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About This Role
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. Our employees around the world work to discover and bring life\-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world.
Organization Overview
Lilly Small Molecule Discovery is an organization purpose\-built to create molecules that make life better for people. We focus on using cutting edge science to unlock new approaches that can treat people suffering from diseases with poor treatment options. We continually challenge ourselves to deliver molecules that can provide breakthrough efficacy with the highest possible safety margins. We are dedicated to optimizing our mindset, technology, and processes for faster, more nimble execution. Our success is built on a culture that empowers innovative problem solving through open collaboration and individual accountability.
Discovery Technology and Platforms is a newly established function within this organization. Its mission is to accelerate molecule discovery by building highly optimized foundational platforms, streamlining lab operations through advanced technologies and data connectivity, and intentionally investing in novel technologies and capabilities.
Frontier AI is a purpose\-built team that fuses scientific agentic AI, lab automation, and unified data platforms to autonomously design, run, and refine experiments—accelerating molecule discovery.
Position Summary
We are rebuilding the Design\-Make\-Test\-Analyze (DMTA) cycle by integrating agentic AI, cloud\-based orchestration, and LIMS infrastructure to connect experimental readouts with tools that accelerate laboratory science.
You will engineer the connective tissue between Agentic AI and physical lab systems building practical integrations with robotic platforms, analytical instruments, and data pipelines. You'll design agent workflows that reason over experimental data, trigger automated actions, and surface insights to scientists. This is a hands\-on engineering role: you'll prototype rapidly, productionize what works, and collaborate with chemists, biologists, and automation engineers to deploy intelligent systems that accelerate molecule discovery tasks.
Research \& Innovation
- Build multi\-agent systems with robust orchestration, state management, error recovery, and tool integration
- Prototype and iterate rapidly on agent planning strategies, memory systems, and human\-in\-the\-loop patterns
- Design agent architectures that interface with lab automation platforms (Hamilton, Tecan, Opentrons) for closed\-loop experimental execution
Solution Deployment
- Partner with automation engineers and scientists to transition prototypes into reliable lab operations
- Deploy and maintain containerized services using Docker and Kubernetes with GitOps and CI/CD practices
- Integrate cloud\-based orchestration frameworks such as Argo on Kubernetes with laboratory control systems
External Engagement
- Represent Frontier AI in the broader AI@Lilly and external AI research community: publish, give talks, review papers, and scout emerging trends.
- Evaluate external vendors, open\-source projects, and academic collaborations for strategic fit.
What Success Looks Like
- Autonomous agents reliably execute experiments on physical laboratory instruments
- Measurable reduction in DMTA turnaround through autonomous planning and execution
- Agents you build become indispensable to the automation engineering community
- Frontier AI platforms scale from pilot deployments to production lab environments
Basic Qualifications
- PhD (or MS \+ 2 yrs / BS \+ 5 yrs equivalent experience) in Chemical / Mechanical Engineering, Robotics, Computer Engineering, or related discipline with demonstrated wet\-lab automation experience.
- Demonstrated experience with laboratory automation systems and LIMS engineering
- Direct experience integrating software control and/or AI systems with lab automation platforms (liquid handlers, analytical instruments, robotic workflows)
- Strong experience with containerization (Docker) and Kubernetes\-based orchestration in production environments
- Experience building scalable and production\-level python applications using tools like Redis, FastAPI, flask/streamlit, pytest, etc. (GitHub portfolio a plus)
Preferred
- Experience with LLM post\-training, fine\-tuning, or RLHF
- Direct experience integrating AI or algorithmic decision systems with laboratory automation
- Proven ability to build and maintain the translation layer between high\-level planning logic and low\-level instrument control
- Demonstrable research experience, evidenced by contributions to projects, and ideally through publications in relevant ML/NLP venues (e.g., NeurIPS, ICML, ICLR, ACL, EMNLP, CVPR
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 Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ\+ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.
Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is
$87,000 \- $222,200
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 $87K-$222K range is below the median for AI/ML Engineer roles in our dataset (median: $180K across 2130 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 4,133 AI roles we're tracking, AI/ML Engineer positions make up 69% 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 $185,000 based on 13,200 positions with disclosed compensation. Senior-level AI roles across all categories have a median of $227,400. This role's midpoint ($154K) sits 16% below the category median. Disclosed range: $87K to $222K.
Across all AI roles, the market median is $200,700. Top-quartile compensation starts at $254,000. The 90th percentile reaches $307,500. For comparison, the highest-paying categories include AI Safety ($274,200) and AI Engineering Manager ($268,700). By seniority level: Entry: $97,760; Mid: $165,778; Senior: $227,400; Director: $250,000; VP: $250,000.
Eli Lilly AI Hiring
Eli Lilly has 4 open AI roles right now. They're hiring across MLOps Engineer, AI/ML Engineer. Positions span San Francisco, CA, US, Indianapolis, IN, US. Compensation range: $165K - $283K.
Location Context
Across all AI roles, 14% (583 positions) offer remote work, while 3,532 require on-site attendance. Top AI hiring metros: New York (2,760 roles, $211,000 median); San Francisco (2,258 roles, $253,000 median); Los Angeles (1,841 roles, $195,000 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 4,133 open positions tracked in our dataset. By seniority: 106 entry-level, 1,901 mid-level, 1,663 senior, and 463 leadership roles (Director, VP, C-Level). Remote roles make up 14% of the market (583 positions). The remaining 3,532 roles require on-site or hybrid attendance.
The market median for AI roles is $200,700. Top-quartile compensation starts at $254,000. The 90th percentile reaches $307,500. Highest-paying categories: AI Safety ($274,200 median, 57 roles); AI Engineering Manager ($268,700 median, 42 roles); Research Engineer ($260,000 median, 442 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 4,133 open positions across 15 role categories. The largest categories by volume: AI/ML Engineer (2,865), Data Scientist (339), AI Software Engineer (313). 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 (1,901) and senior (1,663) 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 463 positions, representing the bottleneck between technical execution and organizational strategy.
Remote work availability sits at 14% of all AI roles (583 positions), with 3,532 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 $200,700. Top-quartile roles start at $254,000, and the 90th percentile reaches $307,500. 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 $274,200 median, while Prompt Engineer roles sit at $140,000. 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 (2,128 postings), Aws (1,324 postings), Azure (1,003 postings), Rag (916 postings), Gcp (817 postings), Pytorch (655 postings), Prompt Engineering (639 postings), Claude (571 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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