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README and docs homepage: results first, and the end-to-end chain from LLM to failure handling - #39

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NingyuSUN merged 2 commits into
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portfolio-readme
Oct 6, 2026
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NingyuSUN merged 2 commits into
mainfrom
portfolio-readme

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@NingyuSUN NingyuSUN commented Oct 6, 2026 •

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Rewrites the homepage README for readers assessing the project. It now leads with:

  • what the toolkit does;
  • a results figure and table (six models, real data);
  • one real run traced step by step: LLM → tool calling → structured output → evaluation → feedback;
  • a failure-handling table mapped to the code;
  • how it works, what it demonstrates, quickstart, real-data cases, limits (including the failed definition check) and the roadmap.

The figure docs/assets/ai_validation_results.svg is rendered from the committed summaries by evaluation/llm_benchmark/plot.py. Its palette was checked with the dataviz validator, and every segment is labelled.

Every number and example is taken from committed results:

  • the VHL / anti-VEGF agent trace is Claude Haiku 4.5's episode in results/agent-pilot;
  • the CL:0002335 → CL:0000173 correction is in results/celltype-test.

Links stay absolute, so the README also renders on PyPI.

Also syncs the docs site homepage (docs/index.md) with the same content and site-relative links, and publishes the single-cell case as a benchmarks page (mkdocs_hooks.py, mkdocs.yml). mkdocs build --strict passes.

Lead with what the toolkit does for AI-assisted curation and the measured
results with six models; show one real run from LLM tool calls through
structured output, evaluation and feedback, and a failure-handling table
mapped to the code; state the limits and the negative result. Add a
results figure rendered from the committed summaries (plot.py).
The site's home page now leads with the same results, the end-to-end
chain and the failure-handling table, with site-relative links; the
single-cell case page joins the benchmarks section.
@NingyuSUN NingyuSUN changed the title README: results first, and the end-to-end chain from LLM to failure handling README and docs homepage: results first, and the end-to-end chain from LLM to failure handling Oct 6, 2026
@NingyuSUN
NingyuSUN merged commit 49d571a into main Oct 6, 2026
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@NingyuSUN
NingyuSUN deleted the portfolio-readme branch October 6, 2026 02:41
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