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rhowardstone/README.md

I build AI-assisted data systems for large, messy, high-stakes datasets, then turn the results into usable software, analysis, and plain-English insight.

What I build

  • Evidence databases for massive document dumps — CaseStack, an engine that turns any document dump into a quarriable evidence database. Its proof-of-concept deployment over 1.38M DOJ documents draws ~15K daily users, and its results have been used by reporters at major and independent outlets. Data exports: Epstein-research-data
  • Scientific extraction pipelines with provenance — Organoid Protocol Atlas, an ongoing effort, is an interface grown from a curated set of academic literature on organoid culture protocols.
  • Bioinformatics tools and high-performance search — AmpliconHunter2, a SIMD-accelerated in silico PCR engine, 5.9× faster than the original (ICCABS 2026)
  • AI-agent workflows for research and software engineering — claude-code-scientist, a 24-skill semi-autonomous research agent with validation hooks and provenance tracking for academic literature acquisition, data acquisition, computational experimentation, synthesis, and peer review. "Self-improving": includes /cortex, which audits prior sessions, diagnoses issues, and generates fixes.

How I use AI

I scaffold AI agents the way you'd onboard a new hire: they work in Git, write findings up as reports, and pass a peer-review check before the output reaches me. claude-code-scientist shows one example of this setup — staged skills, validation hooks, and an automated review pass.

Selected links

Resume · LinkedIn · Google Scholar · ORCID

Website:

ryehowardstone.com

Projects:

AmpliconHunter1 · AmpliconHunter2 · Epstein-data.com · CaseStack · OrganoidProtocolAtlas

Pinned Loading

  1. Epstein-research-data Epstein-research-data Public

    Structured data exports from forensic analysis of the 218GB DOJ Epstein file release — knowledge graph, entity extractions, image catalog, EFTA mapping

    Python 165 29

  2. casestack casestack Public

    Turn any document dump into a searchable evidence database. Semantic, keyword, AI, and reverse image search routes

    Python 10 1

  3. AmpliconHunter2 AmpliconHunter2 Public

    SIMD-accelerated C version of AmpliconHunter; ultra-fast in-silico PCR

    C 7

  4. Claude-Code-Scientist Claude-Code-Scientist Public

    Transform Claude Code into a semi-autonomous, self-improving scientific researcher. Literature review, data acquisition, experimentation, synthesis, peer review

    Python 8

  5. AI-Job-Coach AI-Job-Coach Public

    Democratized access to elite "career coach" methodology via Claude Code, for relationship-focused job searching. Implements networking methodology grounded in career development research (Granovett…

    Python 5

  6. organoid-protocol-atlas organoid-protocol-atlas Public

    Evidence-grounded extraction of organoid culture protocols into a structured, quarriable knowledge base. (Experimental)

    Python