Local RAG for medical guidelines

1. 1Ingest

   PDF parsing and chunking with document and page metadata, plus OCR of figures.

2. 2Route

   Dense retrieval with routing per guideline, and a hard filter when the question names a document.

3. 3Rerank

   A cross-encoder reorders a deep pool of 20 passages. This was the single biggest gain.

4. 4Answer

   Targeted prompting; every answer cites the guideline and the page it comes from.

44 clinical guidelines in nephrology and internal medicine, 3,236 PDF pages. Full run of 99 questions in 3.01 hours, about 109 s per question including grading.

• NVIDIA Jetson AGX Orin
• qwen3:32b via Ollama
• bge-m3 embeddings
• PostgreSQL + pgvector
• Cross-encoder reranker
• Web front end

LLM-as-judge across six configurations, inter-judge agreement checks, grounding analysis (verbatim 6-gram coverage), expert clinical review, ablations and cost/latency measurements.

What it did not reach. The 95% accuracy target was not reached. Before any clinical use the thesis calls for better grounding in the cited evidence, an independent clinical benchmark and a new expert review.

Supervisor Vanni Galli · Host company Alwicom SA · 25 August 2026

• Citation link prediction on DBLP

  LightGBM, XGBoost, Random Forest, MLP and a Graph Convolutional Network, with feature engineering, a data-leakage audit, SHAP, uncertainty estimates and stratified edge subsampling.

  • Graph ML
  • GCN
  • SHAP

• CYP2C19 inhibition prediction

  Cheminformatics with RDKit: ECFP4 fingerprints, physico-chemical descriptors, SHAP, applicability domain and Williams plot.

  • RDKit
  • Cheminformatics

• Lipophilicity prediction

  RDKit descriptors, Spearman correlation matrices, permutation feature importance and forward feature selection.

  • Regression
  • Feature selection

• Autonomous robot navigation

  A DJI RoboMaster EP navigating on its own in a CoppeliaSim simulation.

  • Robotics
  • Simulation

• Penetration testing lab

  Metasploit, antivirus evasion and obfuscation techniques, in a controlled teaching environment.

  • Security