This 3D scene needs WebGL. The legend below lists what it shows.

Dan Peng

M.S. Biomedical Data Science student at Stanford University, working on medical AI.

I build AI that makes healthcare safer and smarter, and the evaluations that show when it isn't.

M.S. Biomedical Data Science @ Stanford University
Pacific time

About

I build AI for medicine that clinicians can trust, and the benchmarks that show when they can't.

My work sits where machine learning meets healthcare and human-centered AI. I believe AI should not only become more powerful, but also safer, more trustworthy, and more useful for clinicians and patients.

On the research side that means evaluation: how LLMs hold up when a patient pushes back, and whether an LLM judge agrees with physicians. It also means building models and agents, from multimodal clinical trial prediction and high-risk order detection to, now at Stanford, an agent that reads 3D medical scans. The work has been cited 40+ times.

I'm a master's student in Biomedical Data Science (AI/ML) at Stanford. Before that I studied Computer Science and Statistics & Analytics at UNC Chapel Hill (Phi Beta Kappa, Honors Carolina), and interned on the engineering side: agentic AI and LLM infrastructure at Takeoff41, and an AI code-review agent at Bandwidth. When I'm not doing research, you'll probably find me writing code, exploring new models, or contributing to open-source projects.

Research

5 publications, 2025 to 2026
2026

SycoEval-EM: Sycophancy Evaluation of Large Language Models in Simulated Clinical Encounters for Emergency Care

D Peng, Y Wang, A Schoeffler, S Hong, B Suffoletto, D Kim, C Preiksaitis, et al.

npj Digital Medicineunder reviewfirst author
2025

SpaGenBench: Large-scale Spatial Variable Gene Atlas for Spatial Transcriptomics

J Chen, J Zhang, D Peng, Y Song, A Ruan, Y Li, D Li

Nature Geneticsunder review
2025

LIFTED: Multimodal Clinical Trial Outcome Prediction via Large Language Models and Mixture-of-Experts

W Zheng, L Wang, D Peng, H Xu, Y Li, H Zhu, T Fu, H Yao

EMNLP 2025 Findings
2025

EchoViT: Self-Supervised Contrastive Learning for Cardiac MR Sequence Classification

Y Wang, H Jung, D Peng, Y Dai, J Wu, H Guan, Y Kato, et al.

MICCAI 2025 Workshop
2025

Artificial Intelligence-Guided Nutritional Therapy in the ICU

D Peng, T Phongpreecha, N Aghaeepour

Current Opinion in Clinical Nutrition and Metabolic Carefirst author

Projects

open a project for the architecture
UNC Chapel Hill2025Flagging high-risk clinical ordersGradient-boosted (XGBoost) anomaly prediction on 10+ engineered feature tables in BigQuery: AUC 0.87, 0.21 above an LSTM baseline, with SHAP reason codes for every flag.
Nature Geneticsunder reviewSpaGenBench, a spatially variable gene atlasA benchmark of 20 methods for detecting spatially variable genes on 662 human slides across 18+ tissue types, and a cross-tissue atlas of those genes.arXivMICCAI 2025 Workshop2025EchoViT, cardiac MR sequence classificationSelf-supervised contrastive learning adapts vision transformers to cardiac MR. It beats supervised training and carries over to external MR datasets.arXiv

Experience

2023 to now

Stanford Universitycurrent

Graduate Research Assistant, Stanford, CA
Sep 2026 – Present

Building an agent that reads 3D medical scans, and the data pipelines behind it.

  • An agentic diagnostic workflow for 3D medical imaging: a Qwen2.5-7B planner orchestrates multi-step tool calls over MCP for frame selection, segmentation, quantitative measurement and diagnostic reasoning.
  • Reasoning trajectories optimized with reinforcement learning (GRPO) on 30K samples: 16.4 points above Gemini 3.8 Flash (via Vertex AI) in VQA balanced accuracy (p < 0.05, paired bootstrap). First-author ICLR 2027 submission.
  • PySpark ETL on UK Biobank (300K participants) that joins 3M medical images with clinical notes, with 15 data-validation checks and augmentation pipelines, saving 3 hours per run.
Qwen2.5-7BGRPOMCPVertex AIPySpark

Takeoff41

Machine Learning Intern, San Francisco, CA
Nov 2025 – May 2026

Deployed an agentic AI reporting system for clinical operations on GCP, taking a run from about 3 hours to under 2 minutes.

  • LangGraph orchestration with async execution, shared state, retrieval and self-reflection loops, and human-in-the-loop review: end-to-end runs from about 3 hours to under 2 minutes.
  • Hybrid RAG retrieval: BM25 plus embedding search in Elasticsearch, with LLM-generated chunk summaries, took Recall@5 from 75.1% to 91.2% on a 10K-query evaluation set.
  • Node- and tool-level tracing and evaluation in LangSmith across 100K simulated queries, tracking latency, tokens, cost and answer quality per agent trajectory, cut inference cost by about 30% with no drop in quality.
  • Inside the vLLM inference engine, KV-cache management and scheduler improvements cut P95 latency 3× while sustaining 5.3K tokens a second on production workloads.
  • A reproducible MLOps pipeline on W&B, Docker and GCP for dataset and model versioning, experiment tracking, automated evaluation gates and production rollback.
LangGraphvLLMElasticsearchLangSmithGCPW&B

Stanford Medicine

Research Intern, remote
Sep 2025 – Aug 2026

First author of SycoEval-EM, an open-source multi-agent benchmark of how LLMs hold up when patients push back in emergency care.

  • A containerized benchmark with patient, physician and evaluator agents over MCP, run across 19 LLMs and 1,425 encounters. Failure-log analysis and prompt engineering raised tool-calling success by 20%.
  • An LLM-as-judge pipeline that agrees with blinded ratings from two physicians at Cohen's κ = 0.96, and keeps 99.4% leave-one-judge-out concordance in sensitivity analysis.
  • Mixed-effects regression showed model identity explained 64% of the variance in safety risk, which informs guardrails and pre-deployment stress tests. Under review at npj Digital Medicine.
Multi-agentMCPLLM-as-judgeMixed-effects modelsDocker

Bandwidth

Software Engineer Co-op
Aug 2025 – Nov 2025

Built PROwl, an event-driven AI code-review agent, and rolled it out across 3 engineering teams.

  • GitHub webhooks trigger the agent on AWS EKS (Kubernetes), which took median time to first review from 6 hours to under 10 minutes.
  • A hybrid knowledge-graph and embedding index, built with LlamaIndex entity and relation extraction and stored in PostgreSQL, over 10 API manuals and 5 repos in S3, grounds feedback in client-specific context.
  • SQL analysis of reviewer accept and reject signals on PR events drove prompt iteration, raising accepted agent comments from 27% to 55%.
  • CI/CD on GitHub Actions with automated test and 97% coverage gates before every agent release.
  • Led weekly technical reviews with 8 engineers to gather workflow and integration requirements, using adoption and efficiency metrics to guide the wider rollout.
AWS EKSKubernetesLlamaIndexPostgreSQLGitHub Actions

UNC Chapel Hill

Student Researcher, Chapel Hill, NC
Aug 2023 – May 2025

Multimodal clinical trial prediction, high-risk order detection, and faster model training.

  • A multimodal mixture-of-experts transformer in PyTorch Lightning for clinical trial outcome prediction, fusing text and drug formulations, state of the art on phases I, II and III. Co-author at EMNLP 2025 Findings.
  • Gradient-boosted (XGBoost) anomaly prediction on 10+ engineered feature tables in BigQuery: AUC 0.87, 0.21 above an LSTM baseline, with SHAP reason codes that flag high-risk clinical orders.
  • Multi-GPU training with PyTorch DDP and mixed precision, from 10 hours to 2.
PyTorch LightningMixture of expertsXGBoostBigQueryDDP

Education and honors

M.S., Biomedical Data Science (AI/ML), Stanford University2026 – 2028
B.S., Computer Science and Statistics & Analytics, UNC Chapel Hill2022 – 2026
Phi Beta Kappa, UNC Chapel Hillhonor
Honors Carolina, UNC Chapel Hillhonor
SURF Fellow, UNC Chapel Hill2024

Stack

45 tools, 6 areas

Languages

5

From research code to production services.

PythonJavaTypeScriptSQLR

ML and training

10

Training, fine-tuning and scaling models.

PyTorchPyTorch LightningHugging FaceXGBoostSHAPDDPPEFT (LoRA)RL fine-tuning (GRPO)TensorFlowDeepSpeed

Agents

8

Agents, their tools, and the evals that keep them honest.

LangGraphLangChainLangSmithMCPTool and function callingAgent orchestrationMulti-agent systemsLLM-as-judge

Retrieval and inference

5

Finding the right context, and serving models fast.

vLLMRAGLlamaIndexElasticsearchVector search

Data

8

From raw records to training-ready data.

BigQueryPostgreSQLPySparkpandasNumPySciPyscikit-learnmatplotlib

Cloud and MLOps

9

Shipping it, and keeping it running.

GCPVertex AIAWS (EKS, S3, Bedrock)DockerKubernetesFastAPIW&BGitHub ActionsLinux

Writing

1 post, notes on models and training

Working on medical AI, LLM evaluation or agents? Let's talk.

Email is the fastest way to reach me. I'm open to ML engineering and research roles, and to collaborations.

LinkedInGitHub