Senior Machine Learning Engineer

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, optimising hardware utilisation for efficient training, and performing model optimisations.

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.

Key responsibilities include:

• Implementing and refining DL pipelines on distributed computing platforms to enhance the speed and efficiency of DL operations, including model training, data handling, model management, and inference.
• Collaborating closely with ML scientists and software engineers to understand current challenges and requirements and ensure that the DL model development pipelines created are perfectly aligned with scientific goals and operational needs.
• Continuously monitoring, evaluating, and optimising DL model training pipelines for performance and scalability.
• Staying up to date with the latest advancements in AI, ML, and related technologies, and quickly learning and adapting new tools and frameworks, if necessary.
• Developing and maintaining robust and reproducible DL pipelines that guarantee that DL pipelines can be reliably executed, maintaining consistency and accuracy of results.
• Driving performance improvements across our stack through profiling, optimisation, and benchmarking. Implementing efficient caching solutions and debugging distributed systems to accelerate both training and evaluation pipelines.
• Acting 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 include:

• 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 containerisation technologies (e.g., Docker) and computing resource orchestration tools (e.g., Kubernetes) for deploying scalable ML/AI solutions.
• Proven track record of developing and optimising 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 (such as HDFS or Parquet on S3), 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 include:

• 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.

Freenome is proud to be an equal-opportunity employer, and we value diversity. Freenome does not discriminate on the basis of race, colour, 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.