Machine Learning Scientist

POSITION SUMMARY: Natera is seeking a Senior Machine Learning Scientist to join our AI team, an advanced R&D and core AI innovation team bridging the gap between molecular discovery and clinical execution. Leveraging a proprietary data moat of over 250,000 oncology patients profiled with longitudinal ctDNA, WES/WGS, digital pathology, and EMR data, you will design and deploy production-grade autonomous AI agents and multi-modal foundation models. Your mission is to architect systems capable of multi-step biological reasoning, converting complex multi-omic datasets into verifiable clinical insights that accelerate biomarker and therapeutic discovery. You will lead the next evolution of our Agentic AI platform, designing autonomous systems capable of reasoning through the complexities of cancer biology, orchestrating proprietary foundation models, and simulating virtual patient trajectories. PRIMARY RESPONSIBILITIES Lead the technical design and deployment of multi-agent systems capable of autonomous hypothesis generation and tool use, including genomic variant calling, LLM fine-tuning, and clinical trial matching pipelines Incorporate and advance Natera’s transformer-based foundation model by integrating DNA, RNA, and H&E imaging modalities for multi-step biological reasoning and tool use Implement advanced LLM reasoning frameworks, such as ReAct and Chain-of-Thought, alongside reinforcement fine-tuning (RFT) to ensure agents provide accurate, explainable clinical rationales Architect systems that autonomously translate complex, multi-modal data into diagnostic and therapeutic insights with human-verifiable reasoning and tracing Own the technical strategy and product roadmap for agentic workflows across the Biopharma Solutions and Therapeutics Discovery division, converting complex clinical challenges into scalable AI systems Establish production-grade machine learning engineering standards and reproducible architectures across the AI team to ensure absolute model transparency and scientific auditability Drive cross-functional alignment and technical consensus by defending agentic architectures and biological reasoning frameworks in rigorous peer reviews QUALIFICATIONS: PhD or Master's degree in Computer Science, Bioinformatics, Statistics, or a related quantitative field 8 or more years of experience in AI research or engineering, with a proven track record of moving multi-agent orchestration architectures or large-scale language model workflows from prototype to production Deep experience with agentic frameworks, such as LangChain or Claude Agent SDK, retrieval-augmented generation (RAG), and validation frameworks for autonomous AI agents Strong understanding of cancer genomics (WES/WTS), mutational signatures, and structure-activity relationships Advanced production-level development experience using PyTorch and experience with distributed training on large GPU clusters, including NVIDIA H100s KNOWLEDGE, SKILLS, AND ABILITIES: Ability to operate with absolute ownership to close operational gaps and independently drive architectural deployment Data-driven decision-making focused on empirical model performance and clinical validity Technical leadership capability to define long-term AI engineering roadmaps Rigor in code architecture, reproducibility, and production-grade software engineering practices Comfort with high intellectual friction and the ability to defend scientific and engineering choices under rigorous internal peer review Focus on translating machine learning outcomes directly into patient-centric clinical utility 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 $169,800 - $212,300 USD Compensation & Total Rewards This range reflects a good-faith estimate of the base pay we reasonablyexpect to offer at the time of hire.Final compensation will vary based on experience, qualifications, and internal equity considerations. This positionis also eligible for additional compensation and benefits throughNatera’s robust Total Rewards program, including: Annual performance incentive bonus Long-term equity awards Comprehensive health benefits (medical, dental, vision) 401(k) with company match Generous paid time off and company holidays Additional wellness and work-life benefits Compensation Range $160,335.12 - $200,418.90 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 . 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: 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