Integrate uniprot info into initial prompt #396
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JuliaS92
requested review from
mschwoer and
boopthesnoot
and removed request for
mschwoer
| dummy_model = LLMIntegration(model_name, api_key="lorem", load_tools=False) | ||
| tokens = dummy_model.estimate_tokens( |
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a bit hacky ;-)
please refactor such that the estimate_tokens becomes static and you can just call LLMIntegration.estimate_tokens here:
def estimate_tokens(
model: str = None, messages: List[Dict[str, str]], average_chars_per_token: float = 3.6
) -> float:
...
| ) | ||
| st.markdown(f"Total tokens: {tokens:.0f}") | ||
| with c5: | ||
| st.checkbox( |
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why do we need the extra checkbox? Can I not just click "update prompt"? (set state[StateKeys.INTEGRATE_UNIPROT]=True after button click)
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You need a way to also revert to an initial prompt that does not contain the uniprot information. Uncheck the box, then update.
| ): | ||
| """Get the initial prompt for the LLM model.""" | ||
| group1 = parameter_dict["group1"] | ||
| group2 = parameter_dict["group2"] | ||
| column = parameter_dict["column"] | ||
| if uniprot_info: | ||
| uniprot_instructions = ( | ||
| f"We have already retireved relevant information from Uniprot for these proteins:{os.linesep}{os.linesep}{uniprot_info}{os.linesep}{os.linesep}" |
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This (and other prompts) are using interpunctation quite sparsely. My knowledge may be outdated, but I learned that the more structured a prompt, the better. Shall we add some backticks or quoatation marks?
just an example:
===
Uniprot information for protein "VCL"
- protein name: `Vinculin (or Metavinculin)`
- entryType of this protein is `UniProtKB reviewed (Swiss-Prot)`.
- primaryAccession of this protein is `P18206`.
- secondaryAccessions of this protein is `Q16450, Q5SWX2, Q7Z3B8, Q8IXU7`.
- XXXXX is `Actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion`
===
===
Uniprot information for protein "XYZ"
instead of
The protein VCL is called Vinculin (or Metavinculin).
Uniprot information:
- entryType of this protein is UniProtKB reviewed (Swiss-Prot).
- primaryAccession of this protein is P18206.
- secondaryAccessions of this protein is Q16450, Q5SWX2, Q7Z3B8, Q8IXU7.
- Actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion
(maybe a different PR)
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I will consider this when I start the next PR on prompt engineering.
| uniprot_instructions = ( | ||
| "You have the ability to retrieve curated information from Uniprot about these proteins. " | ||
| "Please do so for individual proteins if you have little information about a protein or find a protein particularly important in the specific context." | ||
| ) | ||
| return ( | ||
| f"We've recently identified several proteins that appear to be differently regulated in cells " | ||
| f"when comparing {group1} and {group2} in the {column} group. " | ||
| f"From our proteomics experiments, we know that the following ones are upregulated: {', '.join(upregulated_genes)}.{os.linesep}{os.linesep}" | ||
| f"Here is the list of proteins that are downregulated: {', '.join(downregulated_genes)}.{os.linesep}{os.linesep}" |
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also prompt engineering:
Here is a comma-separated list of proteins that are downregulated: `{', '.join(downregulated_genes)}.{os.linesep}{os.linesep}`
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I will consider this when I start the next PR on prompt engineering.
| ): | ||
| """Get the initial prompt for the LLM model.""" | ||
| group1 = parameter_dict["group1"] | ||
| group2 = parameter_dict["group2"] | ||
| column = parameter_dict["column"] | ||
| if uniprot_info: | ||
| uniprot_instructions = ( | ||
| f"We have already retireved relevant information from Uniprot for these proteins:{os.linesep}{os.linesep}{uniprot_info}{os.linesep}{os.linesep}" |
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"proteins" or "genes"? :)
| @@ -24,6 +24,9 @@ def protein_selector(df: pd.DataFrame, title: str, state_key: str) -> List[str]: | |||
| selected_proteins (List[str]): A list of selected proteins. | |||
| """ | |||
| st.write(title) | |||
| if len(df) == 0: | |||
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shall we move this check to 06_LLM.py? e.g. right after st.markdown("##### Genes of interest")? I feel here it's a bit hidden
| def display_uniprot( | ||
| regulated_genes_dict, | ||
| feature_to_repr_map, | ||
| model_name: str = Models.OLLAMA_31_70B, |
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please don't specify a default here
New:
Note: