Principal ML Engineer

Summary

Join Natera as a Principal Machine Learning Engineer to spearhead the development and implementation of cutting-edge AI models for clinical and genomics applications. This role demands a highly technical and results-oriented individual to build, deploy, and refine models impacting precision medicine. You will be at the forefront of clinical AI, leveraging real patient data to create systems for various medical fields. Responsibilities include model selection, tuning, and deployment; agent and workflow development; iterative testing and evaluation; and collaboration with cross-functional teams. The position requires a PhD or equivalent experience, extensive machine learning experience (preferably in healthcare or genomics), and proficiency in various programming languages and tools. Natera offers competitive benefits, including comprehensive medical, dental, vision, life, and disability plans, free testing for employees and their families, fertility care benefits, and more.

Requirements

• PhD in Computer Science, Computational Biology, Bioinformatics, Statistics, or related field, or equivalent practical experience
• 8+ years of experience applying machine learning to real-world problems, preferably in healthcare or genomics domains
• Proficiency in deep learning frameworks such as PyTorch, TensorFlow, or Keras
• Experience with integrating LLMs (e.g., OpenAI, LLaMA, DeepSeek, Claude) into downstream clinical workflows
• Expertise in fine-tuning and optimizing pre-trained models for domain-specific applications
• Familiarity with agent frameworks (e.g., LangChain, Haystack, ReAct) and retrieval-augmented generation (RAG) techniques
• Experience with semantic search, hybrid search, and vector databases
• Strong programming skills in Python; familiarity with libraries such as scikit-learn, pandas, and NumPy
• Experience with containerization (Docker) and orchestration (Kubernetes)
• Knowledge of API development and integration, including RESTful services
• Experience with cloud platforms (AWS, Azure, or GCP) and associated ML services

Responsibilities

• Model Selection, Tuning and Deployment
• Identify and evaluate best-fit models for a wide range of tasks (e.g., clinical entity recognition, summarization, variant interpretation, workflow automation)
• Fine-tune or optimize foundation models (LLMs, transformer, etc.) for targeted clinical/genomic outcomes
• Design for scalability, observability, and maintainability in ML deployments
• Package and serve models for production inference (REST APIs, batch pipelines, or real-time services)
• Agent and Workflow Development
• Build agentic systems that can answer complex clinical or genomic queries
• Automate human-in-the-loop workflows for expert-level decision support
• Navigating longitudinal patient records for best practice recommendation and decision support
• Integrate external tools, databases, or domain-specific knowledge into agentic pipelines
• Iteration and Evaluation
• Rapidly test hypotheses and ship prototypes or MVPs in collaboration with product team
• Define and track evaluation metrics (e.g., extraction accuracy, latency, alignment with ground truth)
• Collaborate with ML scientists, clinicians, bioinformaticians, product and other cross-functional stakeholders to align technical implementation with real-world constraints
• Engineering and Collaboration
• Own the ML engineering stack, from model integration and experimentation to cloud-native deployment
• Contribute to a reusable foundation of tools (prompt libraries, feature extractors, evaluation harnesses, etc.)
• Work with company-wide vector store and document mesh infrastructure to design and optimize high-performance retrieval strategies for LLM pipelines
• Partner with AI, data, platform, and product pods to deliver production-ready features on a complex and evolving platform
• Security and compliance: Ensure all model pipelines adhere to data governance, privacy, and compliance standards in healthcare and genomics

Benefits

• Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents
• Natera employees and their immediate families receive free testing in addition to fertility care benefits
• Other benefits include pregnancy and baby bonding leave, 401k benefits, commuter benefits and much more
• We also offer a generous employee referral program!