Biotherapeutics AI/ML Foundation Models Advisor

100 Eli Lilly and Company; San Diego (CA); On-site; USD 168,000 - 268,000; Full time

Job summary

Lilly seeks an Advisor - AI/ML Generative Foundation Models for Biotherapeutics at the San Diego Biotechnology Center. The role advances de novo design platforms integrating AI/ML, protein engineering, automation, and structural biology to generate and optimize novel biotherapeutics.

Responsibilities include developing model architectures, scaling training on LillyPod, curating data with SMEs, and communicating results to both computational and wet-lab teams.

Qualifications

• PhD in computer science, mathematics, physics, computational biology, or a related quantitative field, or an MS with 3+ years of relevant research experience in machine learning, computational biology, or a related domain.
• Fluency in Python and PyTorch, with hands-on experience training deep learning models on GPUs, including multi-node or distributed runs.

Responsibilities

• Develop model architectures for protein design across sequence-structure generation, epitope conditioning, and confidence prediction.
• Contribute novel technical ideas and research directions for foundation models and generative AI in biotherapeutics.
• Run training at scale on LillyPod, tracking configurations, checkpoints, and results for reproducibility.
• Curate training data including processing and interpretation of structure, sequence, and assay data with SME collaboration.
• Evaluate and calibrate model outputs by connecting to experimental results.
• Diagnose model failures and improve architectures, data strategies, or training approaches.
• Partner with protein scientists and automation colleagues to benchmark performance.
• Communicate results to computational and wet-lab audiences and publish at conferences.

Skills

Python

PyTorch

Distributed training

Education

PhD or MS with relevant ML research

Tools

Geometric deep learning methods

Graph transformers

Diffusion/flow-matching

Job description

Lilly seeks an Advisor - AI/ML Generative Foundation Models for Biotherapeutics at the San Diego Biotechnology Center. The role advances de novo design platforms integrating AI/ML, protein engineering, automation, and structural biology to generate and optimize novel biotherapeutics.

Responsibilities include developing model architectures, scaling training on LillyPod, curating data with SMEs, and communicating results to both computational and wet-lab teams.