Agentic automation, Frontier AI

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 150,000 - 230,000; Full time

Job summary

Lilly in Indianapolis is building Frontier AI to accelerate molecule discovery by integrating agentic AI with lab automation. As an Agent Automation Engineer, you will connect experimental readouts to robotic platforms, develop practical integrations, and prototype workflows that reason over data to surface insights for scientists.

The role requires hands-on coding in Python, experience with Docker/Kubernetes, and collaboration with chemists, biology, and automation engineers to deploy

Qualifications

• MS + 1 yr or BS + 3 yrs equivalent experience in Computer Science, Mathematics, Engineering, or related discipline with demonstrated wet-lab automation experience
• Demonstrated experience with laboratory automation systems and LIMS/ELN integration
• Direct experience integrating software control and/or AI systems with lab automation platforms (e.g., liquid handlers, analytical instruments, robotic workflows, high-throughput experimentation, flow chemistry)
• Experience with containerization (Docker) and Kubernetes-based orchestration in cloud or production environments
• Experience building scalable and production-level Python applications using tools like LangChain/LangGraph, AutoGen, OpenTelemetry, etc. (GitHub portfolio a plus)

Responsibilities

• Transition prototypes into reliable, scalable lab operations with automation engineers
• Deploy containerized services using Docker and Kubernetes with CI/CD
• Integrate Argo on Kubernetes with lab control systems
• Build multi-agent systems with robust orchestration and memory management
• Design agent architectures for lab automation platforms like Hamilton, Tecan, Opentrons
• Represent Frontier AI in external AI community and assess partnerships

Skills

Laboratory automation experience

Python development

Docker and Kubernetes

LangChain/LangGraph

CI/CD and GitOps

Education

MS in Computer Science or related

BS in CS/Engineering or related

Tools

Docker

Kubernetes

Hamilton/Tecan/Opentrons integration

LIMS/ELN integration tooling

OpenTelemetry

Job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us. 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 45,000 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.

Organization Overview

Lilly Small Molecule Discovery is an organization purpose-built to create molecules that make life better for people. We focus on using cutting edge science to unlock new approaches that can treat people suffering from diseases with poor treatment options. We continually challenge ourselves to deliver molecules that can provide breakthrough efficacy with the highest possible safety margins. We are dedicated to optimizing our mindset, technology, and processes for faster, more nimble execution. Our success is built on a culture that empowers innovative problem solving through open collaboration and individual accountability.

Discovery Technology and Platforms

Its mission is to accelerate molecule discovery by building highly optimized foundational platforms, streamlining lab operations through advanced technologies and data connectivity, and intentionally investing in novel technologies and capabilities.

Frontier AI

Frontier AI is a purpose-built team that fuses scientific agentic AI, lab automation, and unified data platforms to autonomously design, run, and refine experiments—accelerating molecule discovery.

Job Title: Agent Automation, Frontier AI

Position Summary

We are rebuilding the Design-Make-Test-Analyze (DMTA) cycle by integrating agentic AI, cloud-based orchestration, and LIMS infrastructure to connect experimental readouts with tools that accelerate laboratory science. You will engineer the connective tissue between Agentic AI and physical lab systems building practical integrations with robotic platforms, analytical instruments, and data pipelines. You'll design agent workflows that reason over experimental data, trigger automated actions, and surface insights to scientists. This is a hands-on engineering role: you'll prototype rapidly, productionize what works, and collaborate with chemists, biologists, and automation engineers to deploy intelligent systems that accelerate molecule discovery tasks.

Research & Innovation

Build multi-agent systems with robust orchestration, state management, error recovery, and tool integration Prototype and iterate rapidly on agent planning strategies, memory systems, and human-in-the-loop patterns Design agent architectures that interface with lab automation platforms (Hamilton, Tecan, Opentrons) for closed-loop experimental execution

Solution Deployment

• Partner with automation engineers and scientists to transition prototypes into reliable lab operations
• Deploy and maintain containerized services using Docker and Kubernetes with GitOps and CI/CD practices
• Integrate cloud-based orchestration frameworks such as Argo on Kubernetes with laboratory control systems

External Engagement

Represent Frontier AI in the broader AI@Lilly and external AI research community: publish, give talks, review papers, and scout emerging trends. Evaluate external vendors, open-source projects, and academic collaborations for strategic fit.

What Success Looks Like

• Autonomous agents reliably execute experiments on physical laboratory instruments
• Measurable reduction in DMTA turnaround through autonomous planning and execution
• Agents you build become indispensable to the automation engineering community
• Frontier AI platforms scale from pilot deployments to production lab environments

Basic Qualifications

• MS + 1 yr or BS + 3 yrs equivalent experience in Computer Science, Mathematics, Engineering, or related discipline with demonstrated wet-lab automation experience
• Demonstrated experience with laboratory automation systems and LIMS/ELN integration
• Direct experience integrating software control and/or AI systems with lab automation platforms (e.g., liquid handlers, analytical instruments, robotic workflows, high-throughput experimentation, flow chemistry)
• Experience with containerization (Docker) and Kubernetes-based orchestration in cloud or production environments
• Experience building scalable and production-level Python applications using tools like LangChain/LangGraph, AutoGen, OpenTelemetry, etc. (GitHub portfolio a plus)

Preferred Experience

• Experience with LLM post-training, fine-tuning, or RLHF
• Experience deploying closed-loop autonomous experimentation, where agents plan, execute, and analyze experiments on physical instruments with minimal human intervention
• Proven ability to build and maintain the translation layer between high-level planning logic and low-level instrument control
• Demonstrable research experience, evidenced by contributions to projects, and ideally through publications in relevant ML/NLP venues (e.g., NeurIPS, ICML, ICLR, ACL, EMNLP, CVPR)

Qualified applicants must be authorized to work in the United States on a full-time basis.

Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions.

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