Update README.md

README.md

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-license: cc-by-nc-4.0
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+---
+license: cc-by-nc-4.0
+---
+
+# Precious3-GPT-Multi-Modal inference
+
+Model inference is running at HuggingFace Inference endpoint
+
+
+## Definitions
+
+- **Signature**: up- and down-gene lists
+
+---
+
+## 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
+    }
+}
+
+```
+
+---
+
+## 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.
+
+---
+
+
+### 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