AI Scientist (Model Building & Training)

Eli Lilly and Company; South San Francisco (CA); Hybrid; USD 168,000 - 268,000; Full time

Benefits offered by this job

Company bonus

401(k) plan

Health benefits

Vacation benefits

Job summary

Eli Lilly and Company is seeking an Advisor – AI Scientist to design and evaluate foundation models across chemistry and biology. You will work at the intersection of ML, chemistry, biology, and physics to translate AI advances into drug discovery breakthroughs.

The role emphasizes rigorous evaluation, collaboration with researchers, and impactful scientific validation, with a hybrid work model in Silicon Valley.

Qualifications

• PhD in a relevant quantitative field with post-PhD research experience.
• Strong ML research track record with generative/predictive models.
• Proficiency in Python and ML frameworks (PyTorch or JAX).

Responsibilities

• Design, train, and evaluate foundation models for chemistry and biology.
• Collaborate with scientists and engineers to apply AI to drug discovery.
• Develop robust evaluation strategies linking model performance to experiments.

Skills

Genomics

Computational Chemistry

Foundation Models

Generative Models

Predictive Models

GPU Training

Collaborative Research

Education

PhD in ML/CS/Computational Biology/Related Field

2+ years post-PhD research experience

Tools

Python

PyTorch

JAX

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.

What You’ll Be Doing As an Advisor – AI Scientist, you will design, train, and evaluate foundation models that advance scientific discovery across chemistry and biology. Working at the intersection of machine learning, chemistry, biology, and physics, you will conduct fundamental research to develop AI approaches that deepen our understanding of molecular and biological systems. Using Lilly’s proprietary experimental data, you will build and validate generative and predictive models that help transform scientific insights into drug discovery breakthroughs.

How You’ll Succeed

• Advance the state of the art in AI for drug discovery by designing and developing generative and predictive models for molecular, chemical, and biological systems.
• Translate machine learning into scientific impact across challenges such as molecular design, target identification, genomics, and structure-based discovery.
• Design rigorous evaluation strategies that connect model performance to meaningful scientific and experimental outcomes.
• Partner closely with researchers, engineers, and domain experts to accelerate the application of AI in discovery programs.
• Drive research from concept to impact, balancing scientific innovation with practical application.

What You Should Bring

• Deep expertise in computational chemistry/biology, genomics, or a related scientific field.
• Recognized expertise in ML research, with significant contributions to generative, predictive, or foundation models for scientific applications.
• Shown impact through publications at leading research venues, patents, open-source contributions, or other notable scientific achievements.
• Advanced proficiency in Python and modern machine learning frameworks (e.g., PyTorch or JAX), with the ability to independently design, implement, train, and evaluate AI models.
• Experience leading complex research initiatives from hypothesis through scientific validation and impact.
• Demonstrated ability to collaborate across scientific and technical disciplines and communicate complex findings to diverse audiences.
• Experience designing, training, and evaluating large neural networks on GPU infrastructure.
• Prior experience applying machine learning to chemical, biological, or other scientific data.

Your Basic Qualifications

• PhD in Machine Learning, Computer Science, Computational Chemistry, Computational Biology, Bioinformatics, Physics, Statistics, or a closely related quantitative field.
• 2 years of relevant research experience beyond the PhD, in industry or in a postdoctoral research position.

Location & Work Flexibility This role is based at our Silicon Valley Hub. We offer a flexible hybrid work model, with three days onsite and two days working remotely each week , supporting both collaboration and work‑life balance.

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

$168,000 – $268,400

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.

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