Senior Machine Learning Platform Engineer (Remote)

South San Francisco, CA
Jun 23, 2022
Biotech Bay
Required Education
Bachelors Degree
Position Type
Full time

About Freenome 

Freenome is a high-growth biotech company on a mission since 2014 to create tools that empower everyone to prevent, detect, and treat their disease.

To achieve this mission, Freenome is developing next-generation blood tests to detect cancer in its earliest, most treatable stages using our multiomics platform and machine learning techniques. Our first blood test will detect early-stage colorectal cancer and advanced adenomas.

As a Senior Machine Learning Research Engineer, you will work on Freenome’s ML research platform, developing and deploying ML pipelines. As part of an interdisciplinary R&D team, you will work in close collaboration with Computational Biologists, Machine Learning Scientists and Software Engineers. You will develop cutting edge solutions at the intersection of Machine Learning, Genetic Sequencing Technology, and Distributed Systems. These contributions will drive our mission to diagnose cancer at its most actionable and early stages.

Your contribution:

  • Work at the intersection of machine learning research, software engineering and biological data
  • Lead the development of Freenome’s ML research framework and internal tools
  • Participate in cutting edge research in statistical modeling and inference of biological problems (including cancer research, genomics, computational biology/bioinformatics, immunology, therapeutics, and more)
  • Build for significant growth and scaling challenges as we transition from research to product development
  • Engineer robust and reproducible data pipelines that enable cutting edge liquid biopsy research
  • Improve the reliability and scalability of our ML platform as it grows
  • Develop software and workflows that support a long term vision for ML research and production
  • Enable data driven science discoveries in biology and healthcare

Your background, perspective and experience: 

  • M.S. in Computer Science or a related technical field (or B.S. and comparable industry experience)
  • 6+ years of industry experience with software engineering, production infrastructure, and automation
  • Expertise in software design and development with Python
  • Expertise building and launching large-scale ML frameworks that supports the experimental needs of a research team
  • Experience in analyzing and troubleshooting data management systems
  • Thorough understanding of ML fundamentals, such as cross-validation, hyper-parameter search, model optimization and bias-variance tradeoff
  • Experience building and launching projects in a production software environment, including use of automated testing, version control, and deployment systems
  • A systematic problem-solving approach, effective communication skills and a strong desire to own and drive your work

Nice to haves:

  • ML and data science tools, such as Sklearn, TensorFlow, pyTorch, Jupyter, or Kubeflow
  • Experience with containerized cloud computing environments, such as Docker in GCP or AWS
  • Data pipelines, such as Metaflow, Flyte, Kafka, Spark, Airflow, Argo, Hadoop, or Flink
  • Experience with high performance programming languages such as C/C++, Go, or Rust
  • Job orchestration and distributed systems, such as Kubernetes, Terraform or Ansible
  • Genomics or bioinformatics background 
  • Large-scale and/or high-performance storage systems, such as PostgreSQL, MySQL, Redis, HBase, Spanner, or Cassandra

COVID safety:

As a condition of employment, you agree to know and comply with our COVID-19 vaccination policy requiring all employees who work on-site and/or attend work-related events to be fully vaccinated and to receive a COVID-19 booster once eligible. Company employees working on-site are required to be fully vaccinated for COVID-19 and to receive a COVID-19 booster once eligible, unless a reasonable accommodation is approved or as otherwise required by law. Absent a reasonable accommodation or legal exception, you agree to provide proof of your vaccination status and to be fully vaccinated by your first day on-site, in accordance with our policy.  If you are currently eligible for a COVID-19 booster, you also agree to provide proof of having received a booster.  If you are not yet eligible for a COVID-19 booster, you must provide proof of receiving a booster within two weeks of becoming eligible.

Freenome is proud to be an equal opportunity employer and we value diversity. Freenome does not discriminate on the basis of race, color, religion, marital status, age, national origin, ancestry, physical or mental disability, medical condition, pregnancy, genetic information, gender, sexual orientation, gender identity or expression, veteran status, or any other status protected under federal, state, or local law.



We have raised more than $1.1B from leading investors including Perceptive Advisors, RA Capital Management, Roche Venture Fund, Kaiser Permanente, Novartis and the American Cancer Society’s BrightEdge Ventures. 


A ‘Freenomer’ is a mission-driven employee who is fueled by the opportunity to make a positive impact on patients' lives, who thrives in a culture of respect and cross collaboration, and whose work makes a significant impact on the company and their career. 

Freenomers are technical, creative, visionary, grounded, empathetic and passionate. We build teams around divergent expertise, allowing us to solve problems and ascertain opportunities in unique ways. Freenomers are some of the most talented experts in their fields, joining together to advance healthcare, one breakthrough at a time. 

Benefits include but are not limited to:

  • Competitive compensation 
  • Pre-IPO equity
  • Flexible PTO (exempt) and generous PTO (non-exempt) 
  • Comprehensive health coverage, including medical, dental, and vision 
  • Wellness and mental health resources, including Employee Assistance Programs (EAPs), Paid maternity and paternity leave
  • 401(k) plan 
  • $250.00 new hire stipend to enhance your home office experience
  • Plus, a variety of other perks, including pre-tax commuter benefits, two paid volunteer days per year, pet insurance, and additional discounts 

Applicants have rights under Federal Employment Laws.  


Notice to agencies:

Our in-house Talent Acquisition Team manages all employment opportunities at Freenome.  Agencies and independent recruiters must be approved as a vendor by Freenome’s Talent Acquisition team before submitting candidates to any Freenome employee. 

We do not accept unsolicited resumes or biographies from agencies under any circumstances. Any unsolicited resumes sent to Freenome, including those sent to a Freenome email address or directly to Freenome employees, will be considered Freenome property. Freenome will NOT pay a fee for any placement resulting from the receipt of an unsolicited resume. Freenome will consider any candidate for whom an Agency has submitted an unsolicited resume to have been referred by the Agency free of any charges or fees. 

Please do not contact Freenome employees directly. Compliance with this request will impact our decision to work with you.