Update app.py

app.py

@@ -10,13 +10,13 @@ import faiss
 st.set_page_config(page_title='KRISSBERT UMLS Linker', layout='wide')
 st.title('🧬 KRISSBERT + UMLS Entity Linker (Local FAISS)')
 
-# File paths
+# Paths & model name
 METADATA_PATH = 'umls_metadata.json'
 EMBED_PATH = 'umls_embeddings.npy'
 INDEX_PATH = 'umls_index.faiss'
 MODEL_NAME = 'microsoft/BiomedNLP-KRISSBERT-PubMed-UMLS-EL'
 
-# Load model & tokenizer
+# 1️⃣ Load model & tokenizer
 @st.cache_resource
 def load_model():
     tokenizer = AutoTokenizer.from_pretrained(MODEL_NAME)
@@ -26,7 +26,7 @@ def load_model():
 
 tokenizer, model = load_model()
 
-# Load UMLS FAISS index + metadata
+# 2️⃣ Load UMLS FAISS index & metadata
 @st.cache_resource
 def load_umls_index():
     meta = json.load(open(METADATA_PATH, 'r'))
@@ -36,7 +36,7 @@ def load_umls_index():
 
 faiss_index, umls_meta = load_umls_index()
 
-# Embed text
+# 3️⃣ Embed text (prefix underscores to avoid caching errors)
 @st.cache_resource
 def embed_text(text, _tokenizer, _model):
     inputs = _tokenizer(text, return_tensors='pt', truncation=True, padding=True)
@@ -45,7 +45,7 @@ def embed_text(text, _tokenizer, _model):
     emb = outputs.last_hidden_state[:, 0, :].squeeze().cpu().numpy()
     return emb / np.linalg.norm(emb)
 
-# UI: examples and input
+# UI: examples + input
 st.markdown('Enter a biomedical sentence to link entities via local UMLS FAISS index and KRISSBERT:')
 examples = [
     'The patient was administered metformin for type 2 diabetes.',
@@ -75,9 +75,9 @@ if st.button('🔗 Link Entities'):
         if results:
             st.success('Top UMLS candidates:')
             for item in results:
-                st.markdown('**' + item['name'] + '** (CUI: `' + item['cui'] + '`)')
+                st.markdown(f"**{item['name']}** (CUI: `{item['cui']}`)")
                 if item['definition']:
-                    st.markdown('> ' + item['definition'] + '\n')
-                st.markdown('_Source: ' + item['source'] + '_\n---')
+                    st.markdown(f"> {item['definition']}\n")
+                st.markdown(f"_Source: {item['source']}_\n---")
         else:
-            st.info('No matches found in UMLS index.')
+            st.info('No matches found in UMLS index.')