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import streamlit as st
import pandas as pd
import torch
from transformers import AutoTokenizer, AutoModelForSeq2SeqLM
from peft import PeftModel
from text_processing import TextProcessor
import gc
import time
from pathlib import Path
# Configure page
st.set_page_config(
page_title="Biomedical Papers Analysis",
page_icon="🔬",
layout="wide"
)
# Initialize session state
if 'processed_data' not in st.session_state:
st.session_state.processed_data = None
if 'summaries' not in st.session_state:
st.session_state.summaries = None
if 'text_processor' not in st.session_state:
st.session_state.text_processor = None
def load_model(model_type):
"""Load appropriate model based on type"""
if model_type == "summarize":
base_model = AutoModelForSeq2SeqLM.from_pretrained("facebook/bart-large-cnn")
model = PeftModel.from_pretrained(base_model, "pendar02/results")
tokenizer = AutoTokenizer.from_pretrained("facebook/bart-large-cnn")
else: # question_focused
base_model = AutoModelForSeq2SeqLM.from_pretrained("GanjinZero/biobart-base")
model = PeftModel.from_pretrained(base_model, "pendar02/biobart-finetune")
tokenizer = AutoTokenizer.from_pretrained("GanjinZero/biobart-base")
return model, tokenizer
@st.cache_data
def process_excel(uploaded_file):
"""Process uploaded Excel file"""
try:
df = pd.read_excel(uploaded_file)
required_columns = ['Abstract', 'Article Title', 'Authors',
'Source Title', 'Publication Year', 'DOI']
# Check required columns
missing_columns = [col for col in required_columns if col not in df.columns]
if missing_columns:
st.error(f"Missing required columns: {', '.join(missing_columns)}")
return None
return df[required_columns]
except Exception as e:
st.error(f"Error processing file: {str(e)}")
return None
def generate_summary(text, model, tokenizer):
"""Generate summary for single abstract"""
inputs = tokenizer(text, return_tensors="pt", max_length=1024, truncation=True)
with torch.no_grad():
summary_ids = model.generate(
**{
"input_ids": inputs["input_ids"],
"attention_mask": inputs["attention_mask"],
"max_length": 150,
"min_length": 50,
"num_beams": 4,
"length_penalty": 2.0,
"early_stopping": True
}
)
return tokenizer.decode(summary_ids[0], skip_special_tokens=True)
def generate_focused_summary(question, abstracts, model, tokenizer):
"""Generate focused summary based on question"""
combined_input = f"Question: {question} Abstracts: " + " [SEP] ".join(abstracts)
inputs = tokenizer(combined_input, return_tensors="pt", max_length=1024, truncation=True)
with torch.no_grad():
summary_ids = model.generate(
**{
"input_ids": inputs["input_ids"],
"attention_mask": inputs["attention_mask"],
"max_length": 200,
"min_length": 50,
"num_beams": 4,
"length_penalty": 2.0,
"early_stopping": True
}
)
return tokenizer.decode(summary_ids[0], skip_special_tokens=True)
def main():
st.title("🔬 Biomedical Papers Analysis")
# Sidebar
st.sidebar.header("About")
st.sidebar.info(
"This app analyzes biomedical research papers. Upload an Excel file "
"containing paper details and abstracts to:"
"\n- Generate individual summaries"
"\n- Get question-focused insights"
)
# Initialize text processor if not already done
if st.session_state.text_processor is None:
with st.spinner("Loading NLP models..."):
st.session_state.text_processor = TextProcessor()
# File upload section
uploaded_file = st.file_uploader(
"Upload Excel file containing papers",
type=['xlsx', 'xls'],
help="File must contain: Abstract, Article Title, Authors, Source Title, Publication Year, DOI"
)
if uploaded_file is not None:
# Process Excel file
if st.session_state.processed_data is None:
with st.spinner("Processing file..."):
df = process_excel(uploaded_file)
if df is not None:
st.session_state.processed_data = df
if st.session_state.processed_data is not None:
df = st.session_state.processed_data
st.write(f"📊 Loaded {len(df)} papers")
# Individual Summaries Section
st.header("📝 Individual Paper Summaries")
if st.session_state.summaries is None and st.button("Generate Individual Summaries"):
try:
with st.spinner("Generating summaries..."):
# Load summarization model
model, tokenizer = load_model("summarize")
# Process abstracts
progress_bar = st.progress(0)
summaries = []
for i, abstract in enumerate(df['Abstract']):
summary = generate_summary(abstract, model, tokenizer)
summaries.append(summary)
progress_bar.progress((i + 1) / len(df))
st.session_state.summaries = summaries
# Clear GPU memory
del model
del tokenizer
torch.cuda.empty_cache()
gc.collect()
except Exception as e:
st.error(f"Error generating summaries: {str(e)}")
if st.session_state.summaries is not None:
# Display summaries with sorting options
col1, col2 = st.columns(2)
with col1:
sort_column = st.selectbox("Sort by:", df.columns)
with col2:
ascending = st.checkbox("Ascending order", True)
# Create display dataframe
display_df = df.copy()
display_df['Summary'] = st.session_state.summaries
sorted_df = display_df.sort_values(by=sort_column, ascending=ascending)
# Show interactive table
st.dataframe(
sorted_df,
column_config={
"Abstract": st.column_config.TextColumn(
"Abstract",
width="medium",
help="Original abstract text"
),
"Summary": st.column_config.TextColumn(
"Summary",
width="medium",
help="Generated summary"
)
},
hide_index=True
)
# Question-focused Summary Section
st.header("❓ Question-focused Summary")
question = st.text_input("Enter your research question:")
if question and st.button("Generate Focused Summary"):
try:
with st.spinner("Analyzing relevant papers..."):
# Find relevant abstracts
results = st.session_state.text_processor.find_most_relevant_abstracts(
question,
df['Abstract'].tolist(),
top_k=5
)
# Show spell-check suggestion if needed
if results['processed_question']['original'] != results['processed_question']['corrected']:
st.info(f"Did you mean: {results['processed_question']['corrected']}?")
# Load question-focused model
model, tokenizer = load_model("question_focused")
# Get relevant abstracts and generate summary
relevant_abstracts = df['Abstract'].iloc[results['top_indices']].tolist()
focused_summary = generate_focused_summary(
results['processed_question']['corrected'],
relevant_abstracts,
model,
tokenizer
)
# Display results
st.subheader("Summary")
st.write(focused_summary)
# Show relevant papers
st.subheader("Most Relevant Papers")
relevant_papers = df.iloc[results['top_indices']][
['Article Title', 'Authors', 'Publication Year', 'DOI']
]
relevant_papers['Relevance Score'] = results['scores']
st.dataframe(relevant_papers, hide_index=True)
# Show identified medical terms
st.subheader("Identified Medical Terms")
st.write(", ".join(results['processed_question']['medical_entities']))
# Clear GPU memory
del model
del tokenizer
torch.cuda.empty_cache()
gc.collect()
except Exception as e:
st.error(f"Error generating focused summary: {str(e)}")
if __name__ == "__main__":
main() |