Delete backend
Browse files- backend/__init__.py +0 -0
- backend/llm_utils.py +0 -34
- backend/main.py +0 -52
- backend/test +0 -0
- backend/umls_linker.py +0 -19
backend/__init__.py
DELETED
File without changes
|
backend/llm_utils.py
DELETED
@@ -1,34 +0,0 @@
|
|
1 |
-
|
2 |
-
"""Utilities for loading the ZeroSearch simulation model and performing simulated searches."""
|
3 |
-
from transformers import AutoModelForCausalLM, AutoTokenizer, pipeline
|
4 |
-
import functools
|
5 |
-
|
6 |
-
MODEL_NAME = "sunhaonlp/SearchSimulation_14B"
|
7 |
-
|
8 |
-
@functools.lru_cache(maxsize=1)
|
9 |
-
def _load_search_pipe():
|
10 |
-
tokenizer = AutoTokenizer.from_pretrained(MODEL_NAME)
|
11 |
-
model = AutoModelForCausalLM.from_pretrained(
|
12 |
-
MODEL_NAME,
|
13 |
-
trust_remote_code=True,
|
14 |
-
device_map="auto"
|
15 |
-
)
|
16 |
-
return pipeline(
|
17 |
-
"text-generation",
|
18 |
-
model=model,
|
19 |
-
tokenizer=tokenizer,
|
20 |
-
max_new_tokens=512,
|
21 |
-
do_sample=False,
|
22 |
-
temperature=0.0,
|
23 |
-
)
|
24 |
-
|
25 |
-
def simulate_search(query: str, k: int = 5):
|
26 |
-
"""Generate *k* synthetic documents for *query*."""
|
27 |
-
pipe = _load_search_pipe()
|
28 |
-
prompt = f"SearchSimulation:\nQuery: {query}\nDocuments:"
|
29 |
-
outputs = pipe(prompt, num_return_sequences=k)
|
30 |
-
docs = []
|
31 |
-
for o in outputs:
|
32 |
-
text = o["generated_text"]
|
33 |
-
docs.append(text.split("Documents:")[-1].strip())
|
34 |
-
return docs
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
backend/main.py
DELETED
@@ -1,52 +0,0 @@
|
|
1 |
-
|
2 |
-
from fastapi import FastAPI
|
3 |
-
from pydantic import BaseModel
|
4 |
-
from .llm_utils import simulate_search
|
5 |
-
from .umls_linker import link_umls
|
6 |
-
from transformers import AutoModelForCausalLM, AutoTokenizer, pipeline
|
7 |
-
import functools
|
8 |
-
|
9 |
-
ANSWER_MODEL = "sunhaonlp/SearchSimulation_14B"
|
10 |
-
|
11 |
-
@functools.lru_cache(maxsize=1)
|
12 |
-
def _load_answer_pipe():
|
13 |
-
tokenizer = AutoTokenizer.from_pretrained(ANSWER_MODEL)
|
14 |
-
model = AutoModelForCausalLM.from_pretrained(
|
15 |
-
ANSWER_MODEL,
|
16 |
-
trust_remote_code=True,
|
17 |
-
device_map="auto"
|
18 |
-
)
|
19 |
-
return pipeline(
|
20 |
-
"text-generation",
|
21 |
-
model=model,
|
22 |
-
tokenizer=tokenizer,
|
23 |
-
max_new_tokens=256,
|
24 |
-
do_sample=False,
|
25 |
-
temperature=0.0,
|
26 |
-
)
|
27 |
-
|
28 |
-
class Query(BaseModel):
|
29 |
-
question: str
|
30 |
-
|
31 |
-
app = FastAPI(
|
32 |
-
title="ZeroSearch Medical Q&A API",
|
33 |
-
description="Ask clinical questions; get answers with UMLS links, no external search APIs.",
|
34 |
-
version="0.1.0",
|
35 |
-
)
|
36 |
-
|
37 |
-
@app.post("/ask")
|
38 |
-
def ask(query: Query):
|
39 |
-
docs = simulate_search(query.question, k=5)
|
40 |
-
context = "\n\n".join(docs)
|
41 |
-
prompt = (
|
42 |
-
"Answer the medical question strictly based on the provided context.\n\n"
|
43 |
-
f"Context:\n{context}\n\n"
|
44 |
-
f"Question: {query.question}\nAnswer:"
|
45 |
-
)
|
46 |
-
answer_pipe = _load_answer_pipe()
|
47 |
-
answer = (
|
48 |
-
answer_pipe(prompt, num_return_sequences=1)[0]["generated_text"]
|
49 |
-
.split("Answer:")[-1].strip()
|
50 |
-
)
|
51 |
-
umls = link_umls(answer)
|
52 |
-
return {"answer": answer, "docs": docs, "umls": umls}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
backend/test
DELETED
File without changes
|
backend/umls_linker.py
DELETED
@@ -1,19 +0,0 @@
|
|
1 |
-
|
2 |
-
"""Simple UMLS linker using SciSpacy."""
|
3 |
-
import spacy
|
4 |
-
from scispacy.linking import UmlsEntityLinker
|
5 |
-
|
6 |
-
nlp = spacy.load("en_core_sci_lg")
|
7 |
-
linker = UmlsEntityLinker(resolve_abbreviations=True, disambiguate=True)
|
8 |
-
nlp.add_pipe(linker)
|
9 |
-
|
10 |
-
def link_umls(text: str):
|
11 |
-
doc = nlp(text)
|
12 |
-
results = []
|
13 |
-
for ent in doc.ents:
|
14 |
-
for cui, score in ent._.kb_ents:
|
15 |
-
results.append(
|
16 |
-
{"text": ent.text, "cui": cui, "score": score}
|
17 |
-
)
|
18 |
-
break # take top candidate
|
19 |
-
return results
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|