Delete pages

pages/1_🏥_Admission.py

@@ -1,174 +0,0 @@
-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
-
-
-from streamlit.components.v1 import html
-
-def nav_page(page_name, timeout_secs=3):
-    nav_script = """
-        <script type="text/javascript">
-            function attempt_nav_page(page_name, start_time, timeout_secs) {
-                var links = window.parent.document.getElementsByTagName("a");
-                for (var i = 0; i < links.length; i++) {
-                    if (links[i].href.toLowerCase().endsWith("/" + page_name.toLowerCase())) {
-                        links[i].click();
-                        return;
-                    }
-                }
-                var elasped = new Date() - start_time;
-                if (elasped < timeout_secs * 1000) {
-                    setTimeout(attempt_nav_page, 100, page_name, start_time, timeout_secs);
-                } else {
-                    alert("Unable to navigate to page '" + page_name + "' after " + timeout_secs + " second(s).");
-                }
-            }
-            window.addEventListener("load", function() {
-                attempt_nav_page("%s", new Date(), %d);
-            });
-        </script>
-    """ % (page_name, timeout_secs)
-    html(nav_script)
-
-    
-# Store the initial value of widgets in session state
-if "visibility" not in st.session_state:
-    st.session_state.visibility = "visible"
-    st.session_state.disabled = False
-
-#nlp = en_core_web_lg.load()
-nlp = spacy.load("en_ner_bc5cdr_md")
-
-st.set_page_config(page_title ='🏥 Admission', 
-                   #page_icon= "Notes",
-                   layout='wide')
-st.title('Clinical Note Summarization - Admission')
-st.markdown(
-    """
-    <style>
-    [data-testid="stSidebar"][aria-expanded="true"] > div:first-child {
-        width: 400px;
-    }
-    [data-testid="stSidebar"][aria-expanded="false"] > div:first-child {
-        width: 400px;
-        margin-left: -230px;
-    }
-    </style>
-    """,
-    unsafe_allow_html=True,
-)
-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} ")
-
-
-##========= Buttons to the 4 tabs ========
-col1, col2, col3, col4 = st.columns(4)
-with col1:
-#    st.button('Admission')
-    if st.button("🏥 Admission"):
-        nav_page('Admission')
-
-with col2:
-    if st.button('📆Daily Narrative'):
-        nav_page('Daily Narrative')
-  
-with col3:
-    if st.button('Discharge Plan'):
-        nav_page('Discharge Plan')
-with col4:
-    if st.button('📝Social Notes'):
-        nav_page('Social Notes')
-    
-
-# 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)
-
-col1, col2 = st.columns([1,1])
-
-with col1:
-    st.button('Summarize')
-    run_model(runtext)
-    sentences=runtext.split('.')
-    st.text_area('Reference text', str(reference_text))#,label_visibility="hidden")
-with col2:
-    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) 
-    

pages/2_📆_Daily Narrative.py

@@ -1,174 +0,0 @@
-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
-
-
-from streamlit.components.v1 import html
-
-def nav_page(page_name, timeout_secs=3):
-    nav_script = """
-        <script type="text/javascript">
-            function attempt_nav_page(page_name, start_time, timeout_secs) {
-                var links = window.parent.document.getElementsByTagName("a");
-                for (var i = 0; i < links.length; i++) {
-                    if (links[i].href.toLowerCase().endsWith("/" + page_name.toLowerCase())) {
-                        links[i].click();
-                        return;
-                    }
-                }
-                var elasped = new Date() - start_time;
-                if (elasped < timeout_secs * 1000) {
-                    setTimeout(attempt_nav_page, 100, page_name, start_time, timeout_secs);
-                } else {
-                    alert("Unable to navigate to page '" + page_name + "' after " + timeout_secs + " second(s).");
-                }
-            }
-            window.addEventListener("load", function() {
-                attempt_nav_page("%s", new Date(), %d);
-            });
-        </script>
-    """ % (page_name, timeout_secs)
-    html(nav_script)
-
-    
-# Store the initial value of widgets in session state
-if "visibility" not in st.session_state:
-    st.session_state.visibility = "visible"
-    st.session_state.disabled = False
-
-#nlp = en_core_web_lg.load()
-nlp = spacy.load("en_ner_bc5cdr_md")
-
-st.set_page_config(page_title ='📆Daily Narrative', 
-                   #page_icon= "Notes",
-                   layout='wide')
-st.title('Clinical Note Summarization - 📆Daily Narrative')
-st.markdown(
-    """
-    <style>
-    [data-testid="stSidebar"][aria-expanded="true"] > div:first-child {
-        width: 400px;
-    }
-    [data-testid="stSidebar"][aria-expanded="false"] > div:first-child {
-        width: 400px;
-        margin-left: -230px;
-    }
-    </style>
-    """,
-    unsafe_allow_html=True,
-)
-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} ")
-
-
-##========= Buttons to the 4 tabs ========
-col1, col2, col3, col4 = st.columns(4)
-with col1:
-#    st.button('Admission')
-    if st.button("🏥 Admission"):
-        nav_page('Admission')
-
-with col2:
-    if st.button('📆Daily Narrative'):
-        nav_page('Daily Narrative')
-  
-with col3:
-    if st.button('Discharge Plan'):
-        nav_page('Discharge Plan')
-with col4:
-    if st.button('📝Social Notes'):
-        nav_page('Social Notes')
-    
-
-# 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)
-
-col1, col2 = st.columns([1,1])
-
-with col1:
-    if st.button('Summarize'):
-        run_model(runtext)
-        sentences=runtext.split('.')
-        st.text_area('Reference text', str(reference_text))#,label_visibility="hidden")
-with col2:
-    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) 
-    

pages/3_🗒️_Discharge Plan.py

@@ -1,175 +0,0 @@
-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
-
-
-from streamlit.components.v1 import html
-
-def nav_page(page_name, timeout_secs=3):
-    nav_script = """
-        <script type="text/javascript">
-            function attempt_nav_page(page_name, start_time, timeout_secs) {
-                var links = window.parent.document.getElementsByTagName("a");
-                for (var i = 0; i < links.length; i++) {
-                    if (links[i].href.toLowerCase().endsWith("/" + page_name.toLowerCase())) {
-                        links[i].click();
-                        return;
-                    }
-                }
-                var elasped = new Date() - start_time;
-                if (elasped < timeout_secs * 1000) {
-                    setTimeout(attempt_nav_page, 100, page_name, start_time, timeout_secs);
-                } else {
-                    alert("Unable to navigate to page '" + page_name + "' after " + timeout_secs + " second(s).");
-                }
-            }
-            window.addEventListener("load", function() {
-                attempt_nav_page("%s", new Date(), %d);
-            });
-        </script>
-    """ % (page_name, timeout_secs)
-    html(nav_script)
-
-    
-# Store the initial value of widgets in session state
-if "visibility" not in st.session_state:
-    st.session_state.visibility = "visible"
-    st.session_state.disabled = False
-
-#nlp = en_core_web_lg.load()
-nlp = spacy.load("en_ner_bc5cdr_md")
-
-st.set_page_config(page_title ='Discharge Plan', 
-                   layout='wide')
-
-st.title('Clinical Note Summarization - Discharge Plan')
-st.markdown(
-    """
-    <style>
-    [data-testid="stSidebar"][aria-expanded="true"] > div:first-child {
-        width: 400px;
-    }
-    [data-testid="stSidebar"][aria-expanded="false"] > div:first-child {
-        width: 400px;
-        margin-left: -230px;
-    }
-    </style>
-    """,
-    unsafe_allow_html=True,
-)
-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} ")
-
-
-
-##========= Buttons to the 4 tabs ========
-col1, col2, col3, col4 = st.columns(4)
-with col1:
-#    st.button('Admission')
-    if st.button("🏥 Admission"):
-        nav_page('Admission')
-
-with col2:
-    if st.button('📆Daily Narrative'):
-        nav_page('Daily Narrative')
-  
-with col3:
-    if st.button('Discharge Plan'):
-        nav_page('Discharge Plan')
-with col4:
-    if st.button('📝Social Notes'):
-        nav_page('Social Notes')
-    
-
-# 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)
-
-col1, col2 = st.columns([1,1])
-
-with col1:
-    st.button('Summarize')
-    run_model(runtext)
-    sentences=runtext.split('.')
-    st.text_area('Reference text', str(reference_text))#,label_visibility="hidden")
-with col2:
-    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) 
-    

pages/4_📝_Social Notes.py

@@ -1,175 +0,0 @@
-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
-
-from streamlit.components.v1 import html
-
-def nav_page(page_name, timeout_secs=3):
-    nav_script = """
-        <script type="text/javascript">
-            function attempt_nav_page(page_name, start_time, timeout_secs) {
-                var links = window.parent.document.getElementsByTagName("a");
-                for (var i = 0; i < links.length; i++) {
-                    if (links[i].href.toLowerCase().endsWith("/" + page_name.toLowerCase())) {
-                        links[i].click();
-                        return;
-                    }
-                }
-                var elasped = new Date() - start_time;
-                if (elasped < timeout_secs * 1000) {
-                    setTimeout(attempt_nav_page, 100, page_name, start_time, timeout_secs);
-                } else {
-                    alert("Unable to navigate to page '" + page_name + "' after " + timeout_secs + " second(s).");
-                }
-            }
-            window.addEventListener("load", function() {
-                attempt_nav_page("%s", new Date(), %d);
-            });
-        </script>
-    """ % (page_name, timeout_secs)
-    html(nav_script)
-
-
-
-# Store the initial value of widgets in session state
-if "visibility" not in st.session_state:
-    st.session_state.visibility = "visible"
-    st.session_state.disabled = False
-
-#nlp = en_core_web_lg.load()
-nlp = spacy.load("en_ner_bc5cdr_md")
-
-st.set_page_config(page_title ='📝Social Notes', 
-                   layout='wide')
-
-st.title('Clinical Note Summarization - 📝Social Notes')
-st.markdown(
-    """
-    <style>
-    [data-testid="stSidebar"][aria-expanded="true"] > div:first-child {
-        width: 400px;
-    }
-    [data-testid="stSidebar"][aria-expanded="false"] > div:first-child {
-        width: 400px;
-        margin-left: -230px;
-    }
-    </style>
-    """,
-    unsafe_allow_html=True,
-)
-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} ")
-
-
-##========= Buttons to the 4 tabs ========
-col1, col2, col3, col4 = st.columns(4)
-with col1:
-#    st.button('Admission')
-    if st.button("🏥 Admission"):
-        nav_page('Admission')
-
-with col2:
-    if st.button('📆Daily Narrative'):
-        nav_page('Daily Narrative')
-  
-with col3:
-    if st.button('Discharge Plan'):
-        nav_page('Discharge Plan')
-with col4:
-    if st.button('📝Social Notes'):
-        nav_page('Social Notes')
-    
-
-
-# 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)
-
-col1, col2 = st.columns([1,1])
-
-with col1:
-    st.button('Summarize')
-    run_model(runtext)
-    sentences=runtext.split('.')
-    st.text_area('Reference text', str(reference_text))#,label_visibility="hidden")
-with col2:
-    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) 
-