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LLM concept annotation #416

Merged
merged 23 commits into from
Jan 14, 2025
Merged

LLM concept annotation #416

merged 23 commits into from
Jan 14, 2025

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kkaris
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@kkaris kkaris commented Jan 13, 2025

This PR adds the capability let ChatGPT attempt to ground the concepts representing the compartments in an ODE.

Further changes:

  • Refactor out openai ODE api to a new file separate from the example ui. See mira/sources/sympy_ode.
  • Attempt concept grounding by default in when using example web UI.
  • Add notebook showing how to extract a template model with groundings from an image of an ODE
  • Complete docstrings for the LLM ODE extraction functions

kkaris added 22 commits January 9, 2025 16:42
@kkaris
Add chat completion method
6a72665
@kkaris
Add json with prompts
d720ea4
@kkaris
Load the constants
0eb4074
@kkaris
Use prompts from JSON file
1882def
@kkaris
Update json
29fcad4
@kkaris
Move text to be in-line instead of in json file
9ad8c4e
@kkaris
Delete prompts json
f0aac30
@kkaris
Move response cleaning to new helper
56abe04
@kkaris
Add new function to get concepts data from string of sympy odes
12cbe57
@kkaris
Optionally run concept data extraction in execute_template_model_from…
5c31fff 
…_sympy_odes
@kkaris
Add test for execute_template_model_from_sympy_odes
f246769
@kkaris
Refactor LLM api to separate module
4dc6129
@kkaris
Attempt grounding for endpoint
b948f51
@kkaris
Update test
8f949bd
@kkaris
Add example ODE image
59553b6
@kkaris
Check for image formats
21d9c35
@kkaris
Remove debug prints
91510f4
@kkaris
Add and use new helpers taking image and returning ODE sympy string
b87052c
@kkaris
Rename function
a2d46ca
@kkaris
Fix comments
b266804
@kkaris
Add and complete docstrings
3a73c3f
@kkaris
Add example notebook of llm ODE extraction from image
c990af6
@kkaris kkaris requested a review from bgyori January 13, 2025 23:02
@bgyori bgyori merged commit 5444ff4 into gyorilab:main Jan 14, 2025
4 checks passed
@kkaris kkaris deleted the llm-annotate branch January 14, 2025 17:50
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@bgyori bgyori bgyori approved these changes

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@kkaris @bgyori