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Update icd9_ui.py
Browse files- icd9_ui.py +543 -543
icd9_ui.py
CHANGED
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# # # Streamlit UI
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# # st.title("
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# # st.
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# # import torch
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# # import pandas as pd
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# # import streamlit as st
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# # from transformers import LongformerTokenizer, LongformerForSequenceClassification
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# # #
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# # model_path = "./clinical_longformer"
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# # tokenizer = LongformerTokenizer.from_pretrained(model_path)
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# # model = LongformerForSequenceClassification.from_pretrained(model_path)
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# # # Load the ICD-9 descriptions from CSV into a dictionary
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# # icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv") # Adjust the path to your CSV file
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# # icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type
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# # icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals for matching
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# # # Load the ICD-9 to ICD-10 mapping
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# # icd9_to_icd10 = {}
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# # with open("2015_I9gem.txt", "r") as file:
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# # for line in file:
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# # parts = line.strip().split()
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# # if len(parts) == 3:
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# # icd9, icd10, _ = parts
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# # icd9_to_icd10[icd9] = icd10
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# # # ICD-9 code columns used during training
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# # icd9_columns = [
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# # '995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
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# # ]
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# # # Function for making
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# # def predict_icd9(texts, tokenizer, model, threshold=0.5):
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# # inputs = tokenizer(
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# # texts,
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# # max_length=512,
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# # return_tensors="pt"
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# # )
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# # with torch.no_grad():
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# # outputs = model(
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# # input_ids=inputs["input_ids"],
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# # logits = outputs.logits
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# # probabilities = torch.sigmoid(logits)
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# # predictions = (probabilities > threshold).int()
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# # predicted_icd9 = []
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# # for pred in predictions:
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# # codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
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# # predicted_icd9.append(codes)
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# # # Fetch descriptions and map to ICD-10 codes
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# # predictions_with_desc = []
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# # for codes in predicted_icd9:
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# # code_with_desc = []
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# # for code in codes:
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# # icd9_stripped = code.replace('.', '')
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# # icd10_code = icd9_to_icd10.get(icd9_stripped, "Mapping not found")
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# # icd9_desc = icd9_descriptions.get(icd9_stripped, "Description not found")
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# # code_with_desc.append((code, icd9_desc, icd10_code))
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# # predictions_with_desc.append(code_with_desc)
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# # return predictions_with_desc
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# # # Streamlit UI
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# # st.title("ICD-9 to ICD-10 Code Prediction")
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# # st.sidebar.header("Model Options")
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# # threshold = st.sidebar.slider("Prediction Threshold", 0.0, 1.0, 0.5, 0.01)
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# # st.write("### Enter Medical Summary")
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# # input_text = st.text_area("Medical Summary", placeholder="Enter clinical notes here...")
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# # if st.button("Predict"):
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# # if input_text.strip():
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# # predictions = predict_icd9([input_text], tokenizer, model, threshold)
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# # st.write("### Predicted ICD-9 and ICD-10 Codes with Descriptions")
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# # for icd9_code, description, icd10_code in predictions[0]:
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# # st.write(f"- ICD-9: {icd9_code} ({description}) -> ICD-10: {icd10_code}")
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# # else:
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# # st.error("Please enter a medical summary.")
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# # import os
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# # import torch
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# # import pandas as pd
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# # import streamlit as st
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# # from PIL import Image
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# # from transformers import LongformerTokenizer, LongformerForSequenceClassification
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# # from phi.agent import Agent
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# # from phi.model.google import Gemini
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# # from phi.tools.duckduckgo import DuckDuckGo
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# # # Load the fine-tuned ICD-9 model and tokenizer
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# # model_path = "./clinical_longformer"
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# # tokenizer = LongformerTokenizer.from_pretrained(model_path)
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# # model = LongformerForSequenceClassification.from_pretrained(model_path)
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# # model.eval() # Set the model to evaluation mode
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# # # Load the ICD-9 descriptions from CSV into a dictionary
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# # icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv") # Adjust the path to your CSV file
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# # icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type for matching
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# # icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals in ICD9 code for matching
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# # # ICD-9 code columns used during training
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# # icd9_columns = [
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# # '038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9',
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# # '287.5', '305.1', '311', '36.15', '37.22', '37.23', '38.91', '38.93', '39.61',
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# # '39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0',
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# # '486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0',
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# # '88.56', '88.72', '93.90', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15',
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# # '995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
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# # ]
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# # # Function for making ICD-9 predictions
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# # def predict_icd9(texts, tokenizer, model, threshold=0.5):
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# # inputs = tokenizer(
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# # texts,
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# # padding="max_length",
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# # truncation=True,
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# # max_length=512,
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# # return_tensors="pt"
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# # )
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# # with torch.no_grad():
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# # outputs = model(
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# # input_ids=inputs["input_ids"],
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# # attention_mask=inputs["attention_mask"]
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# # )
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# # logits = outputs.logits
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# # probabilities = torch.sigmoid(logits)
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# # predictions = (probabilities > threshold).int()
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# # predicted_icd9 = []
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# # for pred in predictions:
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# # codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
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# # predicted_icd9.append(codes)
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# # predictions_with_desc = []
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# # for codes in predicted_icd9:
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# # code_with_desc = [(code, icd9_descriptions.get(code.replace('.', ''), "Description not found")) for code in codes]
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# # predictions_with_desc.append(code_with_desc)
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# # return predictions_with_desc
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# # Streamlit UI
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# # st.title("Medical Diagnosis Assistant")
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# # option = st.selectbox(
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# # "Choose Diagnosis Method",
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# # else:
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# # st.error("Please enter a medical summary.")
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# # Medical Image Analysis
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# # elif option == "Medical Image Analysis":
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# # if "GOOGLE_API_KEY" not in st.session_state:
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# # st.warning("Please enter your Google API Key in the sidebar to continue")
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# # else:
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# # medical_agent = Agent(
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# # model=Gemini(
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# # api_key=st.session_state
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# # id="gemini-2.0-flash-exp"
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# # ),
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# # tools=[DuckDuckGo()],
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# # query = """
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# # You are a highly skilled medical imaging expert with extensive knowledge in radiology and diagnostic imaging. Analyze the patient's medical image and structure your response as follows:
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# # ### 1. Image Type & Region
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# # - Specify imaging modality (X-ray/MRI/CT/Ultrasound/etc.)
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# # - Identify the patient's anatomical region and positioning
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# # - Comment on image quality and technical adequacy
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# # ### 2. Key Findings
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# # - List primary observations systematically
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# # - Note any abnormalities in the patient's imaging with precise descriptions
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# # - Include measurements and densities where relevant
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# # - Describe location, size, shape, and characteristics
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# # - Rate severity: Normal/Mild/Moderate/Severe
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# # ### 3. Diagnostic Assessment
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# # - Provide primary diagnosis with confidence level
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# # - List differential diagnoses in order of likelihood
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# # - Support each diagnosis with observed evidence from the patient's imaging
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# # new_height = int(new_width / aspect_ratio)
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# # resized_image = image.resize((new_width, new_height))
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#
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#
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-
#
|
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-
#
|
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-
#
|
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|
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# import os
|
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# import torch
|
@@ -412,16 +594,6 @@
|
|
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# from phi.model.google import Gemini
|
413 |
# from phi.tools.duckduckgo import DuckDuckGo
|
414 |
|
415 |
-
# # Sidebar for Google API Key input
|
416 |
-
# st.sidebar.title("Settings")
|
417 |
-
# st.sidebar.write("Enter your Google API Key below for the Medical Image Analysis feature.")
|
418 |
-
# api_key = st.sidebar.text_input("Google API Key", type="password")
|
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-
|
420 |
-
# if api_key:
|
421 |
-
# st.session_state["GOOGLE_API_KEY"] = api_key
|
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-
# else:
|
423 |
-
# st.session_state.pop("GOOGLE_API_KEY", None)
|
424 |
-
|
425 |
# # Load the fine-tuned ICD-9 model and tokenizer
|
426 |
# model_path = "./clinical_longformer"
|
427 |
# tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
@@ -429,7 +601,7 @@
|
|
429 |
# model.eval() # Set the model to evaluation mode
|
430 |
|
431 |
# # Load the ICD-9 descriptions from CSV into a dictionary
|
432 |
-
# icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv")
|
433 |
# icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type for matching
|
434 |
# icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals in ICD9 code for matching
|
435 |
|
@@ -452,7 +624,6 @@
|
|
452 |
# max_length=512,
|
453 |
# return_tensors="pt"
|
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# )
|
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-
|
456 |
# with torch.no_grad():
|
457 |
# outputs = model(
|
458 |
# input_ids=inputs["input_ids"],
|
@@ -474,6 +645,9 @@
|
|
474 |
|
475 |
# return predictions_with_desc
|
476 |
|
|
|
|
|
|
|
477 |
# # Streamlit UI
|
478 |
# st.title("Medical Diagnosis Assistant")
|
479 |
# option = st.selectbox(
|
@@ -499,260 +673,86 @@
|
|
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|
500 |
# # Medical Image Analysis
|
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# elif option == "Medical Image Analysis":
|
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#
|
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#
|
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#
|
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#
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#
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#
|
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#
|
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#
|
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-
# tools=[DuckDuckGo()],
|
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-
# markdown=True
|
512 |
-
# )
|
513 |
-
|
514 |
-
# query = """
|
515 |
-
# You are a highly skilled medical imaging expert with extensive knowledge in radiology and diagnostic imaging. Analyze the patient's medical image and structure your response as follows:
|
516 |
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# ### 1. Image Type & Region
|
517 |
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# - Specify imaging modality (X-ray/MRI/CT/Ultrasound/etc.)
|
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# - Identify the patient's anatomical region and positioning
|
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# - Comment on image quality and technical adequacy
|
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# ### 2. Key Findings
|
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# - List primary observations systematically
|
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# - Note any abnormalities in the patient's imaging with precise descriptions
|
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-
# - Include measurements and densities where relevant
|
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# - Describe location, size, shape, and characteristics
|
525 |
-
# - Rate severity: Normal/Mild/Moderate/Severe
|
526 |
-
# ### 3. Diagnostic Assessment
|
527 |
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# - Provide primary diagnosis with confidence level
|
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# - List differential diagnoses in order of likelihood
|
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# - Support each diagnosis with observed evidence from the patient's imaging
|
530 |
-
# - Note any critical or urgent findings
|
531 |
-
# ### 4. Patient-Friendly Explanation
|
532 |
-
# - Explain the findings in simple, clear language that the patient can understand
|
533 |
-
# - Avoid medical jargon or provide clear definitions
|
534 |
-
# - Include visual analogies if helpful
|
535 |
-
# - Address common patient concerns related to these findings
|
536 |
-
# ### 5. Research Context
|
537 |
-
# - Use the DuckDuckGo search tool to find recent medical literature about similar cases
|
538 |
-
# - Provide a list of relevant medical links
|
539 |
-
# - Include key references to support your analysis
|
540 |
-
# """
|
541 |
-
|
542 |
-
# upload_container = st.container()
|
543 |
-
# image_container = st.container()
|
544 |
-
# analysis_container = st.container()
|
545 |
-
|
546 |
-
# with upload_container:
|
547 |
-
# uploaded_file = st.file_uploader(
|
548 |
-
# "Upload Medical Image",
|
549 |
-
# type=["jpg", "jpeg", "png", "dicom"],
|
550 |
-
# help="Supported formats: JPG, JPEG, PNG, DICOM"
|
551 |
-
# )
|
552 |
-
|
553 |
-
# if uploaded_file is not None:
|
554 |
-
# with image_container:
|
555 |
-
# col1, col2, col3 = st.columns([1, 2, 1])
|
556 |
-
# with col2:
|
557 |
-
# image = Image.open(uploaded_file)
|
558 |
-
# width, height = image.size
|
559 |
-
# aspect_ratio = width / height
|
560 |
-
# new_width = 500
|
561 |
-
# new_height = int(new_width / aspect_ratio)
|
562 |
-
# resized_image = image.resize((new_width, new_height))
|
563 |
-
|
564 |
-
# st.image(resized_image, caption="Uploaded Medical Image", use_container_width=True)
|
565 |
-
|
566 |
-
# analyze_button = st.button("π Analyze Image")
|
567 |
-
|
568 |
-
# with analysis_container:
|
569 |
-
# if analyze_button:
|
570 |
-
# image_path = "temp_medical_image.png"
|
571 |
-
# with open(image_path, "wb") as f:
|
572 |
-
# f.write(uploaded_file.getbuffer())
|
573 |
-
|
574 |
-
# with st.spinner("π Analyzing image... Please wait."):
|
575 |
-
# try:
|
576 |
-
# response = medical_agent.run(query, images=[image_path])
|
577 |
-
# st.markdown("### π Analysis Results")
|
578 |
-
# st.markdown(response.content)
|
579 |
-
# except Exception as e:
|
580 |
-
# st.error(f"Analysis error: {e}")
|
581 |
-
# finally:
|
582 |
-
# if os.path.exists(image_path):
|
583 |
-
# os.remove(image_path)
|
584 |
-
# else:
|
585 |
-
# st.info("π Please upload a medical image to begin analysis")
|
586 |
-
|
587 |
-
import os
|
588 |
-
import torch
|
589 |
-
import pandas as pd
|
590 |
-
import streamlit as st
|
591 |
-
from PIL import Image
|
592 |
-
from transformers import LongformerTokenizer, LongformerForSequenceClassification
|
593 |
-
from phi.agent import Agent
|
594 |
-
from phi.model.google import Gemini
|
595 |
-
from phi.tools.duckduckgo import DuckDuckGo
|
596 |
-
|
597 |
-
# Load the fine-tuned ICD-9 model and tokenizer
|
598 |
-
model_path = "./clinical_longformer"
|
599 |
-
tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
600 |
-
model = LongformerForSequenceClassification.from_pretrained(model_path)
|
601 |
-
model.eval() # Set the model to evaluation mode
|
602 |
-
|
603 |
-
# Load the ICD-9 descriptions from CSV into a dictionary
|
604 |
-
icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv")
|
605 |
-
icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type for matching
|
606 |
-
icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals in ICD9 code for matching
|
607 |
-
|
608 |
-
# ICD-9 code columns used during training
|
609 |
-
icd9_columns = [
|
610 |
-
'038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9',
|
611 |
-
'287.5', '305.1', '311', '36.15', '37.22', '37.23', '38.91', '38.93', '39.61',
|
612 |
-
'39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0',
|
613 |
-
'486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0',
|
614 |
-
'88.56', '88.72', '93.90', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15',
|
615 |
-
'995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
|
616 |
-
]
|
617 |
-
|
618 |
-
# Function for making ICD-9 predictions
|
619 |
-
def predict_icd9(texts, tokenizer, model, threshold=0.5):
|
620 |
-
inputs = tokenizer(
|
621 |
-
texts,
|
622 |
-
padding="max_length",
|
623 |
-
truncation=True,
|
624 |
-
max_length=512,
|
625 |
-
return_tensors="pt"
|
626 |
-
)
|
627 |
-
with torch.no_grad():
|
628 |
-
outputs = model(
|
629 |
-
input_ids=inputs["input_ids"],
|
630 |
-
attention_mask=inputs["attention_mask"]
|
631 |
-
)
|
632 |
-
logits = outputs.logits
|
633 |
-
probabilities = torch.sigmoid(logits)
|
634 |
-
predictions = (probabilities > threshold).int()
|
635 |
-
|
636 |
-
predicted_icd9 = []
|
637 |
-
for pred in predictions:
|
638 |
-
codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
|
639 |
-
predicted_icd9.append(codes)
|
640 |
-
|
641 |
-
predictions_with_desc = []
|
642 |
-
for codes in predicted_icd9:
|
643 |
-
code_with_desc = [(code, icd9_descriptions.get(code.replace('.', ''), "Description not found")) for code in codes]
|
644 |
-
predictions_with_desc.append(code_with_desc)
|
645 |
-
|
646 |
-
return predictions_with_desc
|
647 |
-
|
648 |
-
# Define the API key directly in the code
|
649 |
-
GOOGLE_API_KEY = "AIzaSyA24A6egT3L0NAKkkw9QHjfoizp7cJUTaA"
|
650 |
-
|
651 |
-
# Streamlit UI
|
652 |
-
st.title("Medical Diagnosis Assistant")
|
653 |
-
option = st.selectbox(
|
654 |
-
"Choose Diagnosis Method",
|
655 |
-
("ICD-9 Code Prediction", "Medical Image Analysis")
|
656 |
-
)
|
657 |
-
|
658 |
-
# ICD-9 Code Prediction
|
659 |
-
if option == "ICD-9 Code Prediction":
|
660 |
-
st.write("### Enter Medical Summary")
|
661 |
-
input_text = st.text_area("Medical Summary", placeholder="Enter clinical notes here...")
|
662 |
-
|
663 |
-
threshold = st.slider("Prediction Threshold", 0.0, 1.0, 0.5, 0.01)
|
664 |
-
|
665 |
-
if st.button("Predict ICD-9 Codes"):
|
666 |
-
if input_text.strip():
|
667 |
-
predictions = predict_icd9([input_text], tokenizer, model, threshold)
|
668 |
-
st.write("### Predicted ICD-9 Codes and Descriptions")
|
669 |
-
for code, description in predictions[0]:
|
670 |
-
st.write(f"- {code}: {description}")
|
671 |
-
else:
|
672 |
-
st.error("Please enter a medical summary.")
|
673 |
-
|
674 |
-
# Medical Image Analysis
|
675 |
-
elif option == "Medical Image Analysis":
|
676 |
-
medical_agent = Agent(
|
677 |
-
model=Gemini(
|
678 |
-
api_key=GOOGLE_API_KEY,
|
679 |
-
id="gemini-2.0-flash-exp"
|
680 |
-
),
|
681 |
-
tools=[DuckDuckGo()],
|
682 |
-
markdown=True
|
683 |
-
)
|
684 |
|
685 |
-
|
686 |
-
|
687 |
-
|
688 |
-
|
689 |
-
|
690 |
-
|
691 |
-
|
692 |
-
|
693 |
-
|
694 |
-
|
695 |
-
|
696 |
-
|
697 |
-
|
698 |
-
|
699 |
-
|
700 |
-
|
701 |
-
|
702 |
-
|
703 |
-
|
704 |
-
|
705 |
-
|
706 |
-
|
707 |
-
|
708 |
-
|
709 |
-
|
710 |
-
|
711 |
-
|
712 |
-
|
713 |
-
|
714 |
-
|
715 |
-
|
716 |
-
|
717 |
-
|
718 |
-
|
719 |
-
|
720 |
-
|
721 |
-
|
722 |
-
|
723 |
|
724 |
-
|
725 |
-
|
726 |
-
|
727 |
-
|
728 |
-
|
729 |
-
|
730 |
-
|
731 |
-
|
732 |
-
|
733 |
-
|
734 |
|
735 |
-
|
736 |
|
737 |
-
|
738 |
|
739 |
-
|
740 |
-
|
741 |
-
|
742 |
-
|
743 |
-
|
744 |
|
745 |
-
|
746 |
-
|
747 |
-
|
748 |
-
|
749 |
-
|
750 |
-
|
751 |
-
|
752 |
-
|
753 |
-
|
754 |
-
|
755 |
-
|
756 |
-
|
757 |
|
758 |
|
|
|
1 |
+
import streamlit as st
|
2 |
+
import torch
|
3 |
+
from transformers import LongformerTokenizer, LongformerForSequenceClassification
|
4 |
|
5 |
+
# Load the fine-tuned model and tokenizer
|
6 |
+
model_path = "./clinical_longformer"
|
7 |
+
tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
8 |
+
model = LongformerForSequenceClassification.from_pretrained(model_path)
|
9 |
+
model.eval() # Set the model to evaluation mode
|
10 |
|
11 |
+
# ICD-9 code columns used during training
|
12 |
+
icd9_columns = [
|
13 |
+
'038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9',
|
14 |
+
'287.5', '305.1', '311', '36.15', '37.22', '37.23', '38.91', '38.93', '39.61',
|
15 |
+
'39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0',
|
16 |
+
'486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0',
|
17 |
+
'88.56', '88.72', '93.90', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15',
|
18 |
+
'995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
|
19 |
+
]
|
20 |
|
21 |
+
# Function for making predictions
|
22 |
+
def predict_icd9(texts, tokenizer, model, threshold=0.5):
|
23 |
+
inputs = tokenizer(
|
24 |
+
texts,
|
25 |
+
padding="max_length",
|
26 |
+
truncation=True,
|
27 |
+
max_length=512,
|
28 |
+
return_tensors="pt"
|
29 |
+
)
|
30 |
|
31 |
+
with torch.no_grad():
|
32 |
+
outputs = model(
|
33 |
+
input_ids=inputs["input_ids"],
|
34 |
+
attention_mask=inputs["attention_mask"]
|
35 |
+
)
|
36 |
+
logits = outputs.logits
|
37 |
+
probabilities = torch.sigmoid(logits)
|
38 |
+
predictions = (probabilities > threshold).int()
|
39 |
|
40 |
+
predicted_icd9 = []
|
41 |
+
for pred in predictions:
|
42 |
+
codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
|
43 |
+
predicted_icd9.append(codes)
|
44 |
|
45 |
+
return predicted_icd9
|
46 |
|
47 |
+
# Streamlit UI
|
48 |
+
st.title("ICD-9 Code Prediction")
|
49 |
+
st.sidebar.header("Model Options")
|
50 |
+
model_option = st.sidebar.selectbox("Select Model", [ "ClinicalLongformer"])
|
51 |
+
threshold = st.sidebar.slider("Prediction Threshold", 0.0, 1.0, 0.5, 0.01)
|
52 |
+
|
53 |
+
st.write("### Enter Medical Summary")
|
54 |
+
input_text = st.text_area("Medical Summary", placeholder="Enter clinical notes here...")
|
55 |
+
|
56 |
+
if st.button("Predict"):
|
57 |
+
if input_text.strip():
|
58 |
+
predictions = predict_icd9([input_text], tokenizer, model, threshold)
|
59 |
+
st.write("### Predicted ICD-9 Codes")
|
60 |
+
for code in predictions[0]:
|
61 |
+
st.write(f"- {code}")
|
62 |
+
else:
|
63 |
+
st.error("Please enter a medical summary.")
|
64 |
|
65 |
+
# import torch
|
66 |
+
# import pandas as pd
|
67 |
+
# import streamlit as st
|
68 |
+
# from transformers import LongformerTokenizer, LongformerForSequenceClassification
|
69 |
|
70 |
+
# # Load the fine-tuned model and tokenizer
|
71 |
+
# model_path = "./clinical_longformer"
|
72 |
+
# tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
73 |
+
# model = LongformerForSequenceClassification.from_pretrained(model_path)
|
74 |
+
# model.eval() # Set the model to evaluation mode
|
75 |
|
76 |
+
# # Load the ICD-9 descriptions from CSV into a dictionary
|
77 |
+
# icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv") # Adjust the path to your CSV file
|
78 |
+
# icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type for matching
|
79 |
+
# icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals in ICD9 code for matching
|
80 |
|
81 |
+
# # ICD-9 code columns used during training
|
82 |
+
# icd9_columns = [
|
83 |
+
# '038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9',
|
84 |
+
# '287.5', '305.1', '311', '36.15', '37.22', '37.23', '38.91', '38.93', '39.61',
|
85 |
+
# '39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0',
|
86 |
+
# '486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0',
|
87 |
+
# '88.56', '88.72', '93.90', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15',
|
88 |
+
# '995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
|
89 |
+
# ]
|
90 |
|
91 |
+
# # Function for making predictions
|
92 |
+
# def predict_icd9(texts, tokenizer, model, threshold=0.5):
|
93 |
+
# inputs = tokenizer(
|
94 |
+
# texts,
|
95 |
+
# padding="max_length",
|
96 |
+
# truncation=True,
|
97 |
+
# max_length=512,
|
98 |
+
# return_tensors="pt"
|
99 |
+
# )
|
100 |
|
101 |
+
# with torch.no_grad():
|
102 |
+
# outputs = model(
|
103 |
+
# input_ids=inputs["input_ids"],
|
104 |
+
# attention_mask=inputs["attention_mask"]
|
105 |
+
# )
|
106 |
+
# logits = outputs.logits
|
107 |
+
# probabilities = torch.sigmoid(logits)
|
108 |
+
# predictions = (probabilities > threshold).int()
|
109 |
|
110 |
+
# predicted_icd9 = []
|
111 |
+
# for pred in predictions:
|
112 |
+
# codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
|
113 |
+
# predicted_icd9.append(codes)
|
114 |
|
115 |
+
# # Fetch descriptions for the predicted ICD-9 codes from the pre-loaded descriptions
|
116 |
+
# predictions_with_desc = []
|
117 |
+
# for codes in predicted_icd9:
|
118 |
+
# code_with_desc = [(code, icd9_descriptions.get(code.replace('.', ''), "Description not found")) for code in codes]
|
119 |
+
# predictions_with_desc.append(code_with_desc)
|
120 |
|
121 |
+
# return predictions_with_desc
|
122 |
+
|
123 |
+
|
124 |
+
# st.title("ICD-9 Code Prediction")
|
125 |
+
# st.sidebar.header("Model Options")
|
126 |
+
# threshold = st.sidebar.slider("Prediction Threshold", 0.0, 1.0, 0.5, 0.01)
|
127 |
+
|
128 |
+
# st.write("### Enter Medical Summary")
|
129 |
+
# input_text = st.text_area("Medical Summary", placeholder="Enter clinical notes here...")
|
130 |
+
|
131 |
+
# if st.button("Predict"):
|
132 |
+
# if input_text.strip():
|
133 |
+
# predictions = predict_icd9([input_text], tokenizer, model, threshold)
|
134 |
+
# st.write("### Predicted ICD-9 Codes and Descriptions")
|
135 |
+
# for code, description in predictions[0]:
|
136 |
+
# st.write(f"- {code}: {description}")
|
137 |
+
# else:
|
138 |
+
# st.error("Please enter a medical summary.")
|
139 |
+
# import torch
|
140 |
+
# # # # import pandas as pd
|
141 |
+
# # # # import streamlit as st
|
142 |
+
# # # # from transformers import LongformerTokenizer, LongformerForSequenceClassification
|
143 |
+
|
144 |
+
# # # # Load the fine-tuned model and tokenizer
|
145 |
+
# # # model_path = "./clinical_longformer"
|
146 |
+
# # # tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
147 |
+
# # # model = LongformerForSequenceClassification.from_pretrained(model_path)
|
148 |
+
# # # model.eval() # Set the model to evaluation mode
|
149 |
+
|
150 |
+
# # # # Load the ICD-9 descriptions from CSV into a dictionary
|
151 |
+
# # # icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv") # Adjust the path to your CSV file
|
152 |
+
# # # icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type
|
153 |
+
# # # icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals for matching
|
154 |
+
|
155 |
+
# # # # Load the ICD-9 to ICD-10 mapping
|
156 |
+
# # # icd9_to_icd10 = {}
|
157 |
+
# # # with open("2015_I9gem.txt", "r") as file:
|
158 |
+
# # # for line in file:
|
159 |
+
# # # parts = line.strip().split()
|
160 |
+
# # # if len(parts) == 3:
|
161 |
+
# # # icd9, icd10, _ = parts
|
162 |
+
# # # icd9_to_icd10[icd9] = icd10
|
163 |
+
|
164 |
+
# # # # ICD-9 code columns used during training
|
165 |
+
# # # icd9_columns = [
|
166 |
+
# # # '038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9',
|
167 |
+
# # # '287.5', '305.1', '311', '36.15', '37.22', '37.23', '38.91', '38.93', '39.61',
|
168 |
+
# # # '39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0',
|
169 |
+
# # # '486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0',
|
170 |
+
# # # '88.56', '88.72', '93.90', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15',
|
171 |
+
# # # '995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
|
172 |
+
# # # ]
|
173 |
+
|
174 |
+
# # # # Function for making predictions and mapping to ICD-10
|
175 |
+
# # # def predict_icd9(texts, tokenizer, model, threshold=0.5):
|
176 |
+
# # # inputs = tokenizer(
|
177 |
+
# # # texts,
|
178 |
+
# # # padding="max_length",
|
179 |
+
# # # truncation=True,
|
180 |
+
# # # max_length=512,
|
181 |
+
# # # return_tensors="pt"
|
182 |
+
# # # )
|
183 |
+
|
184 |
+
# # # with torch.no_grad():
|
185 |
+
# # # outputs = model(
|
186 |
+
# # # input_ids=inputs["input_ids"],
|
187 |
+
# # # attention_mask=inputs["attention_mask"]
|
188 |
+
# # # )
|
189 |
+
# # # logits = outputs.logits
|
190 |
+
# # # probabilities = torch.sigmoid(logits)
|
191 |
+
# # # predictions = (probabilities > threshold).int()
|
192 |
+
|
193 |
+
# # # predicted_icd9 = []
|
194 |
+
# # # for pred in predictions:
|
195 |
+
# # # codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
|
196 |
+
# # # predicted_icd9.append(codes)
|
197 |
+
|
198 |
+
# # # # Fetch descriptions and map to ICD-10 codes
|
199 |
+
# # # predictions_with_desc = []
|
200 |
+
# # # for codes in predicted_icd9:
|
201 |
+
# # # code_with_desc = []
|
202 |
+
# # # for code in codes:
|
203 |
+
# # # icd9_stripped = code.replace('.', '')
|
204 |
+
# # # icd10_code = icd9_to_icd10.get(icd9_stripped, "Mapping not found")
|
205 |
+
# # # icd9_desc = icd9_descriptions.get(icd9_stripped, "Description not found")
|
206 |
+
# # # code_with_desc.append((code, icd9_desc, icd10_code))
|
207 |
+
# # # predictions_with_desc.append(code_with_desc)
|
208 |
+
|
209 |
+
# # # return predictions_with_desc
|
210 |
+
|
211 |
+
# # # # Streamlit UI
|
212 |
+
# # # st.title("ICD-9 to ICD-10 Code Prediction")
|
213 |
+
# # # st.sidebar.header("Model Options")
|
214 |
+
# # # threshold = st.sidebar.slider("Prediction Threshold", 0.0, 1.0, 0.5, 0.01)
|
215 |
+
|
216 |
+
# # # st.write("### Enter Medical Summary")
|
217 |
+
# # # input_text = st.text_area("Medical Summary", placeholder="Enter clinical notes here...")
|
218 |
+
|
219 |
+
# # # if st.button("Predict"):
|
220 |
+
# # # if input_text.strip():
|
221 |
+
# # # predictions = predict_icd9([input_text], tokenizer, model, threshold)
|
222 |
+
# # # st.write("### Predicted ICD-9 and ICD-10 Codes with Descriptions")
|
223 |
+
# # # for icd9_code, description, icd10_code in predictions[0]:
|
224 |
+
# # # st.write(f"- ICD-9: {icd9_code} ({description}) -> ICD-10: {icd10_code}")
|
225 |
+
# # # else:
|
226 |
+
# # # st.error("Please enter a medical summary.")
|
227 |
+
|
228 |
+
# # # import os
|
229 |
+
# # # import torch
|
230 |
+
# # # import pandas as pd
|
231 |
+
# # # import streamlit as st
|
232 |
+
# # # from PIL import Image
|
233 |
+
# # # from transformers import LongformerTokenizer, LongformerForSequenceClassification
|
234 |
+
# # # from phi.agent import Agent
|
235 |
+
# # # from phi.model.google import Gemini
|
236 |
+
# # # from phi.tools.duckduckgo import DuckDuckGo
|
237 |
+
|
238 |
+
# # # # Load the fine-tuned ICD-9 model and tokenizer
|
239 |
+
# # # model_path = "./clinical_longformer"
|
240 |
+
# # # tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
241 |
+
# # # model = LongformerForSequenceClassification.from_pretrained(model_path)
|
242 |
+
# # # model.eval() # Set the model to evaluation mode
|
243 |
+
|
244 |
+
# # # # Load the ICD-9 descriptions from CSV into a dictionary
|
245 |
+
# # # icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv") # Adjust the path to your CSV file
|
246 |
+
# # # icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type for matching
|
247 |
+
# # # icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals in ICD9 code for matching
|
248 |
+
|
249 |
+
# # # # ICD-9 code columns used during training
|
250 |
+
# # # icd9_columns = [
|
251 |
+
# # # '038.9', '244.9', '250.00', '272.0', '272.4', '276.1', '276.2', '285.1', '285.9',
|
252 |
+
# # # '287.5', '305.1', '311', '36.15', '37.22', '37.23', '38.91', '38.93', '39.61',
|
253 |
+
# # # '39.95', '401.9', '403.90', '410.71', '412', '414.01', '424.0', '427.31', '428.0',
|
254 |
+
# # # '486', '496', '507.0', '511.9', '518.81', '530.81', '584.9', '585.9', '599.0',
|
255 |
+
# # # '88.56', '88.72', '93.90', '96.04', '96.6', '96.71', '96.72', '99.04', '99.15',
|
256 |
+
# # # '995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
|
257 |
+
# # # ]
|
258 |
+
|
259 |
+
# # # # Function for making ICD-9 predictions
|
260 |
+
# # # def predict_icd9(texts, tokenizer, model, threshold=0.5):
|
261 |
+
# # # inputs = tokenizer(
|
262 |
+
# # # texts,
|
263 |
+
# # # padding="max_length",
|
264 |
+
# # # truncation=True,
|
265 |
+
# # # max_length=512,
|
266 |
+
# # # return_tensors="pt"
|
267 |
+
# # # )
|
268 |
+
|
269 |
+
# # # with torch.no_grad():
|
270 |
+
# # # outputs = model(
|
271 |
+
# # # input_ids=inputs["input_ids"],
|
272 |
+
# # # attention_mask=inputs["attention_mask"]
|
273 |
+
# # # )
|
274 |
+
# # # logits = outputs.logits
|
275 |
+
# # # probabilities = torch.sigmoid(logits)
|
276 |
+
# # # predictions = (probabilities > threshold).int()
|
277 |
+
|
278 |
+
# # # predicted_icd9 = []
|
279 |
+
# # # for pred in predictions:
|
280 |
+
# # # codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
|
281 |
+
# # # predicted_icd9.append(codes)
|
282 |
+
|
283 |
+
# # # predictions_with_desc = []
|
284 |
+
# # # for codes in predicted_icd9:
|
285 |
+
# # # code_with_desc = [(code, icd9_descriptions.get(code.replace('.', ''), "Description not found")) for code in codes]
|
286 |
+
# # # predictions_with_desc.append(code_with_desc)
|
287 |
+
|
288 |
+
# # # return predictions_with_desc
|
289 |
|
290 |
# # # Streamlit UI
|
291 |
+
# # # st.title("Medical Diagnosis Assistant")
|
292 |
+
# # # option = st.selectbox(
|
293 |
+
# # # "Choose Diagnosis Method",
|
294 |
+
# # # ("ICD-9 Code Prediction", "Medical Image Analysis")
|
295 |
+
# # # )
|
296 |
+
|
297 |
+
# # # # ICD-9 Code Prediction
|
298 |
+
# # # if option == "ICD-9 Code Prediction":
|
299 |
+
# # # st.write("### Enter Medical Summary")
|
300 |
+
# # # input_text = st.text_area("Medical Summary", placeholder="Enter clinical notes here...")
|
301 |
+
|
302 |
+
# # # threshold = st.slider("Prediction Threshold", 0.0, 1.0, 0.5, 0.01)
|
303 |
+
|
304 |
+
# # # if st.button("Predict ICD-9 Codes"):
|
305 |
+
# # # if input_text.strip():
|
306 |
+
# # # predictions = predict_icd9([input_text], tokenizer, model, threshold)
|
307 |
+
# # # st.write("### Predicted ICD-9 Codes and Descriptions")
|
308 |
+
# # # for code, description in predictions[0]:
|
309 |
+
# # # st.write(f"- {code}: {description}")
|
310 |
+
# # # else:
|
311 |
+
# # # st.error("Please enter a medical summary.")
|
312 |
+
|
313 |
+
# # # Medical Image Analysis
|
314 |
+
# # # elif option == "Medical Image Analysis":
|
315 |
+
# # # if "GOOGLE_API_KEY" not in st.session_state:
|
316 |
+
# # # st.warning("Please enter your Google API Key in the sidebar to continue")
|
317 |
+
# # # else:
|
318 |
+
# # # medical_agent = Agent(
|
319 |
+
# # # model=Gemini(
|
320 |
+
# # # api_key=st.session_state.GOOGLE_API_KEY,
|
321 |
+
# # # id="gemini-2.0-flash-exp"
|
322 |
+
# # # ),
|
323 |
+
# # # tools=[DuckDuckGo()],
|
324 |
+
# # # markdown=True
|
325 |
+
# # # )
|
326 |
+
|
327 |
+
# # # query = """
|
328 |
+
# # # You are a highly skilled medical imaging expert with extensive knowledge in radiology and diagnostic imaging. Analyze the patient's medical image and structure your response as follows:
|
329 |
+
|
330 |
+
# # # ### 1. Image Type & Region
|
331 |
+
# # # - Specify imaging modality (X-ray/MRI/CT/Ultrasound/etc.)
|
332 |
+
# # # - Identify the patient's anatomical region and positioning
|
333 |
+
# # # - Comment on image quality and technical adequacy
|
334 |
+
|
335 |
+
# # # ### 2. Key Findings
|
336 |
+
# # # - List primary observations systematically
|
337 |
+
# # # - Note any abnormalities in the patient's imaging with precise descriptions
|
338 |
+
# # # - Include measurements and densities where relevant
|
339 |
+
# # # - Describe location, size, shape, and characteristics
|
340 |
+
# # # - Rate severity: Normal/Mild/Moderate/Severe
|
341 |
+
|
342 |
+
# # # ### 3. Diagnostic Assessment
|
343 |
+
# # # - Provide primary diagnosis with confidence level
|
344 |
+
# # # - List differential diagnoses in order of likelihood
|
345 |
+
# # # - Support each diagnosis with observed evidence from the patient's imaging
|
346 |
+
# # # - Note any critical or urgent findings
|
347 |
+
|
348 |
+
# # # ### 4. Patient-Friendly Explanation
|
349 |
+
# # # - Explain the findings in simple, clear language that the patient can understand
|
350 |
+
# # # - Avoid medical jargon or provide clear definitions
|
351 |
+
# # # - Include visual analogies if helpful
|
352 |
+
# # # - Address common patient concerns related to these findings
|
353 |
+
|
354 |
+
# # # ### 5. Research Context
|
355 |
+
# # # - Use the DuckDuckGo search tool to find recent medical literature about similar cases
|
356 |
+
# # # - Provide a list of relevant medical links
|
357 |
+
# # # - Include key references to support your analysis
|
358 |
+
# # # """
|
359 |
+
|
360 |
+
# # # upload_container = st.container()
|
361 |
+
# # # image_container = st.container()
|
362 |
+
# # # analysis_container = st.container()
|
363 |
+
|
364 |
+
# # # with upload_container:
|
365 |
+
# # # uploaded_file = st.file_uploader(
|
366 |
+
# # # "Upload Medical Image",
|
367 |
+
# # # type=["jpg", "jpeg", "png", "dicom"],
|
368 |
+
# # # help="Supported formats: JPG, JPEG, PNG, DICOM"
|
369 |
+
# # # )
|
370 |
+
|
371 |
+
# # # if uploaded_file is not None:
|
372 |
+
# # # with image_container:
|
373 |
+
# # # col1, col2, col3 = st.columns([1, 2, 1])
|
374 |
+
# # # with col2:
|
375 |
+
# # # image = Image.open(uploaded_file)
|
376 |
+
# # # width, height = image.size
|
377 |
+
# # # aspect_ratio = width / height
|
378 |
+
# # # new_width = 500
|
379 |
+
# # # new_height = int(new_width / aspect_ratio)
|
380 |
+
# # # resized_image = image.resize((new_width, new_height))
|
381 |
+
|
382 |
+
# # # st.image(resized_image, caption="Uploaded Medical Image", use_container_width=True)
|
383 |
+
|
384 |
+
# # # analyze_button = st.button("π Analyze Image")
|
385 |
+
|
386 |
+
# # # with analysis_container:
|
387 |
+
# # # if analyze_button:
|
388 |
+
# # # image_path = "temp_medical_image.png"
|
389 |
+
# # # with open(image_path, "wb") as f:
|
390 |
+
# # # f.write(uploaded_file.getbuffer())
|
391 |
+
|
392 |
+
# # # with st.spinner("π Analyzing image... Please wait."):
|
393 |
+
# # # try:
|
394 |
+
# # # response = medical_agent.run(query, images=[image_path])
|
395 |
+
# # # st.markdown("### π Analysis Results")
|
396 |
+
# # # st.markdown(response.content)
|
397 |
+
# # # except Exception as e:
|
398 |
+
# # # st.error(f"Analysis error: {e}")
|
399 |
+
# # # finally:
|
400 |
+
# # # if os.path.exists(image_path):
|
401 |
+
# # # os.remove(image_path)
|
402 |
+
# # # else:
|
403 |
+
# # # st.info("π Please upload a medical image to begin analysis")
|
404 |
+
|
405 |
+
# # import os
|
406 |
# # import torch
|
407 |
# # import pandas as pd
|
408 |
# # import streamlit as st
|
409 |
+
# # from PIL import Image
|
410 |
# # from transformers import LongformerTokenizer, LongformerForSequenceClassification
|
411 |
+
# # from phi.agent import Agent
|
412 |
+
# # from phi.model.google import Gemini
|
413 |
+
# # from phi.tools.duckduckgo import DuckDuckGo
|
414 |
|
415 |
+
# # # Sidebar for Google API Key input
|
416 |
+
# # st.sidebar.title("Settings")
|
417 |
+
# # st.sidebar.write("Enter your Google API Key below for the Medical Image Analysis feature.")
|
418 |
+
# # api_key = st.sidebar.text_input("Google API Key", type="password")
|
419 |
+
|
420 |
+
# # if api_key:
|
421 |
+
# # st.session_state["GOOGLE_API_KEY"] = api_key
|
422 |
+
# # else:
|
423 |
+
# # st.session_state.pop("GOOGLE_API_KEY", None)
|
424 |
+
|
425 |
+
# # # Load the fine-tuned ICD-9 model and tokenizer
|
426 |
# # model_path = "./clinical_longformer"
|
427 |
# # tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
428 |
# # model = LongformerForSequenceClassification.from_pretrained(model_path)
|
|
|
430 |
|
431 |
# # # Load the ICD-9 descriptions from CSV into a dictionary
|
432 |
# # icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv") # Adjust the path to your CSV file
|
433 |
+
# # icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type for matching
|
434 |
+
# # icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals in ICD9 code for matching
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
435 |
|
436 |
# # # ICD-9 code columns used during training
|
437 |
# # icd9_columns = [
|
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|
443 |
# # '995.92', 'V15.82', 'V45.81', 'V45.82', 'V58.61'
|
444 |
# # ]
|
445 |
|
446 |
+
# # # Function for making ICD-9 predictions
|
447 |
# # def predict_icd9(texts, tokenizer, model, threshold=0.5):
|
448 |
# # inputs = tokenizer(
|
449 |
# # texts,
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|
452 |
# # max_length=512,
|
453 |
# # return_tensors="pt"
|
454 |
# # )
|
455 |
+
|
456 |
# # with torch.no_grad():
|
457 |
# # outputs = model(
|
458 |
# # input_ids=inputs["input_ids"],
|
|
|
461 |
# # logits = outputs.logits
|
462 |
# # probabilities = torch.sigmoid(logits)
|
463 |
# # predictions = (probabilities > threshold).int()
|
464 |
+
|
465 |
# # predicted_icd9 = []
|
466 |
# # for pred in predictions:
|
467 |
# # codes = [icd9_columns[i] for i, val in enumerate(pred) if val == 1]
|
468 |
# # predicted_icd9.append(codes)
|
469 |
+
|
|
|
470 |
# # predictions_with_desc = []
|
471 |
# # for codes in predicted_icd9:
|
472 |
+
# # code_with_desc = [(code, icd9_descriptions.get(code.replace('.', ''), "Description not found")) for code in codes]
|
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|
473 |
# # predictions_with_desc.append(code_with_desc)
|
474 |
+
|
475 |
# # return predictions_with_desc
|
476 |
|
477 |
# # # Streamlit UI
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|
478 |
# # st.title("Medical Diagnosis Assistant")
|
479 |
# # option = st.selectbox(
|
480 |
# # "Choose Diagnosis Method",
|
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|
497 |
# # else:
|
498 |
# # st.error("Please enter a medical summary.")
|
499 |
|
500 |
+
# # # Medical Image Analysis
|
501 |
# # elif option == "Medical Image Analysis":
|
502 |
# # if "GOOGLE_API_KEY" not in st.session_state:
|
503 |
# # st.warning("Please enter your Google API Key in the sidebar to continue")
|
504 |
# # else:
|
505 |
# # medical_agent = Agent(
|
506 |
# # model=Gemini(
|
507 |
+
# # api_key=st.session_state["GOOGLE_API_KEY"],
|
508 |
# # id="gemini-2.0-flash-exp"
|
509 |
# # ),
|
510 |
# # tools=[DuckDuckGo()],
|
|
|
513 |
|
514 |
# # query = """
|
515 |
# # You are a highly skilled medical imaging expert with extensive knowledge in radiology and diagnostic imaging. Analyze the patient's medical image and structure your response as follows:
|
|
|
516 |
# # ### 1. Image Type & Region
|
517 |
# # - Specify imaging modality (X-ray/MRI/CT/Ultrasound/etc.)
|
518 |
# # - Identify the patient's anatomical region and positioning
|
519 |
# # - Comment on image quality and technical adequacy
|
|
|
520 |
# # ### 2. Key Findings
|
521 |
# # - List primary observations systematically
|
522 |
# # - Note any abnormalities in the patient's imaging with precise descriptions
|
523 |
# # - Include measurements and densities where relevant
|
524 |
# # - Describe location, size, shape, and characteristics
|
525 |
# # - Rate severity: Normal/Mild/Moderate/Severe
|
|
|
526 |
# # ### 3. Diagnostic Assessment
|
527 |
# # - Provide primary diagnosis with confidence level
|
528 |
# # - List differential diagnoses in order of likelihood
|
529 |
# # - Support each diagnosis with observed evidence from the patient's imaging
|
530 |
+
# # - Note any critical or urgent findings
|
531 |
+
# # ### 4. Patient-Friendly Explanation
|
532 |
+
# # - Explain the findings in simple, clear language that the patient can understand
|
533 |
+
# # - Avoid medical jargon or provide clear definitions
|
534 |
+
# # - Include visual analogies if helpful
|
535 |
+
# # - Address common patient concerns related to these findings
|
536 |
+
# # ### 5. Research Context
|
537 |
+
# # - Use the DuckDuckGo search tool to find recent medical literature about similar cases
|
538 |
+
# # - Provide a list of relevant medical links
|
539 |
+
# # - Include key references to support your analysis
|
540 |
+
# # """
|
541 |
+
|
542 |
+
# # upload_container = st.container()
|
543 |
+
# # image_container = st.container()
|
544 |
+
# # analysis_container = st.container()
|
545 |
+
|
546 |
+
# # with upload_container:
|
547 |
+
# # uploaded_file = st.file_uploader(
|
548 |
+
# # "Upload Medical Image",
|
549 |
+
# # type=["jpg", "jpeg", "png", "dicom"],
|
550 |
+
# # help="Supported formats: JPG, JPEG, PNG, DICOM"
|
551 |
+
# # )
|
552 |
+
|
553 |
+
# # if uploaded_file is not None:
|
554 |
+
# # with image_container:
|
555 |
+
# # col1, col2, col3 = st.columns([1, 2, 1])
|
556 |
+
# # with col2:
|
557 |
+
# # image = Image.open(uploaded_file)
|
558 |
+
# # width, height = image.size
|
559 |
+
# # aspect_ratio = width / height
|
560 |
+
# # new_width = 500
|
561 |
+
# # new_height = int(new_width / aspect_ratio)
|
562 |
+
# # resized_image = image.resize((new_width, new_height))
|
|
|
|
|
563 |
|
564 |
+
# # st.image(resized_image, caption="Uploaded Medical Image", use_container_width=True)
|
565 |
|
566 |
+
# # analyze_button = st.button("π Analyze Image")
|
567 |
|
568 |
+
# # with analysis_container:
|
569 |
+
# # if analyze_button:
|
570 |
+
# # image_path = "temp_medical_image.png"
|
571 |
+
# # with open(image_path, "wb") as f:
|
572 |
+
# # f.write(uploaded_file.getbuffer())
|
573 |
|
574 |
+
# # with st.spinner("π Analyzing image... Please wait."):
|
575 |
+
# # try:
|
576 |
+
# # response = medical_agent.run(query, images=[image_path])
|
577 |
+
# # st.markdown("### π Analysis Results")
|
578 |
+
# # st.markdown(response.content)
|
579 |
+
# # except Exception as e:
|
580 |
+
# # st.error(f"Analysis error: {e}")
|
581 |
+
# # finally:
|
582 |
+
# # if os.path.exists(image_path):
|
583 |
+
# # os.remove(image_path)
|
584 |
+
# # else:
|
585 |
+
# # st.info("π Please upload a medical image to begin analysis")
|
586 |
|
587 |
# import os
|
588 |
# import torch
|
|
|
594 |
# from phi.model.google import Gemini
|
595 |
# from phi.tools.duckduckgo import DuckDuckGo
|
596 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
597 |
# # Load the fine-tuned ICD-9 model and tokenizer
|
598 |
# model_path = "./clinical_longformer"
|
599 |
# tokenizer = LongformerTokenizer.from_pretrained(model_path)
|
|
|
601 |
# model.eval() # Set the model to evaluation mode
|
602 |
|
603 |
# # Load the ICD-9 descriptions from CSV into a dictionary
|
604 |
+
# icd9_desc_df = pd.read_csv("D_ICD_DIAGNOSES.csv")
|
605 |
# icd9_desc_df['ICD9_CODE'] = icd9_desc_df['ICD9_CODE'].astype(str) # Ensure ICD9_CODE is string type for matching
|
606 |
# icd9_descriptions = dict(zip(icd9_desc_df['ICD9_CODE'].str.replace('.', ''), icd9_desc_df['LONG_TITLE'])) # Remove decimals in ICD9 code for matching
|
607 |
|
|
|
624 |
# max_length=512,
|
625 |
# return_tensors="pt"
|
626 |
# )
|
|
|
627 |
# with torch.no_grad():
|
628 |
# outputs = model(
|
629 |
# input_ids=inputs["input_ids"],
|
|
|
645 |
|
646 |
# return predictions_with_desc
|
647 |
|
648 |
+
# # Define the API key directly in the code
|
649 |
+
# GOOGLE_API_KEY = "AIzaSyA24A6egT3L0NAKkkw9QHjfoizp7cJUTaA"
|
650 |
+
|
651 |
# # Streamlit UI
|
652 |
# st.title("Medical Diagnosis Assistant")
|
653 |
# option = st.selectbox(
|
|
|
673 |
|
674 |
# # Medical Image Analysis
|
675 |
# elif option == "Medical Image Analysis":
|
676 |
+
# medical_agent = Agent(
|
677 |
+
# model=Gemini(
|
678 |
+
# api_key=GOOGLE_API_KEY,
|
679 |
+
# id="gemini-2.0-flash-exp"
|
680 |
+
# ),
|
681 |
+
# tools=[DuckDuckGo()],
|
682 |
+
# markdown=True
|
683 |
+
# )
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
684 |
|
685 |
+
# query = """
|
686 |
+
# You are a highly skilled medical imaging expert with extensive knowledge in radiology and diagnostic imaging. Analyze the patient's medical image and structure your response as follows:
|
687 |
+
# ### 1. Image Type & Region
|
688 |
+
# - Specify imaging modality (X-ray/MRI/CT/Ultrasound/etc.)
|
689 |
+
# - Identify the patient's anatomical region and positioning
|
690 |
+
# - Comment on image quality and technical adequacy
|
691 |
+
# ### 2. Key Findings
|
692 |
+
# - List primary observations systematically
|
693 |
+
# - Note any abnormalities in the patient's imaging with precise descriptions
|
694 |
+
# - Include measurements and densities where relevant
|
695 |
+
# - Describe location, size, shape, and characteristics
|
696 |
+
# - Rate severity: Normal/Mild/Moderate/Severe
|
697 |
+
# ### 3. Diagnostic Assessment
|
698 |
+
# - Provide primary diagnosis with confidence level
|
699 |
+
# - List differential diagnoses in order of likelihood
|
700 |
+
# - Support each diagnosis with observed evidence from the patient's imaging
|
701 |
+
# - Note any critical or urgent findings
|
702 |
+
# ### 4. Patient-Friendly Explanation
|
703 |
+
# - Explain the findings in simple, clear language that the patient can understand
|
704 |
+
# - Avoid medical jargon or provide clear definitions
|
705 |
+
# - Include visual analogies if helpful
|
706 |
+
# - Address common patient concerns related to these findings
|
707 |
+
# ### 5. Research Context
|
708 |
+
# - Use the DuckDuckGo search tool to find recent medical literature about similar cases
|
709 |
+
# - Provide a list of relevant medical links
|
710 |
+
# - Include key references to support your analysis
|
711 |
+
# """
|
712 |
+
|
713 |
+
# upload_container = st.container()
|
714 |
+
# image_container = st.container()
|
715 |
+
# analysis_container = st.container()
|
716 |
+
|
717 |
+
# with upload_container:
|
718 |
+
# uploaded_file = st.file_uploader(
|
719 |
+
# "Upload Medical Image",
|
720 |
+
# type=["jpg", "jpeg", "png", "dicom"],
|
721 |
+
# help="Supported formats: JPG, JPEG, PNG, DICOM"
|
722 |
+
# )
|
723 |
|
724 |
+
# if uploaded_file is not None:
|
725 |
+
# with image_container:
|
726 |
+
# col1, col2, col3 = st.columns([1, 2, 1])
|
727 |
+
# with col2:
|
728 |
+
# image = Image.open(uploaded_file)
|
729 |
+
# width, height = image.size
|
730 |
+
# aspect_ratio = width / height
|
731 |
+
# new_width = 500
|
732 |
+
# new_height = int(new_width / aspect_ratio)
|
733 |
+
# resized_image = image.resize((new_width, new_height))
|
734 |
|
735 |
+
# st.image(resized_image, caption="Uploaded Medical Image", use_container_width=True)
|
736 |
|
737 |
+
# analyze_button = st.button("π Analyze Image")
|
738 |
|
739 |
+
# with analysis_container:
|
740 |
+
# if analyze_button:
|
741 |
+
# image_path = "temp_medical_image.png"
|
742 |
+
# with open(image_path, "wb") as f:
|
743 |
+
# f.write(uploaded_file.getbuffer())
|
744 |
|
745 |
+
# with st.spinner("π Analyzing image... Please wait."):
|
746 |
+
# try:
|
747 |
+
# response = medical_agent.run(query, images=[image_path])
|
748 |
+
# st.markdown("### π Analysis Results")
|
749 |
+
# st.markdown(response.content)
|
750 |
+
# except Exception as e:
|
751 |
+
# st.error(f"Analysis error: {e}")
|
752 |
+
# finally:
|
753 |
+
# if os.path.exists(image_path):
|
754 |
+
# os.remove(image_path)
|
755 |
+
# else:
|
756 |
+
# st.info("π Please upload a medical image to begin analysis")
|
757 |
|
758 |
|