Update app.py

app.py

@@ -85,14 +85,9 @@ def init_session_states():
     st.session_state['pos_model'] = None
   if 'bio_model' not in st.session_state:
     st.session_state['bio_model'] = None
-  if 'phi_model' not in st.session_state:
-    st.session_state['phi_model'] = None
   if 'ner_bio' not in st.session_state:
     st.session_state['ner_bio'] = None
-  if 'ner_phi' not in st.session_state:
-    st.session_state['ner_phi'] = None
-  if 'aggr' not in st.session_state:
-    st.session_state['aggr'] = None
+  
 
     
     
@@ -109,12 +104,10 @@ def get_pos_arr(input_text,display_area):
 def perform_inference(text,display_area):
   
   if (st.session_state['bio_model'] is None):
-    display_area.text("Loading model 1 of 3. Bio model...")
+    display_area.text("Loading model 1 of 2. Bio model...")
     st.session_state['bio_model'] = bd.BatchInference("bio/desc_a100_config.json",'ajitrajasekharan/biomedical',False,False,DEFAULT_TOP_K,True,True,       "bio/","bio/a100_labels.txt",False)
     
-  if (st.session_state['phi_model'] is None):
-    display_area.text("Loading model 2 of 3. PHI model...")
-    st.session_state['phi_model'] = bd.BatchInference("bbc/desc_bbc_config.json",'bert-base-cased',False,False,DEFAULT_TOP_K,True,True,       "bbc/","bbc/bbc_labels.txt",False)
+
     
   #Load POS model if needed and gets POS tags
   if (SPECIFIC_TAG not in text):
@@ -126,28 +119,14 @@ def perform_inference(text,display_area):
     display_area.text("Initializing BIO module...")
     st.session_state['ner_bio'] = ner.UnsupNER("bio/ner_a100_config.json")
     
-  if (st.session_state['ner_phi'] is None):
-    display_area.text("Initializing PHI module...")
-    st.session_state['ner_phi'] = ner.UnsupNER("bbc/ner_bbc_config.json")
-    
-  if (st.session_state['aggr'] is None):
-    display_area.text("Initializing Aggregation modeule...")
-    st.session_state['aggr'] = aggr.AggregateNER("./ensemble_config.json")
   
   
-  
-  display_area.text("Getting results from BIO model...")
+  display_area.text("Getting predictions from BIO model...")
   bio_descs = st.session_state['bio_model'].get_descriptors(text,pos_arr)
-  display_area.text("Getting results from PHI model...")
-  phi_results = st.session_state['phi_model'].get_descriptors(text,pos_arr)
-  display_area.text("Aggregating BIO & PHI results...")
+  display_area.text("Computing BIO results...")
   bio_ner = st.session_state['ner_bio'].tag_sentence_service(text,bio_descs)
-  phi_ner = st.session_state['ner_phi'].tag_sentence_service(text,phi_results)
   
-  combined_arr = [json.loads(bio_ner),json.loads(phi_ner)]
-
-  aggregate_results = st.session_state['aggr'].fetch_all(text,combined_arr)
-  return aggregate_results
+  return bio_ner
   
 
 sent_arr = [
@@ -156,20 +135,12 @@ sent_arr = [
 "lou gehrig was diagnosed with Parkinson's ",  
 "A eGFR below 60 indicates chronic kidney disease", 
 "Overexpression of EGFR occurs across a wide range of different cancers", 
-"Stanford called", 
 "He was diagnosed with non small cell lung cancer", 
-"I met my girl friends at the pub ",  
-"I met my New York friends at the pub", 
-"I met my XCorp friends at the pub", 
-"I met my two friends at the pub", 
 "Bio-Techne's genomic tools include advanced tissue-based in-situ hybridization assays sold under the ACD brand as well as a portfolio of     assays for prostate cancer diagnosis ",  
 "There are no treatment options specifically indicated for ACD and physicians must utilize agents approved for other dermatology conditions", "As ACD has been implicated in apoptosis-resistant glioblastoma (GBM), there is a high medical need for identifying novel ACD-inducing drugs  ", 
 "Located in the heart of Dublin , in the family home of acclaimed writer Oscar Wilde , ACD provides the perfect backdrop to inspire Irish     (and Irish-at-heart) students to excel in business and the arts", 
 "Patients treated with anticancer chemotherapy drugs ( ACD ) are vulnerable to infectious diseases due to immunosuppression and to the direct impact of ACD on their intestinal microbiota ", 
-"In the LASOR trial , increasing daily imatinib dose from 400 to 600mg induced MMR at 12 and 24 months in 25% and 36% of the patients,        respectively, who had suboptimal cytogenetic responses ", 
-"The sky turned dark in advance of the storm that was coming from the east ", 
-"She loves to watch Sunday afternoon football with her family ", 
-"Paul Erdos died at 83 " 
+"In the LASOR trial , increasing daily imatinib dose from 400 to 600mg induced MMR at 12 and 24 months in 25% and 36% of the patients,        respectively, who had suboptimal cytogenetic responses "
 ]
 
 
@@ -179,21 +150,13 @@ sent_arr_masked = [
 "lou:__entity__ gehrig:__entity__ was diagnosed with Parkinson's:__entity__ ",  
 "A eGFR:__entity__ below 60 indicates chronic kidney disease", 
 "Overexpression of EGFR:__entity__ occurs across a wide range of different cancers", 
-"Stanford:__entity__ called", 
 "He was diagnosed with non:__entity__ small:__entity__ cell:__entity__ lung:__entity__ cancer:__entity__", 
-"I met my girl:__entity__ friends at the pub ",  
-"I met my New:__entity__ York:__entity__ friends at the pub", 
-"I met my XCorp:__entity__ friends at the pub", 
-"I met my two:__entity__ friends at the pub", 
 "Bio-Techne's genomic tools include advanced tissue-based in-situ hybridization assays sold under the ACD:__entity__ brand as well as a portfolio of     assays for prostate cancer diagnosis ",  
 "There are no treatment options specifically indicated for ACD:__entity__ and physicians must utilize agents approved for other dermatology conditions", 
 "As ACD:__entity__ has been implicated in apoptosis-resistant glioblastoma (GBM), there is a high medical need for identifying novel ACD-inducing drugs  ", 
 "Located in the heart of Dublin , in the family home of acclaimed writer Oscar Wilde , ACD:__entity__ provides the perfect backdrop to inspire Irish     (and Irish-at-heart) students to excel in business and the arts", 
 "Patients treated with anticancer chemotherapy drugs ( ACD:__entity__ ) are vulnerable to infectious diseases due to immunosuppression and to the direct impact of ACD on their intestinal microbiota ", 
-"In the LASOR:__entity__ trial:__entity__ , increasing daily imatinib dose from 400 to 600mg induced MMR at 12 and 24 months in 25% and 36% of the patients,        respectively, who had suboptimal cytogenetic responses ", 
-"The sky turned dark:__entity__ in advance of the storm that was coming from the east ", 
-"She loves to watch Sunday afternoon football:__entity__ with her family ", 
-"Paul:__entity__ Erdos:__entity__ died at 83:__entity__ " 
+"In the LASOR:__entity__ trial:__entity__ , increasing daily imatinib dose from 400 to 600mg induced MMR at 12 and 24 months in 25% and 36% of the patients,        respectively, who had suboptimal cytogenetic responses "
 ]
 
 def init_selectbox():
@@ -212,19 +175,19 @@ def main():
 
     init_session_states()
     
-    st.markdown("<h3 style='text-align: center;'>NER using pretrained models with <a href='https://ajitrajasekharan.github.io/2021/01/02/my-first-post.html'>no fine tuning</a></h3>", unsafe_allow_html=True)
+    st.markdown("<h3 style='text-align: center;'>Biomedical NER using a pretrained model with <a href='https://ajitrajasekharan.github.io/2021/01/02/my-first-post.html'>no fine tuning</a></h3>", unsafe_allow_html=True)
     #st.markdown("""
     #<h3 style="font-size:16px; color: #ff0000; text-align: center"><b>App under construction... (not in working condition yet)</b></h3>
   #""", unsafe_allow_html=True)
    
     
-    st.markdown("""
-    <p style="text-align:center;"><img src="https://ajitrajasekharan.github.io/images/1.png" width="700"></p>
-    <br/>
-    <br/>
-  """, unsafe_allow_html=True)
+    #st.markdown("""
+    #<p style="text-align:center;"><img src="https://ajitrajasekharan.github.io/images/1.png" width="700"></p>
+   # <br/>
+   # <br/>
+  #""", unsafe_allow_html=True)
   
-    st.write("This app uses 3 models.  Two Pretrained Bert models (**no fine tuning**) and a POS tagger")
+    st.write("This app uses 2 models.  A  Bert model  pretrained (**no fine tuning**) on biomedical corpus, and a POS tagger")
     
     
     with st.form('my_form'):
@@ -254,7 +217,7 @@ def main():
    # )
    
     st.markdown("""
-    <small style="font-size:16px; color: #7f7f7f; text-align: left"><br/><br/>Models used: <br/>(1) <a href='https://huggingface.co/ajitrajasekharan/biomedical' target='_blank'>Biomedical model</a> pretrained on Pubmed,Clinical trials and BookCorpus subset.<br/>(2) Bert-base-cased (for PHI entities - Person/location/organization etc.)<br/>(3) Flair POS tagger</small>
+    <small style="font-size:16px; color: #7f7f7f; text-align: left"><br/><br/>Models used: <br/>(1) <a href='https://huggingface.co/ajitrajasekharan/biomedical' target='_blank'>Biomedical model</a> pretrained on Pubmed,Clinical trials and BookCorpus subset.<br/>(2) Flair POS tagger</small>
   #""", unsafe_allow_html=True)
     st.markdown("""
     <h3 style="font-size:16px; color: #9f9f9f; text-align: center"><b> <a href='https://huggingface.co/spaces/ajitrajasekharan/Qualitative-pretrained-model-evaluation'   target='_blank'>App link to examine pretrained models</a> used to perform NER without fine tuning</b></h3>