Sr. Deep Learning/AI Engineer - Machine Learning

Company: Illumina
Location: San Diego
Posted on: May 24, 2025

Job Description:

Senior Deep Learning/AI EngineerWhat if the work you did every day could impact the lives of people you know? Or all of humanity? At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for patients.Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world-changing projects, you will do more and become more than you ever thought possible.Our team develops Next Generation Sequencing (NGS) solutions used by researchers and clinicians worldwide, providing sample-to-answer pipelines with high reliability, speed, and accuracy of results. We develop machine learning solutions across Illumina's portfolio, from sequencing functions to analysis and interpretation algorithms. DRAGEN, our secondary analysis platform, has industry-leading performance and is used for clinical and research work. Advanced AI applications drive transformational genetic insights that improve understanding of human biology, cancer, and rare disease.We are seeking an ML Algorithms expert to join our team. This role will develop and implement ML systems across Illumina's products, including DRAGEN, the Constellation technology, and sequencing systems like high-throughput Novaseq X. You will collaborate with cross-functional teams (algorithms, software, bioinformatics, optics and imaging, test) to develop and implement machine learning algorithms operating on a variety of data types (images, sequencing output, population data, DNA, RNA, multi-omics, etc). The ideal candidate is a strong problem-solver with a proven track record of getting things done-someone who takes ownership, works efficiently, and consistently delivers high-quality work.If you have product programming experience and a passion for machine learning, this is a great opportunity to join an exciting team at a leading biotech company.Responsibilities:

• You will design and develop machine learning algorithms for a variety of bioinformatic problems and data types.
• Design machine learning algorithms for unique domain problems and ensure algorithm performance meets product requirements.
• You will develop machine learning algorithms in Python and implement them in C++ (also potentially on FPGA, GPU/CUDA).
• Debug and troubleshoot machine learning models - understand model performance on corner cases and improve model performance.
• You will collaborate with cross-functional teams, including AI/ML researchers, software engineers, bioinformatics domain experts, hardware engineering etc., to implement, optimize and test machine learning models.
• Create and maintain Python and C++ code, documentation, unit tests, complying with software and product development best practice.
• Design, develop, test, deploy, maintain machine learning software solutions (on sequencer, on DRAGEN servers, in the cloud).
• Deliver high quality code, documentation, and test cases.Requirements:
  • Master's or Ph.D. in Machine learning, Computer Science or a related technical field, or equivalent experience.
  • 2+ years of relevant experience in product development focusing on ML systems or high-performance signal processing systems, ideally in Python and modern C++.
  • Experience with large and complex pipelines, using machine learning models to analyze large volumes of data efficiently, from algorithm research and evaluation through detailed implementation; ideally experience in shipping products.
  • Solid knowledge and experience in machine learning algorithms, deep learning, data structures, image processing, numerical optimization, parallel and distributed computing, high-performance computing, embedded systems.
  • Solid knowledge and experience with ML frameworks (Tensorflow, keras, Pytorch, xgboost, sklearn).
  • Experience in debugging ML models and explainable ML frameworks.
  • Solid Python coding skills - demonstrated track of python coding with unit testing, documentation, code reviews, version control.
  • Self-starter, strong problem-solving skills, ability to push forward project objectives both through individual effort and team collaboration.All listed requirements are deemed as essential functions to this position; however, business conditions may require reasonable accommodations for additional task and responsibilities.Additional Nice-to-Haves:
    • Bioinformatics, applied math background and/or experience.
    • Linear algebra and statistics applied to images, tabular data, unstructured multimodal data.
    • NGS knowledge - familiarity with bioinformatics workflows including primary and/or secondary analysis pipelines.
    • Solid C++ programming skills.
    • Experience with ML acceleration technology (FPGA, GPU, etc) and technology infrastructure.
    • Strong Linux/Unix fundamentals.
    • Strong documentation and presentation skills.
    • Project management skills.Degree and Job Experience Requirements:
      • The candidate could have a degree from any of the following fields: Machine learning, Artificial Intelligence, Computer Science, Software Engineering, Applied Math, Bioinformatics, Biology, Physics, related topics.
      • Master's, or Ph.D.
      • Job experience: Ideally the candidate should have 2+ years of experiences in product development with a track record of product shipping.Location: San Diego, CaliforniaThe estimated base salary range for the Senior Deep Learning/AI Engineer role based in the United States of America is: $138,800 - $208,200. Should the level or location of the role change during the hiring process, the applicable base pay range may be updated accordingly. Compensation decisions are dependent on several factors including, but not limited to, an individual's qualifications, location where the role is to be performed, internal equity, and alignment with market data.At Illumina, we strive to foster a diverse and inclusive workplace by cultivating an environment in which everyone contributes to our mission. Built on a strong foundation, Illumina has always been rooted in openness, collaboration, and seeking alternative views and perspectives to propel innovation in genomics. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information.
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Keywords: Illumina, Cathedral City , Sr. Deep Learning/AI Engineer - Machine Learning, Engineering , San Diego, California