Scientific Lead, Applied Intelligence for Discovery

Lilly is developing an AI foundation to transform drug discovery research. The Applied Intelligence for Discovery (AI4D) team seeks a leader to design and deploy core AI systems including retrieval-augmented generation, text-to-SQL interfaces, and agentic workflows that connect scientists to petabyte-scale data.

Key Responsibilities

• Build and optimize RAG pipelines for internal scientific documents, lab notebooks, and study reports
• Create hybrid retrieval systems combining vector search with metadata and ontology-aware filtering
• Develop text-to-SQL systems enabling natural language queries over genomic and proteomics databases
• Design schema documentation and semantic annotations bridging scientist workflows to data storage
• Implement multi-step reasoning approaches to improve accuracy on complex queries
• Engineer agentic workflows automating database queries, bioinformatics tools, and analysis visualization
• Evaluate orchestration frameworks (LangGraph, CrewAI) for scientific applications
• Build evaluation frameworks measuring accuracy, reliability, and scientific validity

Required Qualifications

• PhD in Computer Science/Data Science with 0-3+ years experience OR MS with 5+ years experience

Preferred Qualifications

• Experience with RAG systems, text-to-SQL, agentic workflows, or fine-tuning
• Python proficiency with production-grade systems
• Familiarity with embeddings, vector databases, orchestration frameworks
• LLM evaluation framework design experience
• AWS, Docker, CI/CD familiarity
• Biomedical/pharma/biotech environment experience
• Biomedical ontologies experience (Gene Ontology, MeSH, ChEBI)