Agentic Automation Lead - Frontier AI

Biopharma Careers; South San Francisco (CA); On-site; USD 194,000 - 339,000; Full time

Job summary

Lilly is seeking an experienced Automation AI Scientist to design agentic systems that plan, execute, and learn from physical experiments in a Silicon Valley AI lab partnership with NVIDIA. You own the decision layer, orchestrate experiments, and partner with chemists, biologists, and automation engineers to accelerate discovery.

You will lead a small team of scientist-engineers, prototype against real instruments, productionize successful approaches, and ensure reliability and adoption across

Qualifications

• PhD or MS/BS with substantial experience in AI and decision systems.
• Experience building AI or algorithmic decision systems in production.
• At least one year of direct people management experience.

Responsibilities

• Design and build multi-agent systems with robust orchestration and tool integration for lab workflows.
• Translate high-level scientific intent to instrument control across automation platforms.
• Implement active learning and Bayesian optimization for autonomous experiments.
• Deploy and maintain containerized services using Docker/Kubernetes with CI/CD.
• Lead and grow a small team, setting direction and conducting code reviews.

Skills

AI/algorithmic decision systems

People management

Multi-agent systems

Lab automation integration

Education

PhD in CS or related field

MS + 3 yrs or BS + 6 yrs equivalent

Tools

Docker

Kubernetes

Hamilton automation

Tecan automation

Opentrons

LC/MS/ NMR/ HPLC instrumentation

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.

Where AI Meets Medicine: Build the Future of Drug Discovery in the Heart of Silicon Valley!

Making medicine that’s never been made means doing what’s never been done. If you’re an engineer, scientist, or builder who thrives on problems no one has solved before, this is your invitation, we want you on the team. We are ready to challenge the status quo and push medicine forward, all in the name of health. Are you up for the challenge? If so, join us!

About the Lilly and NVIDIA Partnership

Lilly and NVIDIA are launching a new AI co-innovation lab in the heart of Silicon Valley, an up-to-$1 billion, multi-year commitment to solve drug discovery’s toughest challenges. The lab brings Lilly scientists, technologists, chemists and biologists together with NVIDIA engineers under one roof. Together, we are building purpose-built foundation and frontier AI models trained on Lilly data at scale, tightening the feedback loop between automated wet labs and computational dry labs, designing the next generation of medicines for millions of patients across the globe.

Position Summary

We are looking for an experienced Automation AI Scientist to design and build the agentic systems that plan, execute, and learn from physical experiments. You will own the decision layer of the closed-loop lab: the agents that reason over experimental context, select the next experiment, dispatch it to robotic and analytical platforms, interpret the readout, and update their own strategy, with scientists in the loop at the points where judgment matters.

This is an on-site hands-on scientific engineering role with technical leadership scope. You will prototype rapidly against real instruments and real chemistry, productionize what works, and partner with chemists, biologists, automation engineers, and our NVIDIA counterparts to compress Design-Make-Test-Analyze cycle time from weeks to days. You will also lead a small team of scientist-engineers, set the technical direction for the agentic automation platform, and be accountable for it as a product that other teams depend on, not a collection of prototypes.

Key Responsibilities

Agentic System Design

• Design and build multi-agent systems with robust orchestration, state management, error recovery, and tool integration for laboratory workflows
• Build the translation layer between high-level scientific intent and low-level instrument control across automation platforms (Hamilton, Tecan, Opentrons) and analytical instruments (LC/MS, NMR, HPLC)

Closed-Loop Science

• Implement active learning, Bayesian optimization, and reinforcement-learning approaches for autonomous experiment selection under real-world cost and throughput constraints
• Instrument the loop end-to-end so every experiment produces model-ready data in ELN/LIMS and downstream training corpora

Solution Deployment

• Partner with automation engineers and scientists to transition prototypes into reliable, monitored lab operations
• Deploy and maintain containerized services using Docker and Kubernetes with GitOps and CI/CD practices

Technical Leadership & Platform Ownership

• Lead and grow a small team of scientist-engineers: set technical direction, run design and code review, and hold the bar on engineering quality
• Own the agentic automation platform end to end: roadmap, architecture, reliability, adoption, and deprecation decisions and be accountable for the outcomes it delivers to scientists
• Translate scientific and business priorities into a sequenced technical plan, and communicate progress, trade-offs, and risk to senior R&D leadership

Collaboration & External Engagement

• Work directly with NVIDIA researchers and engineers and with partner teams across the AI@Lilly community
• Evaluate external vendors, open-source projects, and academic collaborations for strategic fit

Basic Qualifications

• PhD (or MS + 3 yrs / BS + 6 yrs equivalent experience) in Computer Science, Chemical Engineering, Robotics, Chemistry, Computational Biology, or a related discipline
• 5+ years of applied experience building AI or algorithmic decision systems, including production LLM agent or multi-agent systems
• At least one year of direct people management experience

Preferred Qualifications

• Demonstrated experience integrating software control and/or AI systems with laboratory automation platforms (liquid handlers, analytical instruments, robotic workflows)
• Track record of owning a platform or product end to end: defining the roadmap, shipping it to real internal or external users, operating it in production, and iterating based on adoption and feedback
• Track record with self-driving labs, autonomous experimentation, or high-throughput experimentation (HTE) workflows
• Working knowledge of LIMS/ELN engineering and scientific data models in a regulated or GxP-adjacent environment
• Experience hiring and building a team from an early stage in a startup, skunkworks, or newly formed function

What Success Looks Like

Autonomous agents reliably execute multi-step experiments on physical laboratory instruments without babysitting

Measurable reduction in DMTA turnaround attributable to autonomous planning and execution

The team you lead grows in capability and autonomy, with people you mentor taking ownership of major platform components

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form ( https://careers.lilly.com/us/en/workplace-accommodation ) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

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.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

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

$193,500 - $338,800

Full-time equivalent employees also will 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.