HypoGeniC

Scope and scientific boundary

This skill covers the ChicagoHAI software repository ChicagoHAI/hypothesis-generation and PyPI package hypogenic. HypoGeniC iteratively proposes and scores textual patterns from labeled data; HypoRefine adds literature-derived information; union workflows combine banks.

Keep these boundaries explicit:

• The output is a bank of candidate textual hypotheses and task-prediction statistics. It is not experimental confirmation, causal evidence, a clinical conclusion, or proof of scientific novelty.
• Predictive accuracy on held-out examples assesses task utility, not truth of a mechanism. Independent scientific validation still needs domain review, suitable controls, preregistered tests where appropriate, and new evidence.
• For researcher-led formulation of mechanisms and falsifiable predictions, use ../hypothesis-generation/SKILL.md. For open-ended ideation, use the scientific brainstorming skill.

Default workflow: local review first

Never start a model call automatically.

1. Classify the request: HypoGeniC software use, general hypothesis formulation, or downstream scientific validation.
2. Record the exact package, source, dataset, model/provider, destination, split policy, output path, and budgets.
3. Validate the local run policy and official task config.
4. Audit dataset checksums, schemas, duplicates, and split leakage.
5. Generate a bounded cost/run plan. Review provider retention and current pricing outside the package.
6. Ask for separate confirmation before any external LLM call, model download, or upload of dataset text.
7. Inspect the resulting hypothesis bank locally.
8. Evaluate once on the preserved test split and report limitations.

The bundled scripts are deterministic, bounded, local-only, and never import hypogenic, contact a model, load .env, enumerate the environment, or execute text found in configs, datasets, hypotheses, or results.

Reproducible installation

The latest stable artifact rechecked on 2026-10-01 is hypogenic==0.3.5 (released 2025-07-16, Python >=3.10, PyPI beta classifier). PyPI provenance links it to tag v0.3.5 and commit 8c3800ccae155e333fac5b530afa8abdaac38300.

uv venv --python 3.12 .venv
uv pip install "hypogenic==0.3.5"

Wheel SHA-256: f4ee8d7fa433cd59c58e0a8fe7df2f481ae29e7465a1b30ccbdac2c216a1b755. Source-distribution SHA-256: 5e1e5590f3612cb606a669909aab117d66577cf078dd56cae0f4123c5e8c44ae. Use a lockfile or hash-verified artifact in reproducible environments. Do not install an unpinned branch tip. See references/upstream.md for package/source alignment and known limitations.

The commands above are installation instructions, not a completed full dependency installation in this review. Bundled tools were tested independently with PyYAML 6.0.3; upstream wrappers were checked with mocked responses.

The dependency set is old and broad, including pinned-compatible ranges around PyTorch 2.4, Transformers 4.45, OpenAI 1.40, and Anthropic 0.32. Resolve it in an isolated environment; do not merge it casually into an unrelated application.

Safe configuration

There are two different configuration layers:

• An official HypoGeniC task config contains task name, train/validation/test paths, optional label/OOD fields, and prompt templates. It does not select a provider or enforce a budget.
• assets/run_config.example.json is this skill's local review policy. It is not an upstream HypoGeniC API. It makes provider, model, credential variable name, data destination, caps, split lock, and logging policy explicit before a run.

Run bundled command examples from the skill directory (or use absolute script paths and set --root to the directory containing the input files). Validate JSON without dependencies:

python3 scripts/validate_config.py run \
  --input assets/run_config.example.json \
  --root .

Validate an official YAML task config only with the reviewed parser version:

uv run --no-project --isolated --with "pyyaml==6.0.3" \
  python scripts/validate_config.py task \
  --input assets/task_config.example.yaml \
  --root .

Add --check-env to the run command to check only the configured, provider-specific name (OPENAI_API_KEY or ANTHROPIC_API_KEY). The report contains only a boolean. Never place a key in JSON/YAML, print it, read an entire .env, or dump the environment.

…