Engineer - MLOps & Scientific Platforms - Data Foundry

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. 

Locations: San Francisco, CA; Louisville, CO; Indianapolis, IN
 

Lilly Small Molecule Discovery is purpose-built to create molecules that make life better for people. Discovery Technology and Platforms (DTP) accelerates molecule discovery by building optimized foundational platforms, streamlining lab operations through advanced technologies and data connectivity, and investing in novel capabilities.

Data Foundry is a multidisciplinary team within DTP that enables AI-native drug discovery through four integrated pillars: Architecture4Insight (data infrastructure and scientific software), Methods4Insight (analytical and computational methods), Automation & Scale4Insight (lab automation and agentic workflows), and Preparedness4Insight (data governance and readiness). These pillars empower every Lilly scientist to make optimal decisions by providing seamless access to data, insights, and AI-driven capabilities—serving both human scientists and autonomous AI agents.

Position Summary

We are seeking an Engineer - MLOps & Scientific Platforms - Data Foundry to operationalize Data Foundry’s scientific tools and analytical methods into actionable-prototypes. You will build the ML deployment pipelines, model serving infrastructure, API layers, and observability guardrails that make our scientific discovery methods and tools reliable, scalable, and consumable, both by discovery scientists and by the Frontier AI group’s autonomous agents.

This role sits at the interface between Methods4Insight (which develops analytical methods) and Architecture4Insight(which provides the agile data infrastructure). Your job is to ensure every scientific tool Data Foundry produces are analytics-ready, well-monitored, and exposed through APIs with the response-time guarantees and error handling that both human users and AI agents require.

Responsibilities

• Build and maintain end-to-end ML deployment pipelines: experiment tracking, model versioning (MLflow, Weights & Biases), containerized model serving, and automated retraining triggers.

• Develop model registry infrastructure and feature engineering pipelines that enable computational scientists to access models.

• Implement monitoring and alerting for data pipelines, APIs, ML models, and agentic systems (LLMOps) to ensure system reliability and performance at scale.

• Build dashboards and metrics tracking for pipeline execution, API latency, token usage, model prediction quality, and system health

• Establish structured logging and tracing infrastructure for debugging and performance optimization across scientific data systems

• Deploy predictive and analytical methods from Methods4Insight (e.g. cheminformatics, structural biology, bioinformatics, reaction informatics) with versioning, structured error handling, and response-time guarantees that enable insight generation in agile manner. Productionize when and where needed in partnerships with Tech@Lilly.

• Build serving infrastructure supporting both synchronous (interactive scientist queries) and asynchronous (batch and agent-invoked) workloads in partnership with Tech@Lilly and Frontier AI.

• Define and implement API contracts, documentation standards, and testing frameworks that ensure scientific tools are analysis ready, robust and consumable by external teams including Frontier AI.

• Build and operate cloud-native model serving infrastructure (AWS, Azure, or GCP) using containers, Kubernetes, and infrastructure-as-code.

• Develop CI/CD pipelines for ML models: automated validation, A/B testing, canary deployments, and rollback procedures.

• Integrate model serving with Data Foundry’s data pipelines, ensuring models have access to properly formatted, versioned training and inference data.

• Partner with the Frontier AI team and Tech@Lilly to ensure Data Foundry’s scientific tools are exposed via well-defined interfaces (REST APIs, MCP-compatible endpoints) that agents can invoke programmatically.

• Collaborate on API performance requirements: latency targets, throughput guarantees, and graceful degradation under load.

• Work with Methods4Insight scientists to ensure deployed models include appropriate uncertainty quantification and confidence metrics.

Basic Requirements

• B.S. or M.S. in Computer Science, Data Science, Machine Learning, Bioinformatics, Computational Biology, or related field.

• 3+ years of experience in MLOps, ML engineering, or scientific platform development

• Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1.

Preferred Qualifications

• Pharmaceutical or biotech research industry experience.

• Strong Python skills; experience with ML frameworks (PyTorch, TensorFlow, scikit-learn) and ML lifecycle tools (MLflow, W&B, Kubeflow, or similar).

• Proven track record building and deploying production model serving infrastructure — containerized endpoints, RESTful/gRPC APIs, and operational monitoring

• Working knowledge of cloud platforms (AWS, Azure, or GCP), Kubernetes, and CI/CD automation.

• Strong communication skills with ability to collaborate across computational scientists, software engineers, and partner teams.

• Experience operationalizing scientific or computational models (cheminformatics, bioinformatics, structural biology, QSAR, molecular simulations, PK/PD, systems biology, or ODE-based models).

• Hands-on experience with model monitoring, drift detection, and automated retraining systems.

• Familiarity with API gateway patterns, event-driven architectures, and service mesh technologies.

• Experience with feature stores, data versioning (DVC), or experiment tracking at scale.

• Exposure to AI agent frameworks (MCP, LangChain) or building APIs that AI systems invoke programmatically.

• Experience with C, C++, CUDA, or GPU-accelerated computing for optimizing model training/inference performance; familiarity with containerizing HPC workloads (Singularity/Apptainer).

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

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