CLI

Install in editable mode before using the command-line interface:

python -m pip install -e ".[dev]"

Simulate

icg-cast simulate --n 1200 --months 72 --seed 7 --outdir outputs/demo

Writes a synthetic cohort, metadata, and optional trajectory plots.

To sample one coefficient-prior realization for the whole cohort:

icg-cast simulate \
  --n 1200 \
  --months 72 \
  --seed 7 \
  --coefficient-mode prior_sample \
  --coefficient-seed 42 \
  --outdir outputs/demo_uncertainty

Make Demo

icg-cast make-demo --n 120 --months 72 --seed 7 --outdir outputs/demo

Runs the reproducible demo workflow:

  • simulate

  • train

  • evaluate

  • graph

  • plot generation

It writes demo_manifest.json alongside the generated cohort, metrics, model bundle, graph exports, and PNG plots.

make-demo accepts the same --coefficient-mode and --coefficient-seed flags as simulate.

Train

icg-cast train \
  --cohort outputs/demo/synthetic_icg_cohort.csv \
  --outdir outputs/demo \
  --seed 7

Writes:

  • model_metrics.csv

  • permutation_importance.csv

  • counterfactual_tests.csv

  • biological_coherence.csv

  • model_bundle.joblib

  • model_card.md

  • modality_auc.png unless plots are disabled

The saved bundle contains the best multiomics_plus_qAOP baseline model and the held-out split indices used during training.

Evaluate

icg-cast evaluate \
  --cohort outputs/demo/synthetic_icg_cohort.csv \
  --model outputs/demo/model_bundle.joblib \
  --outdir outputs/demo

Writes evaluation metrics, calibration diagnostics, counterfactual tests, biological-coherence summary, and a model card. By default the command evaluates on the held-out split stored in the bundle.

Graph

icg-cast graph --outdir outputs/demo

Writes:

  • icg_theory_graph.graphml

  • icg_theory_graph_edges.json

Bench

icg-cast bench list
icg-cast bench info linear_lowhet
icg-cast bench run --cohort linear_lowhet --variant sign_constrained_augmented --seed 7

Benchmark commands run synthetic data-generating-process variants with known mechanistic structure for recovery and intervention-conformity experiments.