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Senior Machine Learning Engineer
Freenome · Brisbane, California
Pay
$162k–227k
Setting
Hybrid
Senior Machine Learning Engineer
Remote
Apply
About this opportunity:
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.
Family & Medical Leave Act (FMLA)
Equal Employment Opportunity (EEO)
Employee Polygraph Protection Act (EPPA)
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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.
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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:
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Listed by Freenome for a position based in the United States. Employers on this board attest they are hiring domestically.
Staff Machine Learning Scientist
Freenome · Brisbane, California
Pay
$200k–284k
Setting
Hybrid
Staff Machine Learning Scientist
Remote
Apply
About this opportunity:
At Freenome, we are seeking a Staff Machine Learning Scientist to help grow the Machine Learning Science team, within the Computational Science department. The ideal candidate has a strong knowledge of artificial intelligence (AI), including machine learning (ML) fundamentals and extensive experience with deep learning (DL) methods, a track record of successfully using these methods to answer complex research questions, the ability to drive independent research and thrive in a highly cross-functional environment.
They will be responsible for the development of algorithms for early, blood-based detection tests for cancer. They will build on a foundation of ML/DL and statistical skills to develop models for identifying molecular signals from blood. They will also work with computational biologists, molecular biologists and ML engineers to design and drive research experiments, and will have a significant impact on the continued growth of an organization dedicated to changing the entire landscape of cancer.
The role reports to the Director, Machine Learning Science. This role can be a Hybrid role based in our Brisbane, California headquarters (2-3 days per week in office), or remote.
What you’ll do:
Independently pursue cutting edge research in AI applied to biological problems (including cancer research, genomics, computational biology, immunology, etc.).
Build new models or fine-tune existing models to identify biological changes resulting from disease.
Build models that achieve high accuracy and that generalize robustly to new data.
Apply contemporary interpretability techniques to provide a deeper understanding of the underlying signal identified by the model, ideally suggesting potential biological mechanisms.
Work closely with ML Engineering partners to ensure that Freenome’s computational infrastructure supports optimal model training and iteration.
Take a mindful, transparent, and humane approach to your work.
Must haves:
PhD or equivalent research experience with an AI emphasis and in a relevant, quantitative field such as Computer Science, Statistics, Mathematics, Engineering, Computational Biology, or Bioinformatics.
6+ years of postdoc or post-PhD industry experience achieving impactful results using relevant modeling techniques.
Expertise demonstrated by research publications or industry achievements, in driving independent research in applied machine learning, deep learning and complex data modeling.
Practical and theoretical understanding of fundamental ML models like generalized linear models, kernel machines, decision trees and forests, neural networks, boosting and model aggregation.
Practical and theoretical understanding of DL models like large language models or other foundation models.
Extensive experience with training paradigms like supervised learning, self-supervised learning, and contrastive learning.
Proficient in current state of the art in ML/DL approaches in different domains, with an ability to envision their applications in biological data.
Proficiency in a general-purpose programming language: Python, R, Java, C, C++, etc.
Proficiency in one or more ML frameworks such as; Pytorch, Tensorflow and Jax; and ML platforms like Hugging Face.
Experience in ML analysis and developer tools like TensorBoard, MLflow or Weights & Biases.
Excellent ability to communicate across disciplines, work collaboratively, and make progress in smaller steps via experimental iterations.
Proficient at productive cross-functional scientific communication and collaboration with software engineers and computational biologists.
A passion for innovation and demonstrated initiative in tackling new areas of research.
Nice to haves:
Deep domain-specific experience in computational biology, genomics, proteomics or a related field.
Experience in building DL models for genomic data, with knowledge of state-of-the-art DNA foundation models.
Experience in NGS data analysis and bioinformatic pipelines.
Experience with containerized cloud computing environments such as Docker in GCP, Azure, or AWS.
Experience in a production software engineering environment, including the use of automated regression testing, version control, and deployment systems.
Benefits and additional information:
The US target range of our base salary for new hires is $199,675 - $283,500. 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)
California applicants please review the CCPA Notice at Collection here:
California Consumer Privacy Act (CCPA)
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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.
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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.
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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.
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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:
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Listed by Freenome for a position based in the United States. Employers on this board attest they are hiring domestically.
Senior Software Engineer II
Freenome · Brisbane, California
Pay
$162k–227k
Setting
Remote
Senior Software Engineer II
Remote
Apply
About this opportunity:
At Freenome, we are seeking a Senior Software Engineer II to join our innovative Engineering team. The ideal candidate is an experienced backend engineer with a strong background in developing scalable and reliable software solutions. You will play a crucial role in designing, building, and maintaining backend services that support our mission to detect cancer early. This position requires a collaborative mindset, as you will work closely with an interdisciplinary team of engineers, scientists, and product managers to deliver high-quality software solutions. You are passionate about software development best practices and will have a significant impact on the continued growth of an organization dedicated to changing the entire landscape of cancer.
The role reports to our engineering management team. This role will be a Remote role.
What you’ll do:
Design, develop, and deploy reliable, maintainable, scalable, and fault-tolerant backend services that power both our internal and external systems.
Collaborate with interdisciplinary teams, including scientists, product managers, and other engineers, to solve complex problems and deliver high-quality software solutions.
Mentor and guide junior engineers, fostering their growth and enhancing the team's technical expertise.
Lead code and design reviews, champion engineering best practices and promote a culture of quality and collaboration.
Contribute to the development of data infrastructure for machine learning applications, ensuring efficient data processing and integration.
Drive the implementation of engineering hygiene practices, ensuring the reliability and maintainability of our systems.
Advocate for and implement innovative software development methodologies and tools to improve team efficiency and product quality.
Must haves:
Bachelor of Science in Computer Science, Engineering, or related field or equivalent training, fellowship, and/or work experience.
At least 8 years of experience as part of a software development team successfully shipping software products, including leading projects from end-to-end and mentoring others.
Proficiency in Python and experience with backend development in a team production environment.
Strong experience with containerization and orchestration technologies such as Docker and Kubernetes.
Familiarity with cloud platforms like AWS, Azure, or Google Cloud Platform.
Proven experience in designing and implementing scalable backend systems, with a focus on reliability and performance.
Excellent written and verbal communication skills, with a mindful and transparent approach to collaboration.
Nice to haves:
Understanding of statistical and machine learning methods, with practical experience in applying them to real-world problems.
Expertise in developing ETL or data pipelines that run at scale, utilizing common workflow management systems like Flyte, Airflow, or similar.
Domain-specific experience in computational biology, genomics, bioinformatics, or a related field.
Experience working in an FDA regulated environment, with a strong understanding of compliance requirements and best practices.
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)
California applicants please review the CCPA Notice at Collection here:
California Consumer Privacy Act (CCPA)
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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.
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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.
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OMB Control Number 1250-0005
Expires 07/31/2029
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
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Listed by Freenome for a position based in the United States. Employers on this board attest they are hiring domestically.
Senior Network Engineer
Freenome · Brisbane, California
Pay
$157k–200k
Setting
Hybrid
Senior Network Engineer
Brisbane, California
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About this opportunity:
At Freenome, we are seeking a Senior Network Engineer with experience managing enterprise and data center network infrastructure. This person will be part of the team tasked with delivering the network infrastructure for Freenome’s HQ campus. Additionally, this person will be responsible to ensure Freenome’s network infrastructure is scalable and following industry best practices. The ideal candidate will have hands-on experience with enterprise network technologies, automation tools, and a background in managing secure network solutions.
The role reports to the Director, IT. This role will be a Hybrid role.
What you’ll do:
Lead the architecture design and implementation of the network infrastructure; both on-prem and in Cloud.
Lead Zero Trust implementation and maintenance.
Work closely with engineering and laboratory teams to gather requirements, analyze, and propose infrastructure solutions.
Contribute to the delivery of a global standard network infrastructure.
Develop and maintain network documentation, including diagrams, policies, procedures, and best practices.
Troubleshoot and remediate any events impacting the operations and availability of the global network infrastructure.
Must haves:
A minimum of 5 years Network Engineering experience.
A minimum of 3 years Firewall security experience.
A minimum of 3 years experience with configuring and managing Palo Alto Network firewalls.
Juniper Networks JNCIP-ENT certification or equivalent experience.
Advanced understanding of network hardware, software, protocols, and technologies.
Experience with enterprise wireless network solutions and deployments.
Hands-on experience with SSL and IPsec VPNs.
Experience with network monitoring, management, and troubleshooting tools.
Ability to work individually, as well as in a dynamic team environment.
Strong communication and problem-solving skills.
Ability to prioritize and manage multiple tasks and projects simultaneously.
Strong documentation skills.
Nice to haves:
Experience working in Clinical Diagnostics or Pharmaceutical Manufacturing.
Expert experience with Juniper Networks products and solutions.
Expert experience with Palo Alto Network Firewalls, Prisma, and Panorama.
Experience with efficient iP SOLIDserver DDI.
Engineering networks in GCP or other cloud providers.
Benefits and additional information:
The US target range of our base salary for new hires is $156,750 - $200,025. 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)
California applicants please review the CCPA Notice at Collection here:
California Consumer Privacy Act (CCPA)
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Can you describe your approach to managing a complex, multi-site enterprise network (specifically using Juniper or similar) on a daily basis? Please highlight how you handle lifecycle management, such as firmware updates or hardware refreshes, with minimal impact on operations.*
This role requires significant hands-on experience with Palo Alto Network firewalls. Can you summarize your experience managing these in a production environment, specifically mentioning any work with Prisma, Panorama, or SSL/IPsec VPNs? *
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Listed by Freenome for a position based in the United States. Employers on this board attest they are hiring domestically.
Senior Software Engineer II
Freenome · Remote
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