
|
| 1005 |
+
|
| 1006 |
+
Explore Milad Saeedi's research, PhD thesis, publications,
|
| 1007 |
+
machine-learning experience, and selected GitHub projects.
|
| 1008 |
+
|
| 1009 |
+
Answers are grounded in retrieved portfolio documents and
|
| 1010 |
+
include supporting sources.
|
| 1011 |
+
"""
|
| 1012 |
+
)
|
| 1013 |
+
|
| 1014 |
+
chatbot = gr.Chatbot(
|
| 1015 |
+
placeholder=(
|
| 1016 |
+
"Ask about Milad's research, publications, "
|
| 1017 |
+
"technical skills, or GitHub projects."
|
| 1018 |
+
),
|
| 1019 |
+
height=550,
|
| 1020 |
+
)
|
| 1021 |
+
|
| 1022 |
+
gr.ChatInterface(
|
| 1023 |
+
fn=research_chat,
|
| 1024 |
+
chatbot=chatbot,
|
| 1025 |
+
examples=[
|
| 1026 |
+
"Summarize Milad Saeedi's research.",
|
| 1027 |
+
"What are the main contributions of his PhD thesis?",
|
| 1028 |
+
"Summarize his GitHub GAN projects.",
|
| 1029 |
+
"Which projects involve computer vision?",
|
| 1030 |
+
"What experience does he have with LoRA and GRPO?",
|
| 1031 |
+
"What did his research show about spatial cross-validation?",
|
| 1032 |
+
"Tell me about his geospatial modeling experience.",
|
| 1033 |
+
"How can I contact Milad?",
|
| 1034 |
+
],
|
| 1035 |
+
save_history=True,
|
| 1036 |
+
flagging_mode="never",
|
| 1037 |
+
)
|
| 1038 |
+
|
| 1039 |
+
gr.Markdown(
|
| 1040 |
+
"""
|
| 1041 |
+
---
|
| 1042 |
+
**ResearchGPT** uses hybrid retrieval, BGE embeddings,
|
| 1043 |
+
FAISS, BM25, cross-encoder reranking, Gemini,
|
| 1044 |
+
and grounded answer generation.
|
| 1045 |
+
"""
|
| 1046 |
+
)
|
| 1047 |
+
|
| 1048 |
+
|
| 1049 |
+
if __name__ == "__main__":
|
| 1050 |
+
demo.queue().launch(server_name="0.0.0.0", server_port=7860)
|
artifacts/chunks.json
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
artifacts/index_config.json
ADDED
|
@@ -0,0 +1,9 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"embedding_model": "BAAI/bge-base-en-v1.5",
|
| 3 |
+
"reranker_model": "cross-encoder/ms-marco-MiniLM-L6-v2",
|
| 4 |
+
"embedding_dimension": 768,
|
| 5 |
+
"number_of_chunks": 1497,
|
| 6 |
+
"chunk_size": 1000,
|
| 7 |
+
"chunk_overlap": 200,
|
| 8 |
+
"query_instruction": "Represent this sentence for searching relevant passages: "
|
| 9 |
+
}
|
artifacts/research_index.faiss
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:8d0cc5b9f80ff3317bd9017fad94dd9bde8a5605c796bcc5214941e668b8aa4f
|
| 3 |
+
size 4598829
|
artifacts/retrieval_texts.json
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
requirements.txt
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
gradio>=5.0
|
| 2 |
+
faiss-cpu
|
| 3 |
+
google-genai
|
| 4 |
+
numpy
|
| 5 |
+
rank-bm25
|
| 6 |
+
sentence-transformers
|
| 7 |
+
torch
|