Machine Learning Engineer

Job Description

Job Description

MyOme is a clinical whole genome analysis company helping individuals and families understand their risk for disease. As a leader in polygenic and AI-based integrative risk modeling, we combine genome sequencing with AI-driven analytics and clinical data to deliver a lifetime of clinically meaningful, actionable insights, from proactive risk assessment to rare disease diagnosis. Our laboratory is CLIA-certified and CAP-accredited, and we're based in Menlo Park, California.

Our team brings together scientists, engineers, clinicians, and professionals across disciplines, united by a shared purpose: making genomic insight a routine part of everyday healthcare. We put patients first and hold ourselves to the scientific and clinical rigor that families and their clinicians depend on.

Joining MyOme means contributing your expertise to work that matters for patients and families. Whether you're advancing our science and technology, supporting the clinicians and patients we serve, or strengthening our operations, you'll help turn genomic discoveries into better care.

Position Overview:

MyOme is a CLIA-certified clinical whole-genome sequencing company building AI risk models that combine clinical data with genomics to predict disease risk years before onset. We are hiring a Machine Learning Engineer with deep expertise in machine learning and advanced deep learning model development. You will develop and improve deep learning risk models and own the path from trained model to a reliable, monitored, clinically reportable service, applying modern AI (LLM and agentic) methods where they add value. You will work directly with model developers and with clinical, regulatory, product, and engineering teams.

What You'll Do:

• Develop and improve deep learning risk models: architecture design, multimodal EHR + genomics fusion, temporal and sequence modeling of patient histories, deep survival models, representation learning, and rigorous ablation and benchmarking.
• Productionize disease risk models as versioned bundles (model weights, survival model coefficients, calibration, PRS scaling), with reproducible training and a model registry.
• Build and maintain inference services (Python, FastAPI, Docker) and integrate them with MyOme's reporting and data platforms.
• Implement calibration, recalibration to new populations, and score reporting (absolute risk over defined horizons, percentiles, risk tiers).
• Stand up deployment monitoring for calibration, discrimination, input drift, and coverage, with defined retraining triggers.
• Run and automate external validation on partner datasets in secure environments.
• Coordinate model evaluation at clinical trial sites with the hiring manager, including site data intake, harmonization, evaluation runs, and results reporting.
• Apply LLMs and agentic methods where they add measurable value, such as structured extraction from clinical notes, automated evaluation, and guardrailed explanation of results.
• Produce validation reports, model cards, and change-control documentation to support CLIA and regulatory review.

What You'll Ne ed:

• MS or PhD in computer science, statistics, biomedical informatics, bioengineering, or a related field (PhD preferred), or equivalent experience; 5+ years developing ML and deep learning models, including at least 3 years with models in production.
• Strong ML fundamentals: supervised learning, survival analysis (Cox and deep survival models), calibration, class imbalance, leakage and cohort shift, and evaluation (AUROC, C-index, calibration curves, decision curves).
• Strong advanced deep learning model development background: designing, training, and debugging modern architectures in PyTorch (transformers, sequence and temporal models, multimodal fusion, deep survival models), with a track record of models that beat strong baselines.
• Rigorous experimental practice: ablations, hyperparameter search, regularization and overfitting control, reproducibility, and honest comparison against baselines.
• Production ML engineering: packaging, APIs, containers, CI/CD, testing, model versioning, and monitoring.
• Experience building and evaluating LLM-based systems (prompting, tool use and agents, retrieval, structured extraction) with quantitative evaluation.
• Strong Python and SQL; comfortable with large tabular datasets and cloud environments (GCP or AWS).
• Clear communicator who can explain model behavior to clinicians and product partners.

Preferred / Bonus Qualifications:

• Experience with EHR data (OMOP, ICD, LOINC, RxNorm, temporal features), ideally All of Us, UK Biobank, or health-system data.
• Familiarity with polygenic risk scores or statistical genetics.
• Experience in regulated environments (CLIA, CAP, HIPAA, FDA SaMD, design controls).
• MLOps tooling (MLflow or similar, Airflow or Prefect, Kubernetes).
• Publications or shipped products in clinical ML.

Location, Compensation, and Benefits:

• Location: Hybrid, 2 to 3 days onsite at our Menlo Park, CA laboratory campus. 
• Compensation: Annual salary range of $170,000 - $200,000, commensurate with experience. This role is eligible for equity. 

San Francisco Bay Area pay range

$170,000—$200,000 USD

Benefits:

• Comprehensive healthcare coverage (Health, Dental, and Vision)
• 401K
• Professional development opportunities
• Company-sponsored off-sites and team meals during in-person meetings
• Direct access to company leadership and the opportunity for career growth

Equal Employment Opportunity and Reasonable Accommodations

MyOme is an equal opportunity employer. We make employment decisions without regard to race, color, ancestry, national origin, religion, age, sex (including pregnancy, childbirth, breastfeeding, and related medical conditions), gender, gender identity or expression, sexual orientation, marital status, physical or mental disability, medical condition, genetic information, military or veteran status, reproductive health decision-making, or any other characteristic protected by applicable law. MyOme provides reasonable accommodations to qualified applicants with disabilities and as otherwise required by law. To request an accommodation during the application or interview process, please contact View email address on ziprecruiter.com.

Why Work at MyOme?

Join us if you:

• Want to make an impact at the intersection of healthcare and technology, changing the way people engage with their health at the genetic level
• Enjoy rolling up your sleeves, taking initiative, and being empowered to lead
• Value humility, transparency, and collaborative problem-solving
• Thrive in fast-moving, dynamic environments with smart, driven teammates
• Appreciate competitive compensation, meaningful equity, and excellent benefits

Learn More: myome.com