Eli Lilly

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.

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 is a newly established function within this organization. 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.

Position Summary:

We are seeking a forward-thinking AI researcher skilled in developing Large Language Models (LLMs), autonomous AI agents, and intelligent lab automation at the intersection of AI and drug discovery. As part of our Agentic Lab initiative, you will help define the DMTA (Design-Make-Test-Analyze) cycle by embedding Agentic AI into with modern wet lab automation workflow. Your work will enable AI systems to autonomously plan, execute, and optimize complex chemistry and biology experiments, accelerating discovery by freeing scientists to focus on the creative, high-impact aspects of discovery.

At its core, Agentic Lab is building a next-generation platform that embeds Agentic AI—built on frontier LLM technologies—directly into wet-lab operations. This platform empowers intelligent systems to plan, reason, and act in the real world, accelerating scientific workflows and learning from each experiment to continuously optimize protocols.

Key Responsibilities:

Laboratory Workflow Automation:

• Create and maintain robust software codebase for laboratory automation tasks, including sample acquisition, and data analytics.
• Integrate automation solutions with commercial laboratory equipment and vendor software stack (e.g., Protocol scripting with Hamilton, OpenTrons, Tecan, Chemspeed).Experience in integrating instruments with APIs or serial ports with laboratory information management systems (LIMS) and databases for accelerated and robust data querying Work proactively with Tech@Lilly to capture and contextualize scientific data

AI Agent & Framework Development:

• Design and enhance enterprise-scale agentic systems that leverage LLMs for complex scientific decision-making, building on existing platforms
• Innovate methods to apply transformer-based models and reinforcement learning techniques to automate chemistry and biology lab operations.
• Train, fine-tune, and deploy Agentic systems tailored to computational biology and cheminformatics.
• Advance the optimization and efficiency of LLM-based models through innovative model quantization and inference-time computation.

Cross-functional Collaboration:

• Collaborate closely with chemists, biologists, computational scientists, and engineers across Lilly's molecule discovery, Tech@Lilly functions, operation lead as well as external vendors.

Basic Qualifications:

• Ph.D. in Computer Science, Computational Chemistry, Computational Biology, Bioinformatics, or a related field with 2-3 years of working experience.
• Demonstrated expertise in agent-based modeling and integration of chemistry/biology software into autonomous workflows.
• Experience in LLM engineering, including prompt engineering, tokenization, and chain-of-thought methodologies.
• Strong proficiency in Python programming, including data science libraries (NumPy stack, PyTorch, Ollama).

Additional Skills/Preferences:

• Excellent communication and teamwork skills, capable of interacting effectively with wet-lab scientists.
• Experience developing AI-driven laboratory automation solutions, preferably with familiarity in automated synthesis and liquid handling, dispensing system.
• Experience in scheduling and orchestration with SiLA, Airflow
• Experience working with commercial automation equipment and robotics, including cobots.
• Familiarity with synthetic biology workflows and analytical pipelines.
• Expertise with cloud computing platforms such as AWS or Azure.
• Track record of leveraging academic insights and recent scientific publications in deep learning and automation research.

At Lilly, we unite caring with discovery to make life better for people around the world. If you are passionate about transforming laboratory operations through AI and automation, join us in shaping the future of medicine discovery at Lilly’s Agentic Labs.

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 does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability or any other legally protected status.

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