Update README.md

README.md

@@ -8,12 +8,14 @@ State is distributed via [`uv`](https://docs.astral.sh/uv). To train models on y
 uv tool install arc-state
 ```
 
-To 
+To generate predictions:
 
 ```code
 state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR>
 ```
 
+This will group the cells in your input AnnData by the specified `pert_col` and run inference with a pretrained ST checkpoint.
+
 ## Running from source
 
 ```bash
@@ -28,7 +30,7 @@ uv venv
 uv tool install -e .
 ```
 
-To generate embeddings given an AnnData:
+To generate predictions:
 
 ```code
 state tx infer --model_dir <ST-Parse_PATH> --pert_col cytokine --adata <INPUT_ADATA>.h5ad --output <OUTPUT_DIR>