Senior Machine Learning Engineer

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 (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: 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. Family & Medical Leave Act (FMLA) Equal Employment Opportunity (EEO) Employee Polygraph Protection Act (EPPA) #LI-REMOTE Create a Job Alert Interested in building your career at Freenome? Get future opportunities sent straight to your email. Create alert Apply for this job * indicates a required field Autofill with MyGreenhouse First Name* Last Name* Email* Phone Country* Phone* Location (City)* Locate me Resume/CV* AttachAttach Dropbox Google Drive Enter manuallyEnter manually Accepted file types: pdf, doc, docx, txt, rtf Cover Letter AttachAttach Dropbox Google Drive Enter manuallyEnter manually Accepted file types: pdf, doc, docx, txt, rtf * * * Have you trained large-scale deep learning models across multiple GPUs using methods like DDP in a cloud environment?* Select... Do you have hands-on experience with Jax, Pytorch and other ML frameworks?* Select... Have you worked with scalable and distributed computing platforms like Ray or DeepSpeed?* Select... Do you have experience managing large datasets, including storage (e.g., HDFS, Parquet) and efficient processing (e.g., PyArrow, Spark)? * Select... Are you fully authorized to work in the United States without need for sponsorship now or in the future?* Select... Voluntary Self-Identification For government reporting purposes, we ask candidates to respond to the below self-identification survey. Completion of the form is entirely voluntary. Whatever your decision, it will not be considered in the hiring process or thereafter. Any information that you do provide will be recorded and maintained in a confidential file. As set forth in Freenome's Equal Employment Opportunity policy, we do not discriminate on the basis of any protected group status under any applicable law. Gender Select... Are you Hispanic/Latino? Select... Race & Ethnicity Definitions If you believe you belong to any of the categories of protected veterans listed below, please indicate by making the appropriate selection. As a government contractor subject to the Vietnam Era Veterans Readjustment Assistance Act (VEVRAA), we request this information in order to measure the effectiveness of the outreach and positive recruitment efforts we undertake pursuant to VEVRAA. Classification of protected categories is as follows: A "disabled veteran" is one of the following: a veteran of the U.S. military, ground, naval or air service who is entitled to compensation (or who but for the receipt of military retired pay would be entitled to compensation) under laws administered by the Secretary of Veterans Affairs; or a person who was discharged or released from active duty because of a service-connected disability. A "recently separated veteran" means any veteran during the three-year period beginning on the date of such veteran's discharge or release from active duty in the U.S. military, ground, naval, or air service. An "active duty wartime or campaign badge veteran" means a veteran who served on active duty in the U.S. military, ground, naval or air service during a war, or in a campaign or expedition for which a campaign badge has been authorized under the laws administered by the Department of Defense. An "Armed forces service medal veteran" means a veteran who, while serving on active duty in the U.S. military, ground, naval or air service, participated in a United States military operation for which an Armed Forces service medal was awarded pursuant to Executive Order 12985. Veteran Status Select... Voluntary Self-Identification of Disability Form CC-305 Page 1 of 1 OMB Control Number 1250-0005 Expires 04/30/2026 Why are you being asked to complete this form? We are a federal contractor or subcontractor. The law requires us to provide equal employment opportunity to qualified people with disabilities. We have a goal of having at least 7% of our workers as people with disabilities. The law says we must measure our progress towards this goal. To do this, we must ask applicants and employees if they have a disability or have ever had one. People can become disabled, so we need to ask this question at least every five years. Completing this form is voluntary, and we hope that you will choose to do so. Your answer is confidential. No one who makes hiring decisions will see it. Your decision to complete the form and your answer will not harm you in any way. If you want to learn more about the law or this form, visit the U.S. Department of Labor's Office of Federal Contract Compliance Programs (OFCCP) website at www.dol.gov/ofccp. How do you know if you have a disability? A disability is a condition that substantially limits one or more of your "major life activities." If you have or have ever had such a condition, you are a person with a disability. Disabilities include, but are not limited to: Alcohol or other substance use disorder (not currently using drugs illegally) Autoimmune disorder, for example, lupus, fibromyalgia, rheumatoid arthritis, HIV/AIDS Blind or low vision Cancer (past or present) Cardiovascular or heart disease Celiac disease Cerebral palsy Deaf or serious difficulty hearing Diabetes Disfigurement, for example, disfigurement caused by burns, wounds, accidents, or congenital disorders Epilepsy or other seizure disorder Gastrointestinal disorders, for example, Crohn's Disease, irritable bowel syndrome Intellectual or developmental disability Mental health conditions, for example, depression, bipolar disorder, anxiety disorder, schizophrenia, PTSD Missing limbs or partially missing limbs Mobility impairment, benefiting from the use of a wheelchair, scooter, walker, leg brace(s) and/or other supports Nervous system condition, for example, migraine headaches, Parkinson's disease, multiple sclerosis (MS) Neurodivergence, for example, attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder, dyslexia, dyspraxia, other learning disabilities Partial or complete paralysis (any cause) Pulmonary or respiratory conditions, for example, tuberculosis, asthma, emphysema Short stature (dwarfism) Traumatic brain injury Disability Status Select... PUBLIC BURDEN STATEMENT: According to the Paperwork Reduction Act of 1995 no persons are required to respond to a collection of information unless such collection displays a valid OMB control number. This survey should take about 5 minutes to complete. Submit application Powered by Greenhouse