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About This Role
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.
Director, AI/ML - Generative Foundation Models for Biotherapeutics
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.
This role is based at the Lilly Biotechnology Center in San Diego, where we are expanding our computational capabilities to build a generative design platform. By bringing together AI/ML, protein engineering, automation, structural biology, and high-throughput experimentation, BioTDR is creating an integrated de novo design platform capable of generating, ranking, and optimizing novel therapeutic antibodies and other biotherapeutics with improved activity, safety, manufacturability, and target coverage. Designs are rapidly evaluated through experimental validation, creating a continuous learning cycle that strengthens both models and discovery outcomes. The program is supported by dedicated capacity on LillyPod, our wholly owned 1,016-GPU NVIDIA Blackwell Ultra SuperPOD.
Help us push the de novo protein design frontier beyond binders to molecules that can become medicines, faster. Ready to make an impact? Join us.
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 lead the development of 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 and scale 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 and reducing the gap between model-ranked and experimentally validated design performance.
- Drive model improvement, resolving underperforming models to root cause across architecture, data, and execution, and making timely decisions to retrain, pivot, or discontinue.
- Drive the advancement of foundation model portfolio, establishing success metrics and ensuring progress translates into measurable experimental outcomes.
- 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 structure-based generative model. Plus, a track record of carrying projects end to end.
- Experience training deep learning models on multi-node 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
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.
#WeAreLilly
Salary Context
This $193K-$338K range is above the 75th percentile for AI/ML Engineer roles in our dataset (median: $178K across 1623 roles with salary data).
View full AI/ML Engineer salary data →Role Details
About This Role
AI/ML Engineers build and deploy machine learning models in production. They work across the full ML lifecycle: data pipelines, model training, evaluation, and serving infrastructure. The role has evolved significantly over the past two years. Where ML Engineers once spent most of their time on model architecture, the job now tilts heavily toward inference optimization, cost management, and integrating LLM capabilities into existing systems. Companies want engineers who can ship production systems, and the experimenter-only role is fading fast.
Day-to-day, you're writing training pipelines, debugging data quality issues, setting up evaluation frameworks, and figuring out why your model performs differently in staging than it did on your dev set. The best ML engineers are obsessive about reproducibility and measurement. They instrument everything. They know that a model is only as good as the data feeding it and the infrastructure serving it.
Across the 9,079 AI roles we're tracking, AI/ML Engineer positions make up 76% of the market. At Eli Lilly, this role fits into their broader AI and engineering organization.
Demand for AI/ML Engineers has been strong and consistent. Unlike some AI roles that spike with hype cycles, ML engineering is a foundational need. Every company deploying AI models needs people who can keep them running, and the gap between research prototypes and production systems keeps growing.
What the Work Looks Like
A typical week might include: debugging a data pipeline that's silently dropping 3% of training examples, running A/B tests on a new model version, writing documentation for a feature flag system that lets you roll back model deployments, and reviewing a junior engineer's PR for a new evaluation metric. Meetings tend to be cross-functional since ML touches product, engineering, and data teams.
Demand for AI/ML Engineers has been strong and consistent. Unlike some AI roles that spike with hype cycles, ML engineering is a foundational need. Every company deploying AI models needs people who can keep them running, and the gap between research prototypes and production systems keeps growing.
Skills Required
Python and PyTorch dominate the requirements. Most roles expect experience with cloud platforms (AWS, GCP, or Azure) and familiarity with ML frameworks like TensorFlow or JAX. RAG (Retrieval-Augmented Generation) has become a top-3 skill requirement as companies integrate LLMs into their products. Docker and Kubernetes show up in about a third of postings, reflecting the production focus of the role.
Beyond the core stack, employers increasingly want experience with experiment tracking tools (MLflow, Weights & Biases), feature stores, and vector databases. Fine-tuning experience is valuable but less common than you'd think from reading Twitter. Most production LLM work is RAG and prompt engineering, not fine-tuning. If you have both, you're in a strong position.
Companies that are serious about AI/ML hiring tend to post specific infrastructure details in the job description: the frameworks they use, their model serving stack, their data pipeline tools. Vague postings that just say 'ML experience required' without specifics are often companies that haven't figured out what they need yet.
Compensation Benchmarks
AI/ML Engineer roles pay a median of $211,950 based on 13,048 positions with disclosed compensation. Director-level AI roles across all categories have a median of $272,300. This role's midpoint ($266K) sits 26% above the category median. Disclosed range: $193K to $338K.
Across all AI roles, the market median is $213,000. Top-quartile compensation starts at $263,911. The 90th percentile reaches $318,400. For comparison, the highest-paying categories include AI Safety ($256,000) and Research Engineer ($252,000). By seniority level: Entry: $111,000; Mid: $193,200; Senior: $229,300; Director: $272,300; VP: $235,830.
Eli Lilly AI Hiring
Eli Lilly has 7 open AI roles right now. They're hiring across AI/ML Engineer, Research Scientist. Positions span Indianapolis, IN, US, IN, US, San Diego, CA, US. Compensation range: $173K - $391K.
Location Context
Across all AI roles, 6% (531 positions) offer remote work, while 8,478 require on-site attendance. Top AI hiring metros: New York (3,078 roles, $221,000 median); San Francisco (2,646 roles, $261,000 median); Los Angeles (1,486 roles, $210,000 median).
Career Path
Common paths into AI/ML Engineer roles include Data Scientist, Software Engineer, Research Engineer.
From here, career progression typically leads toward ML Architect, AI Engineering Manager, Principal ML Engineer.
The fastest path into ML engineering is through software engineering with a self-directed ML education. A CS degree helps, but production engineering skills matter more than academic credentials. Build something that works, deploy it, and measure it. That portfolio project is worth more than a Coursera certificate. For career growth, the fork comes around the senior level: go deep on technical complexity (staff/principal track) or move into managing ML teams.
What to Expect in Interviews
Expect system design questions around ML pipelines: how you'd build a training pipeline for a specific use case, handle data drift, or design A/B testing infrastructure for model deployments. Coding rounds typically involve Python, with emphasis on data manipulation (pandas, numpy) and algorithm implementation. Take-home assignments often ask you to build an end-to-end ML pipeline from raw data to deployed model.
When evaluating opportunities: Companies that are serious about AI/ML hiring tend to post specific infrastructure details in the job description: the frameworks they use, their model serving stack, their data pipeline tools. Vague postings that just say 'ML experience required' without specifics are often companies that haven't figured out what they need yet.
AI Hiring Overview
The AI job market has 9,079 open positions tracked in our dataset. By seniority: 106 entry-level, 4,384 mid-level, 3,343 senior, and 1,246 leadership roles (Director, VP, C-Level). Remote roles make up 6% of the market (531 positions). The remaining 8,478 roles require on-site or hybrid attendance.
The market median for AI roles is $213,000. Top-quartile compensation starts at $263,911. The 90th percentile reaches $318,400. Highest-paying categories: AI Safety ($256,000 median, 66 roles); Research Engineer ($252,000 median, 457 roles); AI Engineering Manager ($251,622 median, 55 roles).
Demand for AI/ML Engineers has been strong and consistent. Unlike some AI roles that spike with hype cycles, ML engineering is a foundational need. Every company deploying AI models needs people who can keep them running, and the gap between research prototypes and production systems keeps growing.
The AI Job Market Today
The AI job market spans 9,079 open positions across 16 role categories. The largest categories by volume: AI/ML Engineer (6,862), AI Product Manager (453), AI Software Engineer (451). These three account for the majority of open positions, though smaller categories often have higher per-role compensation because of specialized skill requirements.
The seniority mix tells a story about where AI teams are in their maturity. Entry-level roles (106) are outnumbered by mid-level (4,384) and senior (3,343) positions, reflecting that most companies are past the 'build a team from scratch' phase and need experienced engineers who can ship production systems. Leadership roles (Director, VP, C-Level) total 1,246 positions, representing the bottleneck between technical execution and organizational strategy.
Remote work availability sits at 6% of all AI roles (531 positions), with 8,478 requiring on-site or hybrid attendance. The remote share has stabilized after the post-pandemic correction. Senior and specialized roles (Research Scientist, ML Architect) are more likely to be remote-eligible than entry-level positions, partly because experienced hires have more negotiating power and partly because these roles require less hands-on mentorship.
AI compensation is structured in clear tiers. The market median sits at $213,000. Top-quartile roles start at $263,911, and the 90th percentile reaches $318,400. These figures include base salary with disclosed compensation. Total compensation (including equity, bonuses, and sign-on) runs 20-40% higher at companies that offer those components.
Category matters for compensation. AI Safety roles lead at $256,000 median, while Prompt Engineer roles sit at $141,440. The spread between highest and lowest-paying categories reflects the premium on specialized technical skills versus broader analytical roles.
The most in-demand skills across all AI postings: Python (1,649 postings), Aws (898 postings), Azure (723 postings), Rag (671 postings), Gcp (536 postings), Pytorch (434 postings), Claude (410 postings), Kubernetes (406 postings). Python dominates, appearing in the vast majority of role descriptions regardless of category. Cloud platform experience (AWS, GCP, Azure) is the second most common requirement. The newer entrants to the top skills list (RAG, vector databases, LLM APIs) reflect the shift from traditional ML toward generative AI applications.
Frequently Asked Questions
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