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Agent guide: [/agents.md](https://www.wearedevelopers.com/agents.md). --- # Machine Learning Research Engineer - **Company:** Freenome - **Location:** Brisbane, CA, United States (Remote available) - **Experience:** Expert - **Salary:** $162,000.0 - $227,000.0 - **Contract:** Permanent contract - **Skills:** Java (Programming Language), Artificial Intelligence, Amazon Web Services, Microsoft Azure, Big Data, Bioinformatics, C++ (Programming Language), Cloud Computing, Configuration Management, Software Quality, Nvidia CUDA, Computer Programming, Continuous Delivery, Continuous Integration, Software Debugging, Programming Tools, Distributed Systems, Github, Hadoop Distributed File System, Linux Kernel, Machine Learning, Tensorflow, Software Engineering, Parquet, Data Processing, Google Cloud, Data Storage Technologies, Pytorch, Large Language Models, Apache Spark, Git, Containerization, Scikit Learn, Kubernetes, Information Technology, Machine Learning Operations, Software Version Control, Docker - **Published:** August 11, 2026 - **Apply:** https://job-boards.greenhouse.io/freenome/jobs/8535248002 ## About the Role 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., * 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., 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. ## Description 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. ## Related Videos - [Geometric deep learning for drug discovery](https://www.wearedevelopers.com/videos/264-geometric-deep-learning-for-drug-discovery) - [Innovating Developer Tools with AI: Insights from GitHub Next](https://www.wearedevelopers.com/videos/1268-innovating-developer-tools-with-ai-insights-from-github-next) - [Docker Compose: Rediscovered](https://www.wearedevelopers.com/videos/1978-docker-compose-rediscovered) - [How a Small Team Shrank a Microsoft Monorepo by 94%](https://www.wearedevelopers.com/videos/1236-how-a-small-team-shrank-a-microsoft-monorepo-by-94) - [Introduction to Azure Machine Learning](https://www.wearedevelopers.com/videos/368-introduction-to-azure-machine-learning) - [Bringing AI Model Testing and Prompt Management to Your Codebase with GitHub Models](https://www.wearedevelopers.com/videos/1536-bringing-ai-model-testing-and-prompt-management-to-your-codebase-with-github-models) ## Related Articles - [Highest Paying Tech Companies for Developers](https://www.wearedevelopers.com/magazine/220-highest-paying-tech-companies-for-developers) - [What Are Large Language Models?](https://www.wearedevelopers.com/magazine/304-what-are-large-language-models) - [How to Become an AI Engineer](https://www.wearedevelopers.com/magazine/331-how-to-become-an-ai-engineer) - [How Much Does a Software Engineer Make? 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