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.

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

Position Summary
 

We are rebuilding the Design-Make-Test-Analyze (DMTA) cycle from the ground up—infusing scientific automation with foundation models, multi-agent systems, and robotics to make scientific discovery intelligent, autonomous, and fast.
 

As an Applied Research Scientist, you will push the state of the art in AI (LLMs, graph ML, reinforcement learning) and translate those advances into working systems that accelerate chemistry and biology at scale. You will prototype novel algorithms, productionize successful ideas, and partner closely with scientists, engineers, and automation teams to reshape how we discover medicines.

Research & Innovation

Lead cutting-edge research on LLMs, Transformer architectures, graph/sequence hybrid models, and agentic RL for molecular design, assay automation.

Integrate LLM reasoning with domain tools (e.g., RDKit, molecular graph ML, ELN/LIMS APIs) to build composite agents that plan, simulate, and execute DMTA tasks.

Rapidly explore new techniques, run ablation studies, and benchmark against internal and external baselines.

Solution Development

Design, implement, and deploy robust ML pipelines that handle  and analyze multi-omics data

Partner with program and product leads to turn scientific opportunities into well-scoped research bets, MVP prototypes, and production roll-outs.

External Engagement

Represent molecule research 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

Measurable reduction in DMTA turnaround through autonomous planning and execution

Tools you build become indispensable to chemists, biologists, and automation engineers

Basic Qualifications

PhD in Bioinformatics, Cheminformatics, Computer Science, or a related technical field.

Hands-on expe