ICD-10 Code Extraction from Medical Diagnosis PDF documents

Welcome to our ICD-10 Code Extraction Tool!

This application helps you extract data from PDF documents using a Vision model and GPT-4 Omnium. Additionally, it offers a virtual assistant to answer your questions about ICD-10 codes powered by RAG system with FAISS and Longchain.

Please note that the assistant is in beta, so the database indexed just contain a short list of conditions. Too check the list find it in the bottom of this README file

Features

• PDF Data Extraction: Upload a PDF to extract and identify conditions in marked fields and provide the most rellevant ICD-10 code (CIE-10 in spanish).
• Image Display: View the pages of your PDF as images.
• CIE-10 Virtual Assistant: Get detailed answers to your questions about CIE-10 codes, this si beta feature, so the db is sampled to a small list of conditions.
• Configuration Settings: Selection of OpenAI model and config of GPT-4 parameters for more accurate data extraction.

Getting Started

Running the Application

• Create a .env file and add your open api key.

• To run the application, execute the following command in your terminal:

sh python main.py

After that you will see a ling to the Interface, the link is composed by a code ended with .gradio.live. example: [https://cb450902f541408b0a.gradio.live/]

Click the link to access to the User Interface.

1. Upload a PDF

To begin, upload a PDF document that you want to extract data from.

1. Click on "Cargar PDF".
2. Choose your PDF file.
3. Select the orientation for image joining of the pdf, by default is set to horizontal.

2. Extract Data

After uploading your PDF:

1. Click on "Enviar" to process the PDF.

2. The extracted fields will appear in the "Campos Extraídos" box.

   Note: The information showed above is a mockup, no real data has been used.

3. Display Images

To view the pages of your uploaded PDF as images:

1. Click on "Mostrar Imágenes".
2. The images will appear in the "Páginas PDF" gallery.

4. Virtual Assistant

Ask the virtual assistant about ICD-10 codes:

1. Enter your question in the "Pregunta" box.
2. Click on "Enviar".
3. The answer will appear in the "Respuesta" box.

5. Download Extracted Data

You can download the extracted data in JSON or Excel format:

• Click on "Descargar en JSON" to download a JSON file.
• Click on "Descargar en Excel" to download an Excel file.

6. Configuration Settings

Adjust the GPT-4 parameters to improve data extraction accuracy:

1. Go to the "Configuration" tab. .
2. Adjust the settings for:
   • Model: The specific OpenAI model to use for data extraction.
   • Temperature: Controls the creativity of the responses.
   • Max Tokens: The maximum number of tokens for the response.
   • Top P: Controls diversity via nucleus sampling
   • Frequency Penalty: Reduces the likelihood of repeated phrases by penalizing frequent tokens.
   • Presence Penalty: Forces the model to talk about new topics by penalizing tokens that have already appeared. .
3. Click on "Save Settings" to apply your changes.

List of conditions for the Assistant

• Adamantinoblastoma
• Adamantinoma
• Quiste, calcificación odontogénica - huesos largos
  • miembro inferior
  • miembro superior
  • maligno
  • mandíbula (hueso)
  • (parte inferior)
  • superior
  • tibial
• Adamantoblastoma
• Adams-Stokes (-Morgagni), enfermedad o síndrome de
• Adaptación, reacción de
• Trastorno, adaptación
• Addison, de
• Anemia (perniciosa)
  • enfermedad (bronceada) o síndrome
  • tuberculoso
  • queloide
• Addison-Biermer, anemia (perniciosa) de
• Addisoniana, crisis
• Addison-Schilder, complejo de
• Adelgazamiento vertebral
• Espondilopatía, especificada NCOC
• Adenitis
• Linfadenitis
• aguda, localización no especificada
• axilar
• aguda
• crónica o subaguda
• Bartolino, glándula de
• cervical
• aguda
• crónica o subaguda
• chancroide (Haemophilus ducreyi)
• conducto de Wharton (supurativa)
  • véase Sialoadenitis
• conducto o glándula de Skene
  • véase Uretritis
• Cowper, glándula de
  • véase Uretritis
  • crónica, localización no especificada
  • debida a Pasteurella multocida (P. septica)
  • epidémica, aguda
• escrófula (tuberculosa)
• estruma, tuberculosa
• ganglio o nódulo linfático, excepto mesentérico
  • aguda
    • véase Linfadenitis, aguda
  • crónica o subaguda
• gangrenosa
• glándula
  • bulbouretral
  • véase Uretritis
  • parótida (supurativa)
  • véase Sialoadenitis
  • salival (cualquiera) (supurativa)
  • véase Sialoadenitis
  • sublingual (supurativa)
  • véase Sialoadenitis
  • submandibular (supurativa)
  • véase Sialoadenitis
  • submaxilar (supurativa)
  • véase Sialoadenitis
  • uretral
  • véase Uretritis
• gonorrea NCOC
• infecciosa (aguda) (epidémica)
• inguinal
  • aguda
  • crónica o subaguda
• mesentérica (aguda) (crónica) (no especificada) (subaguda)
• subaguda, localización no especificada
• tuberculosa
  • véase Tuberculosis, ganglio linfático
• Adenoacantoma
• Neoplasia, maligna, por localización
• Adenoamel