Sr. Principal AI Software Engineer

Lilly • Indianapolis, IN

50d

About The Position

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world. We are seeking an exceptional Senior Principal Engineer to lead the development and deployment of transformative AI solutions across Eli Lilly's global enterprise. In this role, you will architect autonomous AI systems that enhance safety, quality, and operational efficiency across all business functions—from drug discovery and manufacturing to corporate operations in Legal, HR, and Finance. As the technical lead for our pharmaceutical AI initiatives, you will drive the implementation of cutting-edge agent architectures and establish AI development standards for regulated environments. You'll build and guide high-performing technical teams while shaping how artificial intelligence revolutionizes pharmaceutical innovation and patient care. This is a unique opportunity to work at the convergence of advanced AI technology and life sciences, directly impacting how medicines are discovered, developed, and delivered to patients worldwide. The ideal candidate brings deep expertise in AI system design, a proven track record of enterprise-scale implementations, and the vision to transform one of the world's most critical industries through intelligent automation.

Requirements

• Bachelor', Masters or PhD degree in Computer Science, Engineering, or related field
• 8+ years of software engineering experience
• 2+ years architecting and deploying production AI systems
• Proven success delivering AI solutions in regulated or enterprise wide environments

Nice To Haves

• AI Development Proficiency: Demonstrated experience building production applications with AI-powered development tools (GitHub Copilot, Cursor, Claude, ChatGPT, Grok)
• Agent Architecture: Hands-on experience designing and deploying autonomous agent systems, including orchestration patterns, tool selection, and failure handling
• System Integration: Expertise with Model Context Protocols, API integrations, and building extensible AI architectures
• Modern AI Stack: Proficiency in Python, LangChain/LangGraph, vector databases (Pinecone, Weaviate, ChromaDB), embedding models, and advanced prompt engineering
• Experience leading technical teams through AI transformation initiatives
• Ability to communicate complex technical concepts to diverse audiences—from engineering deep-dives to executive strategy sessions
• Track record of mentoring engineers and fostering innovation within teams
• Strategic mindset balancing technical excellence with measurable business outcomes
• End-to-end MLOps implementation (model versioning, monitoring, CI/CD for ML)
• Cloud AI platform expertise (AWS SageMaker, Azure ML, GCP Vertex AI)
• Container orchestration (Kubernetes) and scalable deployment architectures
• AI system observability, performance tuning, and cost optimization

Responsibilities

• Architect Production AI Systems: Design and ship scalable autonomous agent platforms that solve real problems—think multi-agent orchestration, not demos. Own the full stack from LLM integration to production deployment.
• Build on Lilly Cortex: Leverage Lilly's enterprise AI platform to architect sophisticated agentic systems using Model Context Protocol (MCP) for tool integration, Agent-to-Agent (A2A) communication for multi-agent coordination, and dynamic UI frameworks that wrap intelligent experiences around agent workflows. Ship context-aware applications that feel native, not bolted-on.
• Ship Fast with AI Tooling: Be a power user of AI-assisted development. Use AI development tools like GitHub Copilot, and LLM-driven workflows to 10x your output. Set the standard for how modern engineering teams build with AI.
• Define the AI Platform Strategy: Own the technical vision for Studio as the company's AI business platform. Make architectural decisions that scale from prototype to enterprise.
• Level Up the Team: Mentor engineers on modern AI/ML practices, prompt engineering, and agentic patterns. Build a high-trust, high-velocity culture where shipping matters.
• Establish Engineering Standards: Create the playbook—CI/CD for AI systems, evaluation frameworks, observability for agent workflows, and compliance patterns for regulated environments. Balance innovation with reliability.
• Drive Product Impact: Partner with product, operations, and business teams to identify high-leverage AI opportunities. Ship features that move metrics, not science projects.
• Stay on the Edge: Keep the team at the forefront—evaluate new models, test emerging frameworks, and bring the latest research into production before it's mainstream.

Benefits

• Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).
• Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Number of Employees: 5,001-10,000 employees