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import streamlit as st
import pandas as pd
import numpy as np
from math import ceil
from collections import Counter
from string import punctuation
import spacy
from spacy import displacy
import en_ner_bc5cdr_md
nlp = spacy.load("en_ner_bc5cdr_md")
#nlp = en_core_web_lg.load()
st.set_page_config(layout='wide')
st.title('Clinical Note Summarization')
st.sidebar.markdown('Using transformer model')
## Loading in dataset
#df = pd.read_csv('mtsamples_small.csv',index_col=0)
df = pd.read_csv('shpi_w_rouge21Nov.csv')
df['HADM_ID'] = df['HADM_ID'].astype(str).apply(lambda x: x.replace('.0',''))
#Renaming column
df.rename(columns={'SUBJECT_ID':'Patient_ID',
'HADM_ID':'Admission_ID',
'hpi_input_text':'Original_Text',
'hpi_reference_summary':'Reference_text'}, inplace = True)
#data.rename(columns={'gdp':'log(gdp)'}, inplace=True)
#Filter selection
st.sidebar.header("Search for Patient:")
patientid = df['Patient_ID']
patient = st.sidebar.selectbox('Select Patient ID:', patientid)
admissionid = df['Admission_ID'].loc[df['Patient_ID'] == patient]
HospitalAdmission = st.sidebar.selectbox('', admissionid)
# List of Model available
model = st.sidebar.selectbox('Select Model', ('BertSummarizer','BertGPT2','t5seq2eq','t5','gensim','pysummarizer'))
col3,col4 = st.columns(2)
patientid = col3.write(f"Patient ID: {patient} ")
admissionid =col4.write(f"Admission ID: {HospitalAdmission} ")
#text = st.text_area('Input Clinical Note here')
# Query out relevant Clinical notes
original_text = df.query(
"Patient_ID == @patient & Admission_ID == @HospitalAdmission"
)
original_text2 = original_text['Original_Text'].values
runtext =st.text_area('Input Clinical Note here:', str(original_text2), height=300)
reference_text = original_text['Reference_text'].values
def run_model(input_text):
if model == "BertSummarizer":
output = original_text['BertSummarizer'].values
st.write('Summary')
st.success(output[0])
elif model == "BertGPT2":
output = original_text['BertGPT2'].values
st.write('Summary')
st.success(output[0])
elif model == "t5seq2eq":
output = original_text['t5seq2eq'].values
st.write('Summary')
st.success(output)
elif model == "t5":
output = original_text['t5'].values
st.write('Summary')
st.success(output)
elif model == "gensim":
output = original_text['gensim'].values
st.write('Summary')
st.success(output)
elif model == "pysummarizer":
output = original_text['pysummarizer'].values
st.write('Summary')
st.success(output)
if st.button('Summarize'):
run_model(runtext)
sentences=runtext.split('.')
st.text_area('Reference text', str(reference_text))
if st.button('NER'):
doc = nlp(str(original_text2))
colors = { "DISEASE": "pink","CHEMICAL": "orange"}
options = {"ents": [ "DISEASE", "CHEMICAL"],"colors": colors}
ent_html = displacy.render(doc, style="ent", options=options)
st.markdown(ent_html, unsafe_allow_html=True) |