What 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. We also develop algorithms for on-sequencer pipelines including super-resolution, basecalling, denoising. Advanced AI applications drive transformational genetic insights that improve understanding of human biology, cancer and rare disease.

We are seeking a Machine Learning Software Engineer to join our team. This role will develop and implement ML systems across Illumina’s products, including DRAGEN and high-throughput sequencing systems like NovaseqX, the industry-leading platform. You will collaborate with cross-functional teams (algorithms, implementation, bioinformatics, optics and imaging, test) to implement machine learning algorithms operating on a variety of data types (images, sequencing output, population data, DNA, RNA, multi-omics, etc.)

If you have product development experience and a passion for machine learning, this is a great opportunity to join a team developing complex ML algorithms at a leading biotech company.

Responsibilities:

You will develop software infrastructures to support and optimize machine learning algorithms and deliver products that are deployed on the cloud, on sequencers and on local compute servers (using Python, C++, also FPGA, GPU/CUDA)
Create and maintain training, inference, evaluation ML pipelines in various stages of product development (early prototype, feasibility, production)
Debug and troubleshoot ML models – improve the efficiency and agility of the team in supporting large scale deployment of ML systems.
Working closely with other software engineers, researchers and domain experts on AI/ML models and architectures
Work with experts across software engineering, hardware engineering, ML and data science, optics and imaging, embedded systems, test
Help advanced code quality and efficiency throughout ML development; deliver efficient solutions to optimize pipeline speed (DRAGEN is FAST!)
Design, develop, test, deploy, maintain software solutions (on sequencer, on DRAGEN servers, in the cloud)

Qualifications:

Bachelors or Masters in Computer Science, Engineering or a related technical field, or equivalent experience
2+ years of relevant experience in software development focusing on ML systems or high performance signal processing systems, ideally in Python and modern C++, especially high-performance computing
Experience with large and complex pipelines, using machine learning models, signal processing (or similar) to analyze large volumes of data efficiently, from algorithm research and evaluation through detailed implementation; ideally experience in shipping products
Experience in image processing, algorithms and data structures, numerical optimization, parallel and distributed computing, high-performance computing, embedded systems, machine learning
Ideally experience with ML frameworks (Tensorflow, keras, Pytorch, xgboost, sklearn or similar)
Solid Python coding skills – experience with unit testing, code reviews, version control
Statistical skills to identify modeling issues and drive accuracy improvements
Self-starter, good problem-solving skills, ability to push forward project objectives both through individual effort and team collaboration.

Additional Nice-to-Haves:

Bioinformatics, ML, software engineering principles, software test, applied math background and/or experience
Deep learning, structured data machine learning, gradient boosting, linear algebra and statistics applied to images, tabular data, unstructured multimodal data, computer vision
Hardware skills e.g. optical systems, HDL languages, embedded systems
NGS knowledge - familiarity with bioinformatics workflows including primary and/or secondary analysis pipelines, any omics data
Experience with ML frameworks such as Pytorch, Keras, xgboost, sklearn, ONNX, dask, rapids.ai
Experience with revision control (git)
Experience with ML acceleration technology (FPGA, GPU, etc) and technology infrastructure
Strong Linux/Unix fundamentals
Strong documentation and presentation skills
Machine learning experience/knowledge
Project management skills

Degree and Job Experience Requirements:

The candidate could have a degree from any of the following fields: Bioinformatics, Biology, Physics, Electrical Engineering, Computer Science, Software Engineering, Applied Math, related topics
Bachelor’s, Master’s, or Ph.D.
Job experience: experienced professionals with a background in shipping complex technical products (e.g. software, IC development)

Location:

San Diego, California

The estimated base salary range for the Deep Learning/AI Engineer role based in the United States of America is: $115,800 - $173,800. 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. Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off.

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 confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and demonstrate our collective commitment to diversity and inclusion in the communities we live and work. 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. Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws. If you require accommodation to complete the application or interview process, please contact accommodations@illumina.com. To learn more, visit: https://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf. The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants. This role is not eligible for visa sponsorship.

Illumina Software Inc.

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