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yanmingyu92/README.md
Jaime Yan, PhD — Clinical Data Science · Statistical Programming Leader. Kaplan-Meier survival curves. Neofetch-style terminal card with an ASCII portrait. Jaime Yan, PhD: Associate Director, Statistical Programming at Kardigan; previously Merck, Regeneron, Boehringer Ingelheim; 9+ years in Phase 1–3; led statistical programming for the LIPFENDRA NDA; focus on data science leadership, R adoption and GxP AI.

Website LinkedIn Google Scholar py4csr on PyPI r-universe

Hi, I'm Jaime 👋

I lead clinical data science and statistical programming teams, and I help organizations move to open-source R and Python analytics that regulators can trust: reproducible pipelines, CDISC-native data, and AI that runs inside the GxP boundary rather than around it.

  • Associate Director, Statistical Programming @ Kardigan. I manage a programming team, lead statistical programming for the tonlamarsen cardiovascular program, and architected (with IT and QA) a governed clinical analytics platform, from validation framework to user training and adoption.
  • At Merck, I helped drive the move to R. I architected an enterprise GenAI (LLM/RAG) platform whose SAS-to-R conversion tooling was adopted organization-wide.
  • At Merck, I also led statistical programming for LIPFENDRA® (enlicitide) from Phase 2b through the pivotal Phase 3 CORALreef program and owned the NDA eSubmission packages (Define-XML, eCTD, ADRG). FDA approval: July 2026.
  • PhD in Data Science (2026), with research on AI/ML governance, validation and automation in clinical development.
  • Currently exploring digital protocols with CDISC USDM and ICH M11 (usdm-toolkit).

By the numbers: 9+ years in Phase 1–3; 1 FDA approval as NDA lead; 4 sole-author journal papers; 13 PhUSE/PharmaSUG papers; 85+ technical articles.


What my teams deliver: protocol to submission

flowchart TB
    P["Protocol & SAP<br/>USDM · ICH M11"] --> S["SDTM"]
    S --> A["ADaM<br/>admiral · admiralagent"]
    A --> T["TLFs<br/>tlfstack · py4csr"]
    T --> E["eSubmission<br/>Define-XML · eCTD · ADRG"]
    AI(["🤖 LLM agents + validation gates"]) -.-> A
    AI -.-> T
    G(["🛡️ GxP: validation · audit trail · Part 11"]) -.-> S
    G -.-> E
    L(["👥 People · SOPs · CRO oversight · training"]) -.-> S
    L -.-> T
    classDef core fill:#0f766e,stroke:#2dd4bf,color:#ffffff
    classDef layer fill:#4c1d95,stroke:#a78bfa,color:#ffffff
    class P,S,A,T,E core
    class AI,G,L layer
Loading

Featured work

clinical-r-in-practice Quarto book · CC BY-SA 4.0

A free 15-chapter book on the open-source R stack in regulated drug development: pharmaverse, ADaM, ARD, validation and LLM agents.

shiny-gxp-governance R/Shiny · MIT

A governance and validation template for R/Shiny in GxP settings: roles, control gates, risk-tiered validation, QC procedures and a 21 CFR Part 11 mapping.

admiralagent · tlfstack R packages · r-universe

Spec-driven ADaM code generation with LLM-translated layers, and convention-driven RTF TLFs with one code path for batch and interactive use.

clinical-figure-library R + Python · source-available

Reproducible clinical trial figure templates (forest, waterfall, KM and more) with synthetic data and independent numerical QC. Live gallery →

py4csr Python · MIT · on PyPI

A Python framework for clinical study reporting: CDISC-aware tables, listings and figures for CSRs.

pip install py4csr

clinprog-bench · CAVE-Onc Benchmarks · Python

Public benchmarks for clinical statistical-programming automation, plus graph-constrained agentic validation of CDISC oncology submissions.

More open-source work
Project What it does
rval-gateway R package validation gateway: riskmetric screening, decision engine and audit chain
gxp-sce The GxP Statistical Computing Environment: a review and practitioner's guide (CC BY-SA 4.0)
eSubmission-Benchmark Public benchmark submission package (SDTM, ADaM, Define-XML, TLFs) cited at PharmaSUG 2026
clinical-reporting-ir Typed IR schema and parity-validation harness for the Frontiers in Pharmacology paper
sop-knowledge-graph Six-stage pipeline turning pharmaceutical SOPs into a knowledge graph and web explorer
posit-conf-2026-bilingual Modern R in Practice / 现代 R 进阶: a 28-chapter bilingual book with companion labs
usdm-toolkit Toolchain for CDISC USDM / ICH M11 digital protocols
ragql-nav Multi-agent framework routing natural-language clinical data questions to SQL or Neo4j

Selected publications (sole author, 2026)

  • Workflow topology–guided skill loading for agentic AI in clinical trial data pipelines: sequential exploratory evaluation. JMIR Formative Research, 2026. doi:10.2196/100769
  • A non-destructive methodological framework for modernizing legacy clinical reporting systems for AI-driven pharmacoinformatics: a SAS case study. Frontiers in Pharmacology, 2026. doi:10.3389/fphar.2026.1876207 · code
  • CAVE-Onc: graph-constrained agentic validation for cross-domain contradictions in CDISC oncology submissions. PLOS ONE, 2026. doi:10.1371/journal.pone.0350376 · code
  • ClinAgent: AI-assisted methodology for clinical trial data processing and statistical programming. Biology Methods and Protocols (Oxford University Press), 2026. doi:10.1093/biomethods/bpag032

Plus 13 PhUSE / PharmaSUG conference papers (2023–2026). Full list on Google Scholar.


Latest writing

From jaimeyan.com: practical articles on CDISC, R in pharma, GxP and LLM automation. RSS


Toolbox

Skills: R, Python, PostgreSQL, Docker, Linux, Git, GitHub Actions

Shiny Quarto SAS LLM / RAG Neo4j

CDISC pharmaverse GxP Submissions

All demos and benchmarks use synthetic or public test data (e.g. the CDISC Pilot). Views are my own and not those of any employer.

Pinned Loading

  1. admiralagent admiralagent Public

    Spec-Driven ADaM Code Generation with LLM-Translated Layers

    R 3

  2. clinical-r-in-practice clinical-r-in-practice Public

    Clinical R in Practice — free Quarto book on the open-source R stack behind regulated drug development: pharmaverse, ADaM, ARD, validation, LLM agents. 15 chapters, 5 parts.

    CSS 2

  3. py4csr py4csr Public

    Python for Clinical Study Reporting: CDISC-aware tables, listings and figures for CSRs (PyPI)

    Python 2 2

  4. clinprog-bench clinprog-bench Public

    ClinProg-Bench: a public benchmark for clinical-trial statistical-programming automation

    Python 1

  5. clinical-figure-library clinical-figure-library Public

    Reproducible R and Python clinical trial figure templates, synthetic teaching data, independent numerical QC, and Clinical Data Lab demos.

    Python

  6. shiny-gxp-governance shiny-gxp-governance Public

    A governance and validation template for teams running R/Shiny applications in a GxP-regulated environment - roles, control gates, risk-tiered validation, QC procedures, Part 11 mapping.