Senior Machine Learning Engineer

Freenome; United States; Hybrid; USD 161,000 - 227,000; Full time

Job summary

Freenome seeks a Senior Machine Learning Research Engineer to join the MLS team in the Computational Science department. You will design and deploy scalable DL pipelines for massive genomic data in a cloud environment, enabling distributed training and efficient resource use.

You will collaborate with ML scientists and software engineers to push state-of-the-art ML/AI models, optimize performance, and ensure reproducibility.

Qualifications

• MS or equivalent in a quantitative field with emphasis on AI/ML theory/practice
• 5+ years post-MS in AI/ML pipelines
• Proficiency in Python (preferred) or other languages
• Strong ML/DL fundamentals and frameworks such as PyTorch, TensorFlow, Jax, Scikit-learn
• Experience with distributed DL platforms like Ray or DeepSpeed and tools like TensorBoard, Wandb, MLflow
• Cloud experience (AWS/GCP/Azure) and deploying ML in cloud
• Docker and Kubernetes for scalable ML solutions
• Proven track record building/training DL/LLMs on large data
• Experience with large datasets and data processing (PyArrow, Spark, Parquet)
• Git and CI/CD to automate workflows
• Building large-scale ML frameworks in scientific environments
• Excellent cross-functional collaboration and communication

Responsibilities

• Implement and refine DL pipelines on distributed platforms for training, data handling, management, and inference
• Collaborate with ML scientists and software engineers to align pipelines with scientific goals
• Monitor, evaluate, and optimize training pipelines for performance and scalability
• Stay updated with AI/ML advancements and adopt new tools when needed
• Develop and maintain robust, reproducible DL pipelines with consistent results
• Drive performance improvements via profiling, optimization, and caching
• Bridge engineering and science teams, sharing best practices

Skills

Python

ML fundamentals

DL fundamentals

PyTorch

TensorFlow

Jax

Scikit-learn

Ray

DeepSpeed

TensorBoard

Wandb

MLflow

Cloud platforms

Docker

Kubernetes

Git

CI/CD

Spark

PyArrow

HDFS/Parquet

LLMs

Distributed DL pipelines

Education

MS or equivalent

Tools

AWS

Google Cloud

Azure

Docker

Kubernetes

Ray/DeepSpeed

TensorBoard

Wandb

MLflow

PyArrow

Spark

Git

Job description

At Freenome, we are seeking a Senior Machine Learning Research Engineer to join the Machine Learning Science (MLS) team, within the Computational Science department. The ideal candidate has a strong knowledge in designing and building deep learning (DL) pipelines, and expertise in creating reliable, scalable artificial intelligence/machine learning (AI/ML) systems in a cloud environment.

The MLS team at Freenome develops DL models using massive-scale genomic data that presents significant challenges for current training paradigms. The Senior Machine Learning Research Engineer will primarily be responsible for developing and deploying the infrastructure needed to support development of such DL models: enabling distributed DL pipelines, optimizing hardware utilization for efficient training, and performing model optimizations. As part of an interdisciplinary R&D team, they will work in close collaboration with machine learning scientists, computational biologists and software engineers to accelerate the development of state-of-the‑art ML/AI models and help Freenome achieve its mission of reducing cancer mortality via accessible early detection.

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

What you’ll do:

• Implement and refine DL pipelines on distributed computing platforms enhancing the speed and efficiency of DL operations including model training, data handling, model management, and inference.
• Collaborate closely with ML scientists and software engineers to understand current challenges and requirements and ensure that the DL model development pipelines you create are perfectly aligned with scientific goals and operational needs.
• Continuously monitor, evaluate, and optimize DL model training pipelines for performance and scalability.
• Stay up to date with the latest advancements in AI, ML, and related technologies, and quickly learn and adapt new tools and frameworks, if necessary.
• Develop and maintain robust and reproducible DL pipelines that guarantee that DL pipelines can be reliably executed, maintaining consistency and accuracy of results.
• Drive performance improvements across our stack through profiling, optimization, and benchmarking. Implement efficient caching solutions and debug distributed systems to accelerate both training and evaluation pipelines.
• Act as a bridge facilitating communication between the engineering and scientific teams, documenting and sharing best practices to foster a culture of learning and continuous improvement.

Must haves:

• MS or equivalent experience in a relevant, quantitative field such as Computer Science, Statistics, Mathematics, Software Engineering, with an emphasis on AI/ML theory and/or practical development.
• 5+ years of post-MS industry experience working on developing AI/ML software engineering pipelines.
• Proficiency in a general-purpose programming language: Python (preferred), Java, Julia, C, C++, etc.
• Strong knowledge of ML and DL fundamentals and hands‑on experience with machine learning frameworks such as PyTorch, TensorFlow, Jax or Scikit‑learn.
• In‑depth knowledge of scalable and distributed computing platforms that support complex model training (such as Ray or DeepSpeed) and their integration with ML developer tools like TensorBoard, Wandb, or MLflow.
• Experience with cloud platforms (e.g., AWS, Google Cloud, Azure) and how to deploy and manage AI/ML models and pipelines in a cloud environment.
• Understanding of containerization technologies (e.g., Docker) and computing resource orchestration tools (e.g., Kubernetes) for deploying scalable ML/AI solutions.
• Proven track record of developing and optimizing workflows for training DL models, large language models (LLMs), or similar for problems with high data complexity and volume.
• Experience managing large datasets, including data storage (eg: HDFS or Parquet on object storage), retrieval, and efficient data processing techniques (via libraries and executors such as PyArrow and Spark).
• Proficiency in version control systems (e.g., Git) and continuous integration/continuous deployment (CI/CD) practices to maintain code quality and automate development workflows.
• Expertise in building and launching large-scale ML frameworks in a scientific environment that supports the needs of a research team.
• Excellent ability to work effectively with cross‑functional teams and communicate across disciplines.

Nice to haves:

• Experience working with large-scale genomics or biological datasets.
• Experience managing multimodal datasets, such as combinations of sequence, text, image, and other data.
• Experience GPU/Accelerator programming and kernel development (such as CUDA, Triton or XLA).
• Experience with infrastructure-as-code and configuration management.
• Experience cultivating MLOps and ML infrastructure best practices, especially around reliability, provisioning and monitoring.
• Strong track record of contributions to relevant DL projects, e.g. on github.

Benefits and additional information:

The US target range of our base salary for new hires is $161,925 - $227,325 . 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. We invite you to check out our career page @ freenome.com/job-openings/ for additional company information.

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.