An example implementation of RAG with Structured Outputs

[jylee-bcm]

Recently, I implemented a small RAG (Retrieval-Augmented Generation) application using ChatGPT with minimal code. The database it references contains information about patients and medical articles. When you query something related to a patient's condition, such as diseases or symptoms, it accurately retrieves relevant articles featuring similar cases and generates content based on those articles.

I wanted to share it with the group as I utilized the technique of structured outputs, which I recently presented at a basic level, and the code is quite compact (under 100 lines), so there’s plenty of room for improvement or extension.

Link: https://colab.research.google.com/drive/19MDbFZSfASDA69pea5oijzlCIwkjKCA6?usp=sharing

Feel free to leave comments!

Example Input

ask_me_pmc_articles_with_retries("I want to find cases of cerebral palsy with any medication treatment")

Example Output

Thank you for reaching out with your query regarding cases of cerebral palsy (CP) and their medication treatments. I have found several related articles that discuss various treatments and their outcomes. Here is a summary of the shared characteristics and findings across these articles:

Summary of Shared Characteristics

1. Patient Demographics: The patients varied in age from infants to young adults, with many cases involving children born prematurely. The majority had some form of spastic CP, though other types such as dystonic CP were also represented.
2. Treatment Modalities: Treatments included a combination of pharmacotherapy, physical therapy, and in some cases, innovative treatments like stem cell transplantation. Common medications used were baclofen, botulinum toxin, and various anticonvulsants.
3. Outcomes: Improvement in motor functions, reduction in spasticity, and enhanced quality of life were commonly reported outcomes. Some patients showed significant progress in activities of daily living and motor skills post-treatment.
4. Imaging and Diagnostic Tools: MRI and PET-CT scans were frequently used to assess brain abnormalities and monitor treatment progress. Functional assessments like the Functional Independence Measure (FIM) and Gross Motor Function Classification System (GMFCS) were utilized to evaluate outcomes.
5. Ethical Considerations: All studies adhered to ethical guidelines, with informed consent obtained from patients or guardians.

Detailed Case Reports

1. Bone Marrow Mononuclear Cell Transplantation:

   • Patient: A 12-year-old boy with spastic diplegic CP.
   • Treatment: Bone marrow mononuclear cell transplantation combined with intensive neurorehabilitation.
   • Outcome: Significant improvements in trunk strength, upper limb control, and overall functional independence. PET-CT scans showed normalization of brain function.
   • Reference: PMC Article

2. Botulinum Toxin Injections:

   • Patient: A 12-year-old female with mild spastic diplegic CP.
   • Treatment: Physical and occupational therapy, splinting, and botulinum toxin injections.
   • Outcome: Reduction in spasticity and improvement in motor function.
   • Reference: PMC Article

3. Umbilical Cord-derived Mesenchymal Stem Cell Transplantation:

   • Patient: A 6-year-old male with dystonic CP.
   • Treatment: Stem cell transplantation along with baclofen and rehabilitation.
   • Outcome: Partial benefits reported, with improvements in motor functions.
   • Reference: PMC Article

4. Intrathecal Baclofen Therapy:

   • Patient: A 15-year-old girl with spastic quadriplegic CP.
   • Treatment: Intrathecal baclofen pump placement.
   • Outcome: Improved muscle tone and reduced spasticity, leading to better functional outcomes.
   • Reference: PMC Article

5. Pharmacotherapy and Rehabilitation:

   • Patient: A 20-year-old male with CP and mental retardation.
   • Treatment: Combination of cellular therapy and multidisciplinary rehabilitation.
   • Outcome: Enhanced functional independence and social interaction, with improved IQ scores.
   • Reference: PMC Article

These articles collectively provide valuable insights into the various treatment approaches for CP and their effectiveness. If you need more detailed information on any specific case or treatment, feel free to let me know!

Best regards,
[Your Name]

[hyunhwan-bcm]

another idea might be posting this jupyter notebook into the git at tips_and_notebook/3/your_awesome_notebook.ipynb Please PR then share if you agree with :)