Sr. Principal or Engineering Advisor - Agentic Lab Automation Integration

Eli Lilly and Company; South San Francisco (CA); On-site; USD 87,000 - 222,200; Full time

Benefits offered by this job

401(k) and pension

Health, dental, vision benefits

Flexible spending accounts

Employee assistance program

Job summary

Eli Lilly and Company is seeking an experienced engineer to enhance laboratory automation using cutting-edge AI and cloud technologies. The role involves building integrations for systems that accelerate molecule discovery and requires a PhD or equivalent experience in relevant fields. Key responsibilities include collaborating with automation engineers, optimizing workflows, and representing the company at research events. The position offers a competitive salary range of $87,000 - $222,200 and comprehensive benefits including health insurance and retirement plans.

Qualifications

• PhD (or MS + 2 yrs / BS + 5 yrs) in a relevant field with wet-lab automation experience.
• Strong experience with laboratory automation systems and direct AI integration.
• Ability to build production-level Python applications for lab systems.

Responsibilities

• Engineer integrations between AI and lab systems for efficient molecule discovery.
• Collaborate with scientists to transition prototypes into lab operations.
• Publish and represent AI developments in broader research communities.

Skills

Wet-lab automation experience

Laboratory automation systems

Containerization (Docker)

Kubernetes orchestration

Python application development

Education

PhD in Chemical/Mechanical Engineering, Robotics, or related discipline

Tools

Docker

Kubernetes

Redis

FastAPI

Job description

At Lilly, we unite caring with discovery to make life better for people around the world. We are 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.

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 will 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

• PhD (or MS + 2 yrs / BS + 5 yrs equivalent experience) in Chemical / Mechanical Engineering, Robotics, Computer Engineering, or related discipline with demonstrated wet‑lab automation experience.
• Demonstrated experience with laboratory automation systems and LIMS engineering.
• Direct experience integrating software control and/or AI systems with lab automation platforms (liquid handlers, analytical instruments, robotic workflows).
• Strong experience with containerization (Docker) and Kubernetes‑based orchestration in production environments.
• Experience building scalable and production‑level python applications using tools like Redis, FastAPI, flask/streamlit, pytest, etc. (GitHub portfolio a plus).

Preferred Qualifications

• Experience with LLM post‑training, fine‑tuning, or RLHF.
• Direct experience integrating AI or algorithmic decision systems with laboratory automation.
• 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).

EEO Statement

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Compensation and Benefits

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is $87,000 - $222,200.

Full‑time equivalent employees will also be eligible for a company bonus (depending, in part, on company and individual performance). In addition, 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). Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.