[feature] heatmap functionality for transition model

README.md

@@ -59,6 +59,25 @@ options:
   -h, --help  show this help message and exit
 ```
 
+### Double Perturbation Analysis
+
+Generate double perturbation sweeps against a baseline core cell batch:
+
+```bash
+uv run state tx double \
+  --output-dir /path/to/training/run \
+  --target-cell-type RPE1 \
+  --checkpoint last.ckpt
+```
+
+Key arguments:
+- `--target-cell-type`: cell type used to seed the core control cells
+- `--checkpoint`: checkpoint filename inside `<output-dir>/checkpoints`
+- `--results-dir`: optional override for where to dump results; defaults to `<output-dir>/eval_<checkpoint>`
+- `--phase-one-only`: stop after saving single-perturbation predictions
+
+The command emits `.npy` snapshots, AnnData files, and metric reports mirroring the single-perturbation heatmap command.
+
 ## State Transition Model (ST)
 
 To start an experiment, write a TOML file (see `examples/zeroshot.toml` or

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "arc-state"
-version = "0.9.31"
+version = "0.9.32"
 description = "State is a machine learning model that predicts cellular perturbation response across diverse contexts."
 readme = "README.md"
 authors = [
@@ -13,7 +13,7 @@ authors = [
 requires-python = ">=3.10,<3.13"
 dependencies = [
     "anndata>=0.11.4",
-    "cell-load>=0.8.3",
+    "cell-load>=0.8.5",
     "numpy>=2.2.6",
     "pandas>=2.2.3",
     "pyyaml>=6.0.2",