Staff Machine Learning Scientist

Freenome; Brisbane (CA); Hybrid; USD 199,675 - 283,500; Full time

Benefits offered by this job

Equity

Cash bonuses

Medical benefits

Job summary

Freenome is seeking a Staff Machine Learning Scientist to advance AI methods for early cancer detection from blood signals. You will lead research, build and refine models, and work with biologists and ML engineers to drive experiments.

This role emphasizes independent research, cross‑functional collaboration, and innovative problem solving. The position reports to the Director, Machine Learning Science, and offers a hybrid work option based in Brisbane, California, with 2–3 days per week in the

Qualifications

• PhD or equivalent in AI emphasis or quantitative field.
• 6+ years postdoc or post-PhD experience with impactful ML/DL results.
• Publications or industry achievements demonstrating independent research in ML/DL.

Responsibilities

• Independently pursue cutting‑edge AI research for biological problems.
• Build or fine‑tune models to identify biological changes.
• Ensure high accuracy and robust generalization to new data.
• Apply interpretability techniques to reveal potential biological mechanisms.
• Collaborate with ML Engineering to support model training and iteration.
• Maintain mindful, transparent, and humane approach to work.

Skills

PhD in AI

Independent research

Cross-functional collaboration

Python programming

Education

PhD or equivalent in AI/CS/Math/Engineering

Tools

PyTorch

TensorFlow

JAX

Job description

At Freenome, we are seeking a Staff Machine Learning Scientist to help grow the Machine Learning Science team, within the Computational Science department. The ideal candidate has a strong knowledge of artificial intelligence (AI), including machine learning (ML) fundamentals and extensive experience with deep learning (DL) methods, a track record of successfully using these methods to answer complex research questions, and the ability to drive independent research and thrive in a highly cross‑functional environment.

They will be responsible for the development of algorithms for early, blood‑based detection tests for cancer. They will build on a foundation of ML/DL and statistical skills to develop models for identifying molecular signals from blood. They will also work with computational biologists, molecular biologists and ML engineers to design and drive research experiments, and will have a significant impact on the continued growth of an organization dedicated to changing the entire landscape of cancer.

The role reports to the Director, Machine Learning Science. This role can be a Hybrid role based in our Brisbane, California headquarters (2–3 days per week in office), or remote.

What you’ll do:

• Independently pursue cutting‑edge research in AI applied to biological problems (including cancer research, genomics, computational biology, immunology, etc.).
• Build new models or fine‑tune existing models to identify biological changes resulting from disease.
• Build models that achieve high accuracy and that generalize robustly to new data.
• Apply contemporary interpretability techniques to provide a deeper understanding of the underlying signal identified by the model, ideally suggesting potential biological mechanisms.
• Work closely with ML Engineering partners to ensure that Freenome’s computational infrastructure supports optimal model training and iteration.
• Take a mindful, transparent, and humane approach to your work.

Must haves:

• PhD or equivalent research experience with an AI emphasis and in a relevant, quantitative field such as Computer Science, Statistics, Mathematics, Engineering, Computational Biology, or Bioinformatics.
• 6+ years of postdoc or post‑PhD industry experience achieving impactful results using relevant modeling techniques.
• Expertise demonstrated by research publications or industry achievements, in driving independent research in applied machine learning, deep learning and complex data modeling.
• Practical and theoretical understanding of fundamental ML models such as generalized linear models, kernel machines, decision trees and forests, neural networks, boosting and model aggregation.
• Practical and theoretical understanding of DL models such as large language models or other foundation models.
• Extensive experience with training paradigms like supervised learning, self‑supervised learning, and contrastive learning.
• Proficiency in current state of the art ML/DL approaches in different domains, with an ability to envision their applications in biological data.
• Proficiency in a general‑purpose programming language: Python, R, Java, C, C++, etc.
• Proficiency in one or more ML frameworks such as Pytorch, Tensorflow and Jax, and ML platforms like Hugging Face.
• Experience in ML analysis and developer tools like TensorBoard, MLflow or Weights & Biases.
• Excellent ability to communicate across disciplines, work collaboratively, and make progress in smaller steps via experimental iterations.
• Proficiency at productive cross‑functional scientific communication and collaboration with software engineers and computational biologists.
• A passion for innovation and demonstrated initiative in tackling new areas of research.

Nice to haves:

• Deep domain‑specific experience in computational biology, genomics, proteomics or a related field.
• Experience in building DL models for genomic data, with knowledge of state‑of‑the‑art DNA foundation models.
• Experience in NGS data analysis and bioinformatic pipelines.
• Experience with containerized cloud computing environments such as Docker in GCP, Azure, or AWS.
• Experience in a production software engineering environment, including the use of automated regression testing, version control, and deployment systems.

Benefits and additional information:

The US target range of our base salary for new hires is $199,675 - $283,500. You will also be eligible to receive equity, cash bonuses, and a full range of medical, financial, and other benefits depending on the position offered. Please note that individual total compensation for this position will be determined at the Company’s sole discretion and may vary based on several factors, including but not limited to, location, skill level, years and depth of relevant experience, and education.

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.

Applicants have rights under Federal Employment Laws.