Senior Machine Learning Engineer

About this role

<p><strong>About this opportunity:</strong></p> <p><span style="font-weight: 300;">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.&nbsp;</span></p> <p><span style="font-weight: 300;">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&amp;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.&nbsp;</span></p> <p><span style="font-weight: 300;">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.<br></span></p> <p><strong>What you’ll do:</strong></p> <ul> <li style="font-weight: 300;"><span style="font-weight: 300;">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.</span></li> <li style="font-weight: 300;"><span style="font-weight: 300;">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.</span></li> <li style="font-weight: 300;"><span style="font-weight: 300;">Continuously monitor, evaluate, and optimize DL model training pipelines for performance and scalability.</span></li> <li style="font-weight: 300;"><span style="font-weight: 300;">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. </span></li> <li style="font-weight: 300;"><span style="font-weight: 300;">Develop and maintain robust and reproducible DL pipelines that guarantee that DL pipelines can be reliably executed, maintaining consistency and accuracy of results.</span></li> <li style="font-weight: 300;"><span style="font-weight: 300;">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.</span></li> <li style="font-weight: 300;"><span style="font-weight: 300;">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.<br></span></li> </ul> <p><strong>Must haves:</strong><strong><br></strong></p> <ul> <li><span style="font-weight: 300;">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.&nbsp;<br></span></li> <li><span style="font-weight: 300;">5+ years of post-MS industry experience working on developing AI/ML software engineering pipelines.<br></span></li> <li><span style="font-weight: 300;">Proficiency in a general-purpose programming language: Python (preferred), Java, Julia, C, C++, etc.<br></span></li> <li><span style="font-weight: 300;">Strong knowledge of ML and DL fundamentals and hands-on experience with machine learning frameworks such as PyTorch, TensorFlow, Jax or Scikit-learn.<br></span></li> <li><span style="font-weight: 300;">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.&nbsp;<br></span></li> <li><span style="font-weight: 300;">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.<br></span></li> <li><span style="font-weight: 300;">Understanding of containerization technologies (e.g., Docker) and computing resource orchestration tools (e.g., Kubernetes) for deploying scalable ML/AI solutions.<br></span></li> <li><span style="font-weight: 300;">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.<br></span></li> <li><span style="font-weight: 300;">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).<br></span></li> <li><span style="font-weight: 300;">Proficiency in version control systems (e.g., Git) and continuous integration/continuous deployment (CI/CD) practices to maintain code quality and automate development workflows.<br></span></li> <li><span style="font-weight: 300;">Expertise in building and launching large-scale ML frameworks in a scientific environment that supports the needs of a research team.<br></span></li> <li><span style="font-weight: 300;">Excellent ability to work effectively with cross-functional teams and communicate across disciplines.&nbsp;<br></span></li> </ul> <p><strong>Nice to haves:</strong></