Advisor - AI/ML Generative Foundation Models for Biotherapeutics
Eli Lilly and Company4 days ago
San Diego, CA, USASenior
Base Salary
$168k - $268k/yr
Responsibilities
- Develop, adapt, and invent model architectures for protein design, including sequence-structure generation, epitope conditioning, and confidence prediction.
- Develop novel research methods and directions for foundation models and generative AI applied to biotherapeutics.
- Run and track large-scale training and fine-tuning experiments on dedicated LillyPod GPU capacity, including distributed runs.
- Curate and interpret internal structure, sequence, and assay data with subject matter experts.
- Build evaluations connecting model outputs with experimental results and calibrate model performance.
- Diagnose model failure modes and improve architectures, data strategies, and training approaches.
- Collaborate with computational scientists, protein scientists, and automation colleagues to benchmark models.
- Present results to computational and wet-lab audiences and publish in conferences and the scientific community.
Requirements
- Ph.D. in computer science, mathematics, physics, computational biology, or a related quantitative field, or an M.S. with 3+ years of relevant research experience in machine learning, computational biology, or a related domain.
- Fluency in Python and PyTorch and hands-on experience training deep learning models on GPUs, including multi-node or distributed training.
- Experience with geometric deep learning, equivariant networks, diffusion or flow-matching methods, or graph transformers applied to structure-based generative models is preferred.
- Peer-reviewed publications or equivalent public contributions applying machine learning to molecular or biological data are preferred.
- Ability to develop and implement new deep learning methods and maintain clean, tested, reproducible research code and shared version-controlled training pipelines.
- Open-source contributions such as released code, models, benchmarks, or other widely used work are preferred.
- Experience working with noisy and negative wet-lab data and collaborating with experimental scientists is preferred.
- Experience mentoring interns or junior scientists or leading a small technical sub-project is preferred.
- Proficiency with antibody or VHH molecules is desired but not required.
- Strong written and verbal communication skills and the ability to work across computational and experimental disciplines.
Benefits
- Full-time employees may be eligible for a company bonus based partly on company and individual performance.
- Benefits may include a 401(k), pension, vacation, medical, dental, vision, prescription drug, flexible spending, life insurance, leave, well-being, fitness, employee assistance, and employee club benefits.
- The role is based at the Lilly Biotechnology Center in San Diego.
Categories
AI ResearchML Engineering
About Eli Lilly and Company
Eli Lilly and Company researches, develops, manufactures, and markets prescription medicines and biologics for patients, sold through healthcare providers, pharmacies, and payers. Core therapeutic areas include diabetes, oncology, immunology, neuroscience, and obesity. Founded in 1876 and headquartered in Indianapolis, it is a public company (NYSE: LLY) with global operations and is building a new advanced manufacturing site for gene therapy and other modalities in Lebanon, Indiana.