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license: cc-by-nc-4.0
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# Precious3-GPT-Multi-Modal inference

Model inference is running at HuggingFace Inference endpoint


## Definitions

- **Signature**: up- and down-gene lists

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## Generation config .json Overview

In the following example all possible configuration fields are specified. You can leave some meta-data fields in ```inputs``` section empty string(```""```) or empty list(```[]```). 

For example, if you want to generate signature given specific meta-data you can use the following configuration. Note, ```up``` and ```down``` fields are empty lists as you want to generate them. 

Another example - predict compound based on signature. You can take 

```json
{
    "inputs": {
        "instruction": "compound2diff2compound",
        "tissue": ["whole blood"],
        "cell": "u937",
        "efo": "Orphanet_139399",
        "datatype": "",
        "drug": "",
        "dose": "",
        "time": "",
        "case": "",
        "control": "",
        "age": "",
        "dataset_type": "expression",
        "gender": "m",
        "species": "human",
        "up": [],
        "down": []
    },
    "mode": "meta2diff",
    "parameters": {
        "temperature": 0.8,
        "top_p": 0.2,
        "top_k": 3550,
        "n_next_tokens": 50
    }
}

```

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## Generation Modes (`mode` in config)

Choose the appropriate mode based on your requirements:

1. **meta2diff**: Generate signature given meta-data such as tissue, compound, gender, etc.
2. **diff2compound**: Predict compounds based on signature.
3. **meta2diff2compound**: Generate signatures given meta-data and then predict compounds based on generated signatures.

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### Instruction (`inputs.instruction` in config)

You can use the following instructions (one or several at a time):

1. disease2diff2disease - generate signature for disease
2. compound2diff2compound - generate signature for compound
3. age_group2diff2age_group - generate signature for age-group
4. Under development:
   - pathway2gene_list2pathway
   - crispr_pert2diff2crispr_pert
   - sh_crispr_pert2diff2sh_crispr_pert
   - oe_lincs_pert2diff2oe_lincs_pert


### Other meta-data (`inputs.` in config)
Full list of available values for each meta-data item you can find in ```p3_entities_with_type.csv```


## Multi-Modality