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Browse files- app.py +653 -0
- requirements.txt +26 -0
app.py
ADDED
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@@ -0,0 +1,653 @@
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| 1 |
+
import os
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| 2 |
+
import json
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| 3 |
+
import csv
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| 4 |
+
import asyncio
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| 5 |
+
import xml.etree.ElementTree as ET
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| 6 |
+
from typing import Any, Dict, Optional, Tuple, Union, List
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| 7 |
+
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| 8 |
+
import httpx
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| 9 |
+
import gradio as gr
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| 10 |
+
import torch
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| 11 |
+
from dotenv import load_dotenv
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| 12 |
+
from loguru import logger
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| 13 |
+
from huggingface_hub import login
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| 14 |
+
from openai import OpenAI
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| 15 |
+
from reportlab.pdfgen import canvas
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| 16 |
+
from transformers import (
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| 17 |
+
AutoTokenizer,
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| 18 |
+
AutoModelForSequenceClassification,
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| 19 |
+
MarianMTModel,
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| 20 |
+
MarianTokenizer,
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| 21 |
+
)
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| 22 |
+
import pandas as pd
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| 23 |
+
import altair as alt
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| 24 |
+
import spacy
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| 25 |
+
import spacy.cli
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| 26 |
+
import PyPDF2 # For PDF reading
|
| 27 |
+
|
| 28 |
+
# Ensure spaCy model is downloaded
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| 29 |
+
try:
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| 30 |
+
nlp = spacy.load("en_core_web_sm")
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| 31 |
+
except OSError:
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| 32 |
+
logger.info("Downloading SpaCy 'en_core_web_sm' model...")
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| 33 |
+
spacy.cli.download("en_core_web_sm")
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| 34 |
+
nlp = spacy.load("en_core_web_sm")
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| 35 |
+
|
| 36 |
+
# Logging
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| 37 |
+
logger.add("error_logs.log", rotation="1 MB", level="ERROR")
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| 38 |
+
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| 39 |
+
# Load environment variables
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| 40 |
+
load_dotenv()
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| 41 |
+
HUGGINGFACE_TOKEN = os.getenv("HF_TOKEN")
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| 42 |
+
OPENAI_API_KEY = os.getenv("OPENAI_API_KEY")
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| 43 |
+
ENTREZ_EMAIL = os.getenv("ENTREZ_EMAIL")
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| 44 |
+
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| 45 |
+
# Basic checks
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| 46 |
+
if not HUGGINGFACE_TOKEN or not OPENAI_API_KEY:
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| 47 |
+
logger.error("Missing Hugging Face or OpenAI credentials.")
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| 48 |
+
raise ValueError("Missing credentials for Hugging Face or OpenAI.")
|
| 49 |
+
|
| 50 |
+
# API endpoints
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| 51 |
+
PUBMED_SEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
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| 52 |
+
PUBMED_FETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
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| 53 |
+
EUROPE_PMC_BASE_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/search"
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| 54 |
+
|
| 55 |
+
# Hugging Face login
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| 56 |
+
login(HUGGINGFACE_TOKEN)
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| 57 |
+
|
| 58 |
+
# Initialize OpenAI
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| 59 |
+
client = OpenAI(api_key=OPENAI_API_KEY)
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| 60 |
+
|
| 61 |
+
# Device setting
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| 62 |
+
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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| 63 |
+
logger.info(f"Using device: {device}")
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| 64 |
+
|
| 65 |
+
# Model settings
|
| 66 |
+
MODEL_NAME = "mgbam/bert-base-finetuned-mgbam"
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| 67 |
+
try:
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| 68 |
+
model = AutoModelForSequenceClassification.from_pretrained(
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| 69 |
+
MODEL_NAME, use_auth_token=HUGGINGFACE_TOKEN
|
| 70 |
+
).to(device)
|
| 71 |
+
tokenizer = AutoTokenizer.from_pretrained(
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| 72 |
+
MODEL_NAME, use_auth_token=HUGGINGFACE_TOKEN
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| 73 |
+
)
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| 74 |
+
except Exception as e:
|
| 75 |
+
logger.error(f"Model load error: {e}")
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| 76 |
+
raise
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| 77 |
+
|
| 78 |
+
# Translation model settings
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| 79 |
+
try:
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| 80 |
+
translation_model_name = "Helsinki-NLP/opus-mt-en-fr"
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| 81 |
+
translation_model = MarianMTModel.from_pretrained(
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| 82 |
+
translation_model_name, use_auth_token=HUGGINGFACE_TOKEN
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| 83 |
+
).to(device)
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| 84 |
+
translation_tokenizer = MarianTokenizer.from_pretrained(
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| 85 |
+
translation_model_name, use_auth_token=HUGGINGFACE_TOKEN
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| 86 |
+
)
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| 87 |
+
except Exception as e:
|
| 88 |
+
logger.error(f"Translation model load error: {e}")
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| 89 |
+
raise
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| 90 |
+
|
| 91 |
+
LANGUAGE_MAP: Dict[str, Tuple[str, str]] = {
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| 92 |
+
"English to French": ("en", "fr"),
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| 93 |
+
"French to English": ("fr", "en"),
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| 94 |
+
}
|
| 95 |
+
|
| 96 |
+
### Utility Functions ###
|
| 97 |
+
def safe_json_parse(text: str) -> Union[Dict, None]:
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| 98 |
+
"""Safely parse JSON string into a Python dictionary."""
|
| 99 |
+
try:
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| 100 |
+
return json.loads(text)
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| 101 |
+
except json.JSONDecodeError as e:
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| 102 |
+
logger.error(f"JSON parsing error: {e}")
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| 103 |
+
return None
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| 104 |
+
|
| 105 |
+
def parse_pubmed_xml(xml_data: str) -> List[Dict[str, Any]]:
|
| 106 |
+
"""Parses PubMed XML data and returns a list of structured articles."""
|
| 107 |
+
root = ET.fromstring(xml_data)
|
| 108 |
+
articles = []
|
| 109 |
+
for article in root.findall(".//PubmedArticle"):
|
| 110 |
+
pmid = article.findtext(".//PMID")
|
| 111 |
+
title = article.findtext(".//ArticleTitle")
|
| 112 |
+
abstract = article.findtext(".//AbstractText")
|
| 113 |
+
journal = article.findtext(".//Journal/Title")
|
| 114 |
+
pub_date_elem = article.find(".//JournalIssue/PubDate")
|
| 115 |
+
pub_date = None
|
| 116 |
+
if pub_date_elem is not None:
|
| 117 |
+
year = pub_date_elem.findtext("Year")
|
| 118 |
+
month = pub_date_elem.findtext("Month")
|
| 119 |
+
day = pub_date_elem.findtext("Day")
|
| 120 |
+
if year and month and day:
|
| 121 |
+
pub_date = f"{year}-{month}-{day}"
|
| 122 |
+
else:
|
| 123 |
+
pub_date = year
|
| 124 |
+
articles.append({
|
| 125 |
+
"PMID": pmid,
|
| 126 |
+
"Title": title,
|
| 127 |
+
"Abstract": abstract,
|
| 128 |
+
"Journal": journal,
|
| 129 |
+
"PublicationDate": pub_date,
|
| 130 |
+
})
|
| 131 |
+
return articles
|
| 132 |
+
|
| 133 |
+
### Async Functions for Europe PMC ###
|
| 134 |
+
async def fetch_articles_by_nct_id(nct_id: str) -> Dict[str, Any]:
|
| 135 |
+
params = {"query": nct_id, "format": "json"}
|
| 136 |
+
async with httpx.AsyncClient() as client_http:
|
| 137 |
+
try:
|
| 138 |
+
response = await client_http.get(EUROPE_PMC_BASE_URL, params=params)
|
| 139 |
+
response.raise_for_status()
|
| 140 |
+
return response.json()
|
| 141 |
+
except Exception as e:
|
| 142 |
+
logger.error(f"Error fetching articles for {nct_id}: {e}")
|
| 143 |
+
return {"error": str(e)}
|
| 144 |
+
|
| 145 |
+
async def fetch_articles_by_query(query_params: str) -> Dict[str, Any]:
|
| 146 |
+
parsed_params = safe_json_parse(query_params)
|
| 147 |
+
if not parsed_params or not isinstance(parsed_params, dict):
|
| 148 |
+
return {"error": "Invalid JSON."}
|
| 149 |
+
query_string = " AND ".join(f"{k}:{v}" for k, v in parsed_params.items())
|
| 150 |
+
params = {"query": query_string, "format": "json"}
|
| 151 |
+
async with httpx.AsyncClient() as client_http:
|
| 152 |
+
try:
|
| 153 |
+
response = await client_http.get(EUROPE_PMC_BASE_URL, params=params)
|
| 154 |
+
response.raise_for_status()
|
| 155 |
+
return response.json()
|
| 156 |
+
except Exception as e:
|
| 157 |
+
logger.error(f"Error fetching articles: {e}")
|
| 158 |
+
return {"error": str(e)}
|
| 159 |
+
|
| 160 |
+
### PubMed Integration ###
|
| 161 |
+
async def fetch_pubmed_by_query(query_params: str) -> Dict[str, Any]:
|
| 162 |
+
parsed_params = safe_json_parse(query_params)
|
| 163 |
+
if not parsed_params or not isinstance(parsed_params, dict):
|
| 164 |
+
return {"error": "Invalid JSON for PubMed."}
|
| 165 |
+
|
| 166 |
+
search_params = {
|
| 167 |
+
"db": "pubmed",
|
| 168 |
+
"retmode": "json",
|
| 169 |
+
"email": ENTREZ_EMAIL,
|
| 170 |
+
"retmax": parsed_params.get("retmax", "10"),
|
| 171 |
+
"term": parsed_params.get("term", ""),
|
| 172 |
+
}
|
| 173 |
+
|
| 174 |
+
async with httpx.AsyncClient() as client_http:
|
| 175 |
+
try:
|
| 176 |
+
search_response = await client_http.get(PUBMED_SEARCH_URL, params=search_params)
|
| 177 |
+
search_response.raise_for_status()
|
| 178 |
+
search_data = search_response.json()
|
| 179 |
+
id_list = search_data.get("esearchresult", {}).get("idlist", [])
|
| 180 |
+
if not id_list:
|
| 181 |
+
return {"result": ""}
|
| 182 |
+
|
| 183 |
+
fetch_params = {
|
| 184 |
+
"db": "pubmed",
|
| 185 |
+
"id": ",".join(id_list),
|
| 186 |
+
"retmode": "xml",
|
| 187 |
+
"email": ENTREZ_EMAIL,
|
| 188 |
+
}
|
| 189 |
+
fetch_response = await client_http.get(PUBMED_FETCH_URL, params=fetch_params)
|
| 190 |
+
fetch_response.raise_for_status()
|
| 191 |
+
return {"result": fetch_response.text}
|
| 192 |
+
except Exception as e:
|
| 193 |
+
logger.error(f"Error fetching PubMed articles: {e}")
|
| 194 |
+
return {"error": str(e)}
|
| 195 |
+
|
| 196 |
+
### Crossref Integration ###
|
| 197 |
+
async def fetch_crossref_by_query(query_params: str) -> Dict[str, Any]:
|
| 198 |
+
parsed_params = safe_json_parse(query_params)
|
| 199 |
+
if not parsed_params or not isinstance(parsed_params, dict):
|
| 200 |
+
return {"error": "Invalid JSON for Crossref."}
|
| 201 |
+
CROSSREF_API_URL = "https://api.crossref.org/works"
|
| 202 |
+
async with httpx.AsyncClient() as client_http:
|
| 203 |
+
try:
|
| 204 |
+
response = await client_http.get(CROSSREF_API_URL, params=parsed_params)
|
| 205 |
+
response.raise_for_status()
|
| 206 |
+
return response.json()
|
| 207 |
+
except Exception as e:
|
| 208 |
+
logger.error(f"Error fetching Crossref data: {e}")
|
| 209 |
+
return {"error": str(e)}
|
| 210 |
+
|
| 211 |
+
### Core Functions ###
|
| 212 |
+
def summarize_text(text: str) -> str:
|
| 213 |
+
"""Summarize text using OpenAI."""
|
| 214 |
+
if not text.strip():
|
| 215 |
+
return "No text provided for summarization."
|
| 216 |
+
try:
|
| 217 |
+
response = client.chat.completions.create(
|
| 218 |
+
model="gpt-3.5-turbo",
|
| 219 |
+
messages=[{"role": "user", "content": f"Summarize the following clinical data:\n{text}"}],
|
| 220 |
+
max_tokens=200,
|
| 221 |
+
temperature=0.7,
|
| 222 |
+
)
|
| 223 |
+
return response.choices[0].message.content.strip()
|
| 224 |
+
except Exception as e:
|
| 225 |
+
logger.error(f"Summarization Error: {e}")
|
| 226 |
+
return "Summarization failed."
|
| 227 |
+
|
| 228 |
+
def predict_outcome(text: str) -> Union[Dict[str, float], str]:
|
| 229 |
+
"""Predict outcomes (classification) using a fine-tuned model."""
|
| 230 |
+
if not text.strip():
|
| 231 |
+
return "No text provided for prediction."
|
| 232 |
+
try:
|
| 233 |
+
inputs = tokenizer(text, return_tensors="pt", truncation=True, padding=True)
|
| 234 |
+
inputs = {k: v.to(device) for k, v in inputs.items()}
|
| 235 |
+
with torch.no_grad():
|
| 236 |
+
outputs = model(**inputs)
|
| 237 |
+
probabilities = torch.nn.functional.softmax(outputs.logits, dim=-1)[0]
|
| 238 |
+
return {f"Label {i+1}": float(prob.item()) for i, prob in enumerate(probabilities)}
|
| 239 |
+
except Exception as e:
|
| 240 |
+
logger.error(f"Prediction Error: {e}")
|
| 241 |
+
return "Prediction failed."
|
| 242 |
+
|
| 243 |
+
def generate_report(text: str, filename: str = "clinical_report.pdf") -> Optional[str]:
|
| 244 |
+
"""Generate a PDF report from the given text."""
|
| 245 |
+
try:
|
| 246 |
+
if not text.strip():
|
| 247 |
+
logger.warning("No text provided for the report.")
|
| 248 |
+
c = canvas.Canvas(filename)
|
| 249 |
+
c.drawString(100, 750, "Clinical Research Report")
|
| 250 |
+
lines = text.split("\n")
|
| 251 |
+
y = 730
|
| 252 |
+
for line in lines:
|
| 253 |
+
if y < 50:
|
| 254 |
+
c.showPage()
|
| 255 |
+
y = 750
|
| 256 |
+
c.drawString(100, y, line)
|
| 257 |
+
y -= 15
|
| 258 |
+
c.save()
|
| 259 |
+
logger.info(f"Report generated: {filename}")
|
| 260 |
+
return filename
|
| 261 |
+
except Exception as e:
|
| 262 |
+
logger.error(f"Report Generation Error: {e}")
|
| 263 |
+
return None
|
| 264 |
+
|
| 265 |
+
def visualize_predictions(predictions: Dict[str, float]) -> Optional[alt.Chart]:
|
| 266 |
+
"""Visualize model prediction probabilities using Altair."""
|
| 267 |
+
try:
|
| 268 |
+
data = pd.DataFrame(list(predictions.items()), columns=["Label", "Probability"])
|
| 269 |
+
chart = (
|
| 270 |
+
alt.Chart(data)
|
| 271 |
+
.mark_bar()
|
| 272 |
+
.encode(
|
| 273 |
+
x=alt.X("Label:N", sort=None),
|
| 274 |
+
y="Probability:Q",
|
| 275 |
+
tooltip=["Label", "Probability"],
|
| 276 |
+
)
|
| 277 |
+
.properties(title="Prediction Probabilities", width=500, height=300)
|
| 278 |
+
)
|
| 279 |
+
return chart
|
| 280 |
+
except Exception as e:
|
| 281 |
+
logger.error(f"Visualization Error: {e}")
|
| 282 |
+
return None
|
| 283 |
+
|
| 284 |
+
def translate_text(text: str, translation_option: str) -> str:
|
| 285 |
+
"""Translate text between English and French."""
|
| 286 |
+
if not text.strip():
|
| 287 |
+
return "No text provided for translation."
|
| 288 |
+
try:
|
| 289 |
+
if translation_option not in LANGUAGE_MAP:
|
| 290 |
+
return "Unsupported translation option."
|
| 291 |
+
inputs = translation_tokenizer(text, return_tensors="pt", padding=True).to(device)
|
| 292 |
+
translated_tokens = translation_model.generate(**inputs)
|
| 293 |
+
return translation_tokenizer.decode(translated_tokens[0], skip_special_tokens=True)
|
| 294 |
+
except Exception as e:
|
| 295 |
+
logger.error(f"Translation Error: {e}")
|
| 296 |
+
return "Translation failed."
|
| 297 |
+
|
| 298 |
+
def perform_named_entity_recognition(text: str) -> str:
|
| 299 |
+
"""Perform Named Entity Recognition (NER) using spaCy."""
|
| 300 |
+
if not text.strip():
|
| 301 |
+
return "No text provided for NER."
|
| 302 |
+
try:
|
| 303 |
+
doc = nlp(text)
|
| 304 |
+
entities = [(ent.text, ent.label_) for ent in doc.ents]
|
| 305 |
+
if not entities:
|
| 306 |
+
return "No named entities found."
|
| 307 |
+
return "\n".join(f"{ent_text} -> {ent_label}" for ent_text, ent_label in entities)
|
| 308 |
+
except Exception as e:
|
| 309 |
+
logger.error(f"NER Error: {e}")
|
| 310 |
+
return "Named Entity Recognition failed."
|
| 311 |
+
|
| 312 |
+
### Enhanced EDA ###
|
| 313 |
+
def perform_enhanced_eda(df: pd.DataFrame) -> Tuple[str, Optional[alt.Chart], Optional[alt.Chart]]:
|
| 314 |
+
"""
|
| 315 |
+
Perform a more advanced EDA given a DataFrame:
|
| 316 |
+
- Show dataset info (columns, shape, numeric summary).
|
| 317 |
+
- Generate a correlation heatmap (for numeric columns).
|
| 318 |
+
- Generate distribution plots (histograms) for numeric columns.
|
| 319 |
+
Returns (text_summary, correlation_chart, distribution_chart).
|
| 320 |
+
"""
|
| 321 |
+
try:
|
| 322 |
+
# Basic info
|
| 323 |
+
columns_info = f"Columns: {list(df.columns)}"
|
| 324 |
+
shape_info = f"Shape: {df.shape[0]} rows x {df.shape[1]} columns"
|
| 325 |
+
|
| 326 |
+
# Use describe with "include='all'" to show all columns summary
|
| 327 |
+
with pd.option_context("display.max_colwidth", 200, "display.max_rows", None):
|
| 328 |
+
describe_info = df.describe(include="all").to_string()
|
| 329 |
+
|
| 330 |
+
summary_text = (
|
| 331 |
+
f"--- Enhanced EDA Summary ---\n"
|
| 332 |
+
f"{columns_info}\n{shape_info}\n\n"
|
| 333 |
+
f"Summary Statistics:\n{describe_info}\n"
|
| 334 |
+
)
|
| 335 |
+
|
| 336 |
+
# Correlation heatmap
|
| 337 |
+
numeric_cols = df.select_dtypes(include="number")
|
| 338 |
+
corr_chart = None
|
| 339 |
+
if numeric_cols.shape[1] >= 2:
|
| 340 |
+
corr = numeric_cols.corr()
|
| 341 |
+
corr_melted = corr.reset_index().melt(id_vars="index")
|
| 342 |
+
corr_melted.columns = ["Feature1", "Feature2", "Correlation"]
|
| 343 |
+
corr_chart = (
|
| 344 |
+
alt.Chart(corr_melted)
|
| 345 |
+
.mark_rect()
|
| 346 |
+
.encode(
|
| 347 |
+
x="Feature1:O",
|
| 348 |
+
y="Feature2:O",
|
| 349 |
+
color="Correlation:Q",
|
| 350 |
+
tooltip=["Feature1", "Feature2", "Correlation"]
|
| 351 |
+
)
|
| 352 |
+
.properties(width=400, height=400, title="Correlation Heatmap")
|
| 353 |
+
)
|
| 354 |
+
|
| 355 |
+
# Distribution plots (histograms) for numeric columns
|
| 356 |
+
distribution_chart = None
|
| 357 |
+
if numeric_cols.shape[1] >= 1:
|
| 358 |
+
df_long = numeric_cols.melt(var_name='Column', value_name='Value')
|
| 359 |
+
distribution_chart = (
|
| 360 |
+
alt.Chart(df_long)
|
| 361 |
+
.mark_bar()
|
| 362 |
+
.encode(
|
| 363 |
+
alt.X("Value:Q", bin=alt.Bin(maxbins=30)),
|
| 364 |
+
alt.Y('count()'),
|
| 365 |
+
alt.Facet('Column:N', columns=2),
|
| 366 |
+
tooltip=["Value"]
|
| 367 |
+
)
|
| 368 |
+
.properties(
|
| 369 |
+
title='Distribution of Numeric Columns',
|
| 370 |
+
width=300,
|
| 371 |
+
height=200
|
| 372 |
+
)
|
| 373 |
+
.interactive()
|
| 374 |
+
)
|
| 375 |
+
|
| 376 |
+
return summary_text, corr_chart, distribution_chart
|
| 377 |
+
|
| 378 |
+
except Exception as e:
|
| 379 |
+
logger.error(f"Enhanced EDA Error: {e}")
|
| 380 |
+
return f"Enhanced EDA failed: {e}", None, None
|
| 381 |
+
|
| 382 |
+
### File Handling ###
|
| 383 |
+
def read_uploaded_file(uploaded_file: Optional[gr.File]) -> str:
|
| 384 |
+
"""
|
| 385 |
+
Reads the content of an uploaded file (txt, csv, xls, xlsx, pdf).
|
| 386 |
+
Returns the extracted text or CSV-like content.
|
| 387 |
+
"""
|
| 388 |
+
if uploaded_file is None:
|
| 389 |
+
return ""
|
| 390 |
+
|
| 391 |
+
file_name = uploaded_file.name
|
| 392 |
+
file_ext = os.path.splitext(file_name)[1].lower()
|
| 393 |
+
|
| 394 |
+
try:
|
| 395 |
+
# For text
|
| 396 |
+
if file_ext == ".txt":
|
| 397 |
+
return uploaded_file.read().decode("utf-8")
|
| 398 |
+
|
| 399 |
+
# For CSV
|
| 400 |
+
elif file_ext == ".csv":
|
| 401 |
+
return uploaded_file.read().decode("utf-8")
|
| 402 |
+
|
| 403 |
+
# For Excel
|
| 404 |
+
elif file_ext in [".xls", ".xlsx"]:
|
| 405 |
+
# We'll just return empty here and parse it later into a DataFrame
|
| 406 |
+
# because we can read the binary directly into pd.read_excel().
|
| 407 |
+
# Or store as bytes for later use in EDA.
|
| 408 |
+
return "EXCEL_FILE_PLACEHOLDER" # We'll handle it differently in EDA step
|
| 409 |
+
|
| 410 |
+
# For PDF
|
| 411 |
+
elif file_ext == ".pdf":
|
| 412 |
+
pdf_reader = PyPDF2.PdfReader(uploaded_file)
|
| 413 |
+
text_content = []
|
| 414 |
+
for page in pdf_reader.pages:
|
| 415 |
+
text_content.append(page.extract_text())
|
| 416 |
+
return "\n".join(text_content)
|
| 417 |
+
|
| 418 |
+
else:
|
| 419 |
+
return f"Unsupported file format: {file_ext}"
|
| 420 |
+
except Exception as e:
|
| 421 |
+
logger.error(f"File read error: {e}")
|
| 422 |
+
return f"Error reading file: {e}"
|
| 423 |
+
|
| 424 |
+
def parse_excel_file(uploaded_file) -> pd.DataFrame:
|
| 425 |
+
"""
|
| 426 |
+
Parse an Excel file into a pandas DataFrame.
|
| 427 |
+
We assume the user wants the first sheet or we can guess.
|
| 428 |
+
"""
|
| 429 |
+
try:
|
| 430 |
+
# For Excel, we can do:
|
| 431 |
+
df = pd.read_excel(uploaded_file, engine="openpyxl")
|
| 432 |
+
return df
|
| 433 |
+
except Exception as e:
|
| 434 |
+
logger.error(f"Excel parsing error: {e}")
|
| 435 |
+
raise
|
| 436 |
+
|
| 437 |
+
def parse_csv_content(csv_content: str) -> pd.DataFrame:
|
| 438 |
+
"""
|
| 439 |
+
Attempt to parse CSV content with both utf-8 and utf-8-sig to handle BOM issues.
|
| 440 |
+
"""
|
| 441 |
+
from io import StringIO
|
| 442 |
+
errors = []
|
| 443 |
+
for encoding_try in ["utf-8", "utf-8-sig"]:
|
| 444 |
+
try:
|
| 445 |
+
df = pd.read_csv(StringIO(csv_content), encoding=encoding_try)
|
| 446 |
+
return df
|
| 447 |
+
except Exception as e:
|
| 448 |
+
errors.append(f"Encoding {encoding_try} failed: {e}")
|
| 449 |
+
error_msg = "Could not parse CSV content.\n" + "\n".join(errors)
|
| 450 |
+
logger.error(error_msg)
|
| 451 |
+
raise ValueError(error_msg)
|
| 452 |
+
|
| 453 |
+
### Gradio Interface ###
|
| 454 |
+
with gr.Blocks() as demo:
|
| 455 |
+
gr.Markdown("# ✨ Advanced Clinical Research Assistant with Enhanced EDA ✨")
|
| 456 |
+
gr.Markdown("""
|
| 457 |
+
Welcome to the **Enhanced** AI-Powered Clinical Assistant!
|
| 458 |
+
- **Summarize** large blocks of clinical text.
|
| 459 |
+
- **Predict** outcomes with a fine-tuned model.
|
| 460 |
+
- **Translate** text between English & French.
|
| 461 |
+
- **Perform Named Entity Recognition** with spaCy.
|
| 462 |
+
- **Fetch** from PubMed, Crossref, Europe PMC.
|
| 463 |
+
- **Generate** professional PDF reports.
|
| 464 |
+
- **Perform Enhanced EDA** on CSV/Excel data with correlation heatmaps & distribution plots.
|
| 465 |
+
""")
|
| 466 |
+
|
| 467 |
+
# Inputs
|
| 468 |
+
with gr.Row():
|
| 469 |
+
text_input = gr.Textbox(label="Input Text", lines=5, placeholder="Enter clinical text or query...")
|
| 470 |
+
file_input = gr.File(
|
| 471 |
+
label="Upload File (txt/csv/xls/xlsx/pdf)",
|
| 472 |
+
file_types=[".txt", ".csv", ".xls", ".xlsx", ".pdf"]
|
| 473 |
+
)
|
| 474 |
+
|
| 475 |
+
action = gr.Radio(
|
| 476 |
+
[
|
| 477 |
+
"Summarize",
|
| 478 |
+
"Predict Outcome",
|
| 479 |
+
"Generate Report",
|
| 480 |
+
"Translate",
|
| 481 |
+
"Perform Named Entity Recognition",
|
| 482 |
+
"Perform Enhanced EDA",
|
| 483 |
+
"Fetch Clinical Studies",
|
| 484 |
+
"Fetch PubMed Articles (Legacy)",
|
| 485 |
+
"Fetch PubMed by Query",
|
| 486 |
+
"Fetch Crossref by Query",
|
| 487 |
+
],
|
| 488 |
+
label="Select an Action",
|
| 489 |
+
)
|
| 490 |
+
translation_option = gr.Dropdown(
|
| 491 |
+
choices=list(LANGUAGE_MAP.keys()),
|
| 492 |
+
label="Translation Option",
|
| 493 |
+
value="English to French"
|
| 494 |
+
)
|
| 495 |
+
query_params_input = gr.Textbox(
|
| 496 |
+
label="Query Parameters (JSON Format)",
|
| 497 |
+
placeholder='{"term": "cancer", "retmax": "5"}'
|
| 498 |
+
)
|
| 499 |
+
nct_id_input = gr.Textbox(label="NCT ID for Article Search")
|
| 500 |
+
report_filename_input = gr.Textbox(
|
| 501 |
+
label="Report Filename",
|
| 502 |
+
placeholder="clinical_report.pdf",
|
| 503 |
+
value="clinical_report.pdf"
|
| 504 |
+
)
|
| 505 |
+
export_format = gr.Dropdown(["None", "CSV", "JSON"], label="Export Format")
|
| 506 |
+
|
| 507 |
+
# Outputs
|
| 508 |
+
output_text = gr.Textbox(label="Output", lines=10)
|
| 509 |
+
|
| 510 |
+
with gr.Row():
|
| 511 |
+
output_chart = gr.Plot(label="Visualization 1")
|
| 512 |
+
output_chart2 = gr.Plot(label="Visualization 2")
|
| 513 |
+
|
| 514 |
+
output_file = gr.File(label="Generated File")
|
| 515 |
+
|
| 516 |
+
submit_button = gr.Button("Submit")
|
| 517 |
+
|
| 518 |
+
# Async function for handling actions
|
| 519 |
+
async def handle_action(
|
| 520 |
+
action: str,
|
| 521 |
+
text: str,
|
| 522 |
+
file_up: gr.File,
|
| 523 |
+
translation_opt: str,
|
| 524 |
+
query_params: str,
|
| 525 |
+
nct_id: str,
|
| 526 |
+
report_filename: str,
|
| 527 |
+
export_format: str
|
| 528 |
+
) -> Tuple[Optional[str], Optional[Any], Optional[Any], Optional[str]]:
|
| 529 |
+
|
| 530 |
+
# Read the uploaded file
|
| 531 |
+
file_content = read_uploaded_file(file_up)
|
| 532 |
+
combined_text = (text + "\n" + file_content).strip() if file_content else text
|
| 533 |
+
|
| 534 |
+
# Branch by action
|
| 535 |
+
if action == "Summarize":
|
| 536 |
+
return summarize_text(combined_text), None, None, None
|
| 537 |
+
|
| 538 |
+
elif action == "Predict Outcome":
|
| 539 |
+
predictions = predict_outcome(combined_text)
|
| 540 |
+
if isinstance(predictions, dict):
|
| 541 |
+
chart = visualize_predictions(predictions)
|
| 542 |
+
return json.dumps(predictions, indent=2), chart, None, None
|
| 543 |
+
return predictions, None, None, None
|
| 544 |
+
|
| 545 |
+
elif action == "Generate Report":
|
| 546 |
+
file_path = generate_report(combined_text, filename=report_filename)
|
| 547 |
+
msg = f"Report generated: {file_path}" if file_path else "Report generation failed."
|
| 548 |
+
return msg, None, None, file_path
|
| 549 |
+
|
| 550 |
+
elif action == "Translate":
|
| 551 |
+
return translate_text(combined_text, translation_opt), None, None, None
|
| 552 |
+
|
| 553 |
+
elif action == "Perform Named Entity Recognition":
|
| 554 |
+
ner_result = perform_named_entity_recognition(combined_text)
|
| 555 |
+
return ner_result, None, None, None
|
| 556 |
+
|
| 557 |
+
elif action == "Perform Enhanced EDA":
|
| 558 |
+
# We expect the user to either upload a CSV or Excel, or paste CSV content.
|
| 559 |
+
if file_up is None and not combined_text:
|
| 560 |
+
return "No data provided for EDA.", None, None, None
|
| 561 |
+
|
| 562 |
+
# If Excel was uploaded
|
| 563 |
+
if file_up and file_up.name.lower().endswith((".xls", ".xlsx")):
|
| 564 |
+
try:
|
| 565 |
+
df_excel = parse_excel_file(file_up)
|
| 566 |
+
eda_summary, corr_chart, dist_chart = perform_enhanced_eda(df_excel)
|
| 567 |
+
return eda_summary, corr_chart, dist_chart, None
|
| 568 |
+
except Exception as e:
|
| 569 |
+
return f"Excel EDA failed: {e}", None, None, None
|
| 570 |
+
|
| 571 |
+
# If CSV was uploaded
|
| 572 |
+
if file_up and file_up.name.lower().endswith(".csv"):
|
| 573 |
+
try:
|
| 574 |
+
df_csv = parse_csv_content(file_content)
|
| 575 |
+
eda_summary, corr_chart, dist_chart = perform_enhanced_eda(df_csv)
|
| 576 |
+
return eda_summary, corr_chart, dist_chart, None
|
| 577 |
+
except Exception as e:
|
| 578 |
+
return f"CSV EDA failed: {e}", None, None, None
|
| 579 |
+
|
| 580 |
+
# If user just pasted CSV content (no file)
|
| 581 |
+
if not file_up and "," in combined_text:
|
| 582 |
+
try:
|
| 583 |
+
df_csv = parse_csv_content(combined_text)
|
| 584 |
+
eda_summary, corr_chart, dist_chart = perform_enhanced_eda(df_csv)
|
| 585 |
+
return eda_summary, corr_chart, dist_chart, None
|
| 586 |
+
except Exception as e:
|
| 587 |
+
return f"CSV EDA failed: {e}", None, None, None
|
| 588 |
+
|
| 589 |
+
# Otherwise, not supported
|
| 590 |
+
return "No valid CSV/Excel data found for EDA.", None, None, None
|
| 591 |
+
|
| 592 |
+
elif action == "Fetch Clinical Studies":
|
| 593 |
+
if nct_id:
|
| 594 |
+
result = await fetch_articles_by_nct_id(nct_id)
|
| 595 |
+
elif query_params:
|
| 596 |
+
result = await fetch_articles_by_query(query_params)
|
| 597 |
+
else:
|
| 598 |
+
return "Provide either an NCT ID or valid query parameters.", None, None, None
|
| 599 |
+
|
| 600 |
+
articles = result.get("resultList", {}).get("result", [])
|
| 601 |
+
if not articles:
|
| 602 |
+
return "No articles found.", None, None, None
|
| 603 |
+
|
| 604 |
+
formatted_results = "\n\n".join(
|
| 605 |
+
f"Title: {a.get('title')}\nJournal: {a.get('journalTitle')} ({a.get('pubYear')})"
|
| 606 |
+
for a in articles
|
| 607 |
+
)
|
| 608 |
+
return formatted_results, None, None, None
|
| 609 |
+
|
| 610 |
+
elif action in ["Fetch PubMed Articles (Legacy)", "Fetch PubMed by Query"]:
|
| 611 |
+
pubmed_result = await fetch_pubmed_by_query(query_params)
|
| 612 |
+
xml_data = pubmed_result.get("result")
|
| 613 |
+
if xml_data:
|
| 614 |
+
articles = parse_pubmed_xml(xml_data)
|
| 615 |
+
if not articles:
|
| 616 |
+
return "No articles found.", None, None, None
|
| 617 |
+
formatted = "\n\n".join(
|
| 618 |
+
f"{a['Title']} - {a['Journal']} ({a['PublicationDate']})"
|
| 619 |
+
for a in articles if a['Title']
|
| 620 |
+
)
|
| 621 |
+
return formatted if formatted else "No articles found.", None, None, None
|
| 622 |
+
return "No articles found or error fetching data.", None, None, None
|
| 623 |
+
|
| 624 |
+
elif action == "Fetch Crossref by Query":
|
| 625 |
+
crossref_result = await fetch_crossref_by_query(query_params)
|
| 626 |
+
items = crossref_result.get("message", {}).get("items", [])
|
| 627 |
+
if not items:
|
| 628 |
+
return "No results found.", None, None, None
|
| 629 |
+
formatted = "\n\n".join(
|
| 630 |
+
f"Title: {item.get('title', ['No title'])[0]}, DOI: {item.get('DOI')}"
|
| 631 |
+
for item in items
|
| 632 |
+
)
|
| 633 |
+
return formatted, None, None, None
|
| 634 |
+
|
| 635 |
+
return "Invalid action.", None, None, None
|
| 636 |
+
|
| 637 |
+
submit_button.click(
|
| 638 |
+
handle_action,
|
| 639 |
+
inputs=[
|
| 640 |
+
action,
|
| 641 |
+
text_input,
|
| 642 |
+
file_input,
|
| 643 |
+
translation_option,
|
| 644 |
+
query_params_input,
|
| 645 |
+
nct_id_input,
|
| 646 |
+
report_filename_input,
|
| 647 |
+
export_format,
|
| 648 |
+
],
|
| 649 |
+
outputs=[output_text, output_chart, output_chart2, output_file],
|
| 650 |
+
)
|
| 651 |
+
|
| 652 |
+
# Launch the Gradio app
|
| 653 |
+
demo.launch(server_name="0.0.0.0", server_port=7860, share=True)
|
requirements.txt
ADDED
|
@@ -0,0 +1,26 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
streamlit
|
| 2 |
+
gradio
|
| 3 |
+
openai>=0.27.8
|
| 4 |
+
torch>=2.0.0
|
| 5 |
+
transformers>=4.33.0
|
| 6 |
+
huggingface-hub>=0.16.0
|
| 7 |
+
python-dotenv>=1.0.0
|
| 8 |
+
reportlab>=3.6.0
|
| 9 |
+
matplotlib>=3.7.1
|
| 10 |
+
pandas>=2.0.3
|
| 11 |
+
altair>=4.2.2
|
| 12 |
+
loguru>=0.7.0
|
| 13 |
+
spacy>=3.6.0
|
| 14 |
+
PyPDF2>=3.0.0
|
| 15 |
+
pdfplumber>=0.9.0
|
| 16 |
+
Pillow>=10.0.0
|
| 17 |
+
sentencepiece
|
| 18 |
+
sacremoses>=0.0.53
|
| 19 |
+
httpx
|
| 20 |
+
numpy
|
| 21 |
+
reportlab
|
| 22 |
+
requests
|
| 23 |
+
openpyxl
|
| 24 |
+
|
| 25 |
+
|
| 26 |
+
|