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skills/hypogenic/references/sources.md

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Dated sources

Research and access date: 2026-07-23.

Only official project, package-index, repository, publisher, and provider sources were used for behavioral claims. Parallel web search/extract identified the canonical pages; GitHub and PyPI APIs were used to verify exact refs, metadata, file hashes, and source files.

Package and source

  1. PyPI: hypogenic — latest stable 0.3.5, released 2025-07-16; Python requirement, beta classifier, dependencies, files, SHA-256 values, project links, trusted-publisher provenance, source tag/commit. Accessed 2026-07-23.
  2. ChicagoHAI/hypothesis-generation — official repository, README, license, default branch, package layout, examples, task-config instructions, and current project links. Repository default commit checked 2026-07-23.
  3. Release v0.3.5 source tree — immutable source used for API/CLI review. Commit dated 2025-07-16; accessed 2026-07-23.
  4. GitHub releases — release/tag history through v0.3.5. Accessed 2026-07-23.
  5. Master commit history — four post-tag logging/debug commits ending at bd37a3129a2f98ee586f545a57b10b59496eedad on 2025-07-17. Accessed 2026-07-23.
  6. Pinned pyproject.toml — version, Python requirement, dependencies, optional dev dependencies, console entry points, license, and project URLs. Accessed 2026-07-23.
  7. Pinned generation CLI and inference CLI — exact parser flags, defaults, execution flow, logging, output, and metric behavior. Accessed 2026-07-23.
  8. Pinned task loader and prompt implementation — YAML fields, split-path resolution, sampling, and prompt-template access. Accessed 2026-07-23.
  9. Pinned model wrappers — OpenAI, Anthropic, Transformers, vLLM, local registration, cost table, and model-loading behavior. Accessed 2026-07-23.
  10. Pinned output serializer and SummaryInformation — hypothesis-bank JSON shape and stored statistics. Accessed 2026-07-23.
  11. Pinned Redis cache — local Redis prompt/response caching and pickle serialization. Accessed 2026-07-23.

Datasets

  1. ChicagoHAI/HypoBench-datasets — current official GitHub data/config repository; no releases. Default revision 7e4bbc341ee90b7efaa607f67a81543cd68cdf2e, dated 2025-07-09; accessed 2026-07-23.
  2. Pinned HypoBench dataset tree — task families, configs, and split files used for the manifest example. Accessed 2026-07-23.
  3. ChicagoHAI/HypoGeniC-datasets on Hugging Face — official alternate dataset publication. Observed revision 613860dcbcda9e522a6163ee9edf78c261ebe4bb, last modified 2025-04-23; accessed 2026-07-23.

Papers and evaluation scope

  1. Hypothesis Generation with Large Language Models — Zhou et al., Proceedings of the 1st Workshop on NLP for Science, November 2024, DOI 10.18653/v1/2024.nlp4science-1.10. Data-driven HypoGeniC algorithm, classification evaluations, and paper claims. Accessed 2026-07-23.
  2. Literature Meets Data: A Synergistic Approach to Hypothesis Generation — Liu et al.; submitted 2024-10-22, version 3 dated 2025-01-08. HypoRefine, literature/data integration, union methods, five-dataset evaluation, and human decision-support study. Accessed 2026-07-23.
  3. HypoBench: Towards Systematic and Principled Benchmarking for Hypothesis Generation — Liu et al.; submitted 2025-04-15, version 2 dated 2026-02-10. Seven real-world tasks, five synthetic task families, 194 datasets, evaluation dimensions, and documented remaining limitations. Accessed 2026-07-23.
  4. HypoBench OpenReview record — TMLR submission metadata and revisions; submitted 2025-08-31, modified 2026-02-25, recorded as rejected. Used only to distinguish publication status from the arXiv version. Accessed 2026-07-23.

Provider authentication and privacy

  1. OpenAI developer quickstart — OPENAI_API_KEY and automatic SDK environment lookup. Accessed 2026-07-23.
  2. OpenAI enterprise privacy — business/API training defaults, up-to-30-day API retention, exceptions, and eligible ZDR requests. Page search result dated 2026-01-08; accessed 2026-07-23.
  3. Anthropic get started — ANTHROPIC_API_KEY and automatic SDK environment lookup. Accessed 2026-07-23.
  4. Anthropic API and data retention — standard policy links, eligible ZDR, feature exclusions, legal/misuse exceptions, HIPAA readiness, and model-specific retention. Accessed 2026-07-23.
  5. Anthropic commercial data retention — automatic API input/output deletion within 30 days. Updated 2026-07-01; accessed 2026-07-23.
  6. Anthropic covered-model retention — 30-day retention requirement for designated covered models, including effects on ZDR arrangements. Updated 2026-07-09; accessed 2026-07-23.

Local model behavior

  1. Transformers installation and offline mode — Hub downloads, caches, pre-download workflows, and local reload. Accessed 2026-07-23.
  2. Transformers pipelines — model/path loading and trust_remote_code warning. Accessed 2026-07-23.