Engineer - MLOps & Scientific Platforms - Data Foundry

Locations San Diego, CA; San Francisco, CA; Boston, MA; Louisville, CO; Indianapolis, IN 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 MLOps & Model Lifecycle Management 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. Scientific Tool Agile Deployment Deploy predictive and analytical methods from Methods4Insight (cheminformatics, structural biology, bioinformatics, reaction informatics) with versioning, structured error handling, and response‑time guarantees that enable insight generation in an agile manner. Productionize when and where needed in partnership with View email address on click.appcast.io. Build serving infrastructure supporting both synchronous (interactive scientist queries) and asynchronous (batch and agent‑invoked) workloads in partnership with View email address on click.appcast.io 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. Platform Engineering & Integration 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. Frontier AI Interface & Collaboration Partner with the Frontier AI team and View email address on click.appcast.io 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 ( 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. Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is $66,000 - $165,000. 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. #J-18808-Ljbffr