Director, AI/ML - Generative Foundation Models for Biotherapeutics

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.

At Lilly, we unite caring with discovery to make life better for people around the world. For more than 25 years, Lilly's Biotechnology Discovery Research (BioTDR) organization has advanced novel antibody and peptide therapeutics from concept through clinical development to market in areas of high unmet medical need.

Our protein AI/ML models currently helps design, select, and optimize antibody and peptide leads, with measurable impact on portfolio programs. We are now expanding the computational team to build a generative design platform linking de novo design directly to the biology we want, delivering molecules with better activity, safety, and manufacturability. Targets are chosen by therapeutic need, including difficult classes like GPCRs, and validated designs are advanced directly into Lilly's portfolio.

This role is based at the Lilly Biotechnology Center in San Diego, where computational science, protein engineering, automation, and biology sit in one building. Designs are made and tested here on a fast cycle, and every result, including the negatives, feeds closed-loop learning. You'll train at scale from day one. The program has dedicated capacity on LillyPod, our wholly owned 1,016-GPU NVIDIA Blackwell Ultra SuperPOD. Compute isn't the constraint here, talent is.

Primary Responsibilities

Our Generative Design platform has three pillars: Generative Foundation Models , Generative Protein Design & Optimization , and Active Learning & Design Validation . The director of Generative Foundation Models will develop protein and antibody foundation models and validate their performance against experimental outcomes, not just published baselines. You will be accountable for the program's generative model families end to end, across architecture choice, training strategy, and validation, and co-define the program's technical agenda with leadership. You will lead a team of AI researchers and ML infrastructure engineers while staying hands-on and giving direct technical guidance on every model in your workstream. This is an opportunity for a scientific leader who wants to build technologies that directly shape therapeutic molecule discovery.

- Lead generative AI and protein foundation model development, driving state-of-the-art machine learning approaches for representation learning, generative protein design, sequence-structure-function modeling, and multimodal biological learning.
- Set training strategy, developing the pre-training and fine-tuning approach for your models across architecture choice, model family, training curriculum, and evaluation.
- Devise training infrastructure, designing and steering the training lifecycle and scaling approach against LillyPod capacity, accountable for reproducibility, checkpointing, and throughput, with the ML infrastructure engineers on your team.
- Direct confidence and calibration work, treating it as a first-class research objective, accountable for reducing the gap between model-ranked and oracle-backed design performance on held-out data.
- Drive model improvement, resolving underperforming models to root cause across architecture, data, and execution, and making timely decisions to retrain, pivot, or discontinue.
- Leverage multimodal and proprietary biological data, creating differentiated learning advantages by bringing proprietary sequence, structure, binding, functional, developability, and other biological measurements into model development.
- Lead a high-performing team and provide scientific and technical leadership, recruiting and developing AI researchers and engineers on your team and providing sustained technical mentorship. Guide model architecture choices, experimental design, technical prioritization, and research direction while remaining sufficiently close to the science and technology to challenge assumptions and identify new opportunities.
- Evaluate and incorporate external innovation, staying current with rapidly evolving advances in foundation models, generative AI, protein design, structural modeling, and related technologies. Evaluate external methods and collaborations and determine when to build, adapt, or partner.
- Communicate scientific strategy and impact, presenting technical progress, experimental validation, key learnings, and strategic recommendations to scientific leadership and broader R&D stakeholders. Contribute to publications, external collaborations, and scientific presentations where appropriate.

Basic Requirements

- Ph.D. in computer science, mathematics, physics, computational biology, or a related quantitative field, with 3+ years of relevant research experience following the Ph.D. (or an M.S. with 6+ years), including experience as technical lead of a multi-person modeling effort.
- First-author or equivalently attributable contribution to a generative or predictive model for protein structure, sequence design, or molecular interaction, plus a track record of carrying projects end to end.
- Experience training deep learning models on multi-GPU infrastructure; strong Python and PyTorch.

Additional Preferences

- Depth in equivariant architectures, diffusion or flow matching on structure, and graph transformers.
- Experience with inverse folding, side-chain packing, all-atom generation, or conformational ensembles.
- Work on uncertainty quantification or confidence prediction validated against experimental outcomes, not only against held-out structures.
- Contribution to a de novo binder or antibody design effort that reached experimentally validated designs.
- Antibody or VHH experience is desired but not required.
- Experience improving model efficiency, building smaller or faster models at equal accuracy.
- Experience mentoring junior AI researchers or ML engineers.
- Experience taking a model from research prototype to a system other scientists use routinely.
- Open-source release, public benchmark, or tooling contribution the community uses.
- Ability to work productively in an interdisciplinary environment.
- Comfort with ambiguity and close collaboration with wet-lab scientists, with the communication skills to explain model behavior and limitations to non-computational colleagues.

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

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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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