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icd9_ui.py

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+import streamlit as st
+import torch
+from transformers import LongformerTokenizer, LongformerForSequenceClassification
+
+# Load the fine-tuned model and tokenizer
+model_path = "./clinical_longformer"
+tokenizer = LongformerTokenizer.from_pretrained(model_path)
+model = LongformerForSequenceClassification.from_pretrained(model_path)
+model.eval()  # Set the model to evaluation mode
+
+# ICD-9 code columns used during training
+icd9_columns = [
+    '038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9',
+    '287.5', '305.1', '311', '36.15', '37.22', '37.23', '38.91', '38.93', '39.61',
+    '39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0',
+    '486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0',
+    '88.56', '88.72', '93.90', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15',
+    '995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
+]
+
+# Function for making predictions
+def predict_icd9(texts, tokenizer, model, threshold=0.5):
+    inputs = tokenizer(
+        texts,
+        padding="max_length",
+        truncation=True,
+        max_length=512,
+        return_tensors="pt"
+    )
+    
+    with torch.no_grad():
+        outputs = model(
+            input_ids=inputs["input_ids"],
+            attention_mask=inputs["attention_mask"]
+        )
+        logits = outputs.logits
+        probabilities = torch.sigmoid(logits)
+        predictions = (probabilities > threshold).int()
+    
+    predicted_icd9 = []
+    for pred in predictions:
+        codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
+        predicted_icd9.append(codes)
+    
+    return predicted_icd9
+
+# Streamlit UI
+st.title("ICD-9 Code Prediction")
+st.sidebar.header("Model Options")
+model_option = st.sidebar.selectbox("Select Model", [ "ClinicalLongformer"])
+threshold = st.sidebar.slider("Prediction Threshold", 0.0, 1.0, 0.5, 0.01)
+
+st.write("### Enter Medical Summary")
+input_text = st.text_area("Medical Summary", placeholder="Enter clinical notes here...")
+
+if st.button("Predict"):
+    if input_text.strip():
+        predictions = predict_icd9([input_text], tokenizer, model, threshold)
+        st.write("### Predicted ICD-9 Codes")
+        for code in predictions[0]:
+            st.write(f"- {code}")
+    else:
+        st.error("Please enter a medical summary.")

requirements.txt

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+streamlit==1.19.0
+torch==1.13.1
+transformers==4.34.0
+pandas==1.5.3
+scikit-learn==1.2.2
+numpy==1.23.5
+matplotlib==3.7.1
+scipy==1.10.0