Machine Learning Scientist​/Sr Scientist - Antibody Property Prediction & Generative Design

Machine Learning Scientist / Sr Scientist – Antibody Property Prediction & Generative Design

Join to apply for the Machine Learning Scientist / Sr Scientist – Antibody Property Prediction & Generative Design role at Eli Lilly and Company
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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, working to discover and bring life‑changing medicines, improve disease management, and give back through philanthropy and volunteerism. We put people first and look for individuals determined to make a difference.

Lilly Tune Lab is an AI‑powered drug discovery platform that provides biotech companies with access to machine learning models trained on Lilly’s extensive proprietary pharmaceutical research data. Through federated learning, the platform allows Lilly to build models on broad, diverse datasets from across the biotech ecosystem while preserving partner data privacy and competitive advantages. This collaborative approach accelerates drug discovery by continuously improving AI models that benefit both Lilly and our partners.

• Build multi‑task learning frameworks for antibody properties (binding affinity, specificity, stability, immunogenicity, develop ability) using sequence and structural features.
• Develop and implement generative models (transformers, diffusion, evolutionary) for antibody design, including CDR optimization, humanization, and affinity maturation while preserving structural integrity.
• Integrate structural modeling and prediction (Alpha Fold, ESMFold) with generative approaches to ensure generated antibodies maintain proper folding, CDR loop conformations, and epitope recognition.
• Create models that simultaneously optimise for multiple develop ability criteria such as expression yield, solubility, viscosity, and post‑translational modifications, critical for manufacturing and formulation.
• Design antibodies with desired species cross‑reactivity profiles for preclinical development, leveraging cross‑species binding data.
• Develop models for predicting antibody‑antigen interactions, epitope mapping, and paratope design, incorporating both sequence and structural information.

• PhD in Computational Biology, Protein Engineering, Immunology, Biochemistry, or a related accredited field.
• Minimum of 2 years of experience in antibody or protein therapeutic development within the biopharmaceutical industry.
• Strong experience with protein sequence analysis and structural biology.
• Proven track record in applying machine learning to biological sequences.
• Deep understanding of antibody structure‑function relationships and immunology.

• Experience with immune repertoire sequencing and analysis.
• Publications on antibody design, protein engineering, or therapeutic development.
• Expertise in protein language models and transformer architectures.
• Knowledge of antibody manufacturing and CMC considerations.
• Experience with display technologies (phage, yeast, mammalian).
• Understanding of clinical immunogenicity and prediction methods.
• Proficiency in protein modeling tools (Rosetta, MOE, Schrodinger Bio Luminate).
• Familiarity with antibody‑drug conjugates and bispecific platforms.
• Experience with federated learning in biological applications.
• Portfolio mindset balancing innovation with practical develop ability.

This role is based at a Lilly site in Indianapolis, South San Francisco, or Boston with up to 10% travel. Relocation is provided.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce. If you require accommodation to submit a resume, please complete the accommodation request form () for further assistance. This is for individuals to request an accommodation as part of the application process; 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.

The anticipated wage for this position is $151,500 – $244,200.

Full‑time employees are eligible for a company bonus based on performance and a comprehensive benefits program, including 401(k) participation, pension, vacation, medical, dental, vision, prescription drug coverage, flexible spending accounts, life insurance, and wellness benefits.

Mid‑Senior level

Full‑time

Other

Pharmaceutical Manufacturing