Principal ML Engineer

Principal ML Engineer 

We’re looking for a Principal Machine Learning Engineer to lead the implementation of advanced AI models across the clinical and genomics applications. This role is ideal for someone who is both highly technical and impact-driven - focused on rapidly building, deploying, and iterating on models that drive real-world results in precision medicine. You’ll be at the frontier of clinical AI, working with real-world patient data to build systems that power precision medicine, from cancer care to reproductive health.

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

​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. 

The pay range is listed and actual compensation packages are based on a wide array of factors unique to each candidate, including but not limited to skill set, years & depth of experience, certifications and specific office location. This may differ in other locations due to cost of labor considerations.Remote USA$178,900—$223,650 USD

OUR OPPORTUNITY

Natera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women’s health, and organ health. Our aim is to make personalized genetic testing and diagnostics part of the standard of care to protect health and enable earlier and more targeted interventions that lead to longer, healthier lives.

The Natera team consists of highly dedicated statisticians, geneticists, doctors, laboratory scientists, business professionals, software engineers and many other professionals from world-class institutions, who care deeply for our work and each other. When you join Natera, you’ll work hard and grow quickly. Working alongside the elite of the industry, you’ll be stretched and challenged, and take pride in being part of a company that is changing the landscape of genetic disease management.

WHAT WE OFFER

Competitive Benefits - Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents. Additionally, 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!

For more information, visit www.natera.com.

Natera is proud to be an Equal Opportunity Employer. We are committed to ensuring a diverse and inclusive workplace environment, and welcome people of different backgrounds, experiences, abilities and perspectives. Inclusive collaboration benefits our employees, our community and our patients, and is critical to our mission of changing the management of disease worldwide.

All qualified applicants are encouraged to apply, and will be considered without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, age, veteran status, disability or any other legally protected status. We also consider qualified applicants regardless of criminal histories, consistent with applicable laws.

If you are based in California, we encourage you to read this important information for California residents. 

Link: https://www.natera.com/notice-of-data-collection-california-residents/

Please be advised that Natera will reach out to candidates with a @natera.com email domain ONLY. Email communications from all other domain names are not from Natera or its employees and are fraudulent. Natera does not request interviews via text messages and does not ask for personal information until a candidate has engaged with the company and has spoken to a recruiter and the hiring team. Natera takes cyber crimes seriously, and will collaborate with law enforcement authorities to prosecute any related cyber crimes.

For more information:
- BBB announcement on job scams 
- FBI Cyber Crime resource page