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At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the p...

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Selected role

Principal AI/Deep Learning Engineer

Nautilus Biotechnology Seattle, WA

$224k - $337k Senior Full-time

At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome – one of the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing hard scientific problems with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines.

We’re hiring a
Principal AI/Deep Learning Engineer
to drive AI strategy and adoption across the organization. This role combines strategic leadership with hands-on contribution in software and data engineering. You will be directly collaborating with chemists, biologists, hardware engineers, bioinformaticians, marketing, finance, HR, and leadership. We’re seeking a motivated self-starter who thrives in ambiguity and is eager to build innovative solutions from the ground up. This position is a unique opportunity to impact human health by interfacing AI directly with frontier proteomics data of unprecedented resolution and scale.

Responsibilities:

Establish Nautilus Biotechnology as the premier proteomics data source for AI applications.
Lead organization-wide AI strategy, identifying high-impact use cases and driving adoption across teams.
Collaborate with data engineers to build robust infrastructure supporting AI/ML model training, deployment, and monitoring.
Establish best-practices in AI-enhanced software engineering
Integrate AI/ML solutions into production environments, ensuring reliability, scalability, and maintainability.
Work with product, bioinformatics, and software teams to add AI features to our data analysis portal, helping customers quickly extract biological insights from Nautilus data.
Ensure customers can readily interface their Nautilus data with popular AI tooling.
Marry cutting edge AI/ML approaches with our unique single-molecule, intact protein data to reveal previously inaccessible biological information.

Requirements:

PhD or Master's degree in Data Science, Artificial Intelligence, Computer Science, Statistics, Mathematics, or a related field highly desired
8+ years of experience in designing, developing, and deploying machine learning models and data science solutions
4+ years in hands-on GenAI application development
Experience developing and implementing bespoke deep-learning approaches. Biological / proteomics context preferred but not required
Demonstrated ability to translate research prototypes into robust, scalable production systems
Strong background in data engineering, including data pipelines, ETL processes, and data warehouses supporting traditional and AI-driven applications
Experience with MLOps: model deployment, monitoring, and lifecycle management in cloud or on-prem environments, debugging ML models
Experience with explainable AI and inferential machine learning models preferred
Familiarity with best practices in software engineering including code quality, testing, version control, and maintainability
Experience leading cross-functional strategy and execution
Strong problem-solver who collaborates well across disciplines
Effective communicator with both technical and non-technical audiences
Passionate about science and advancing human health

Nautilus Team Culture

We are curious go-getters: this is a team of life-long learners who aren’t afraid to tackle the big challenges, and we embrace the journey
We are detail-oriented: we do great science by working smart & with diligence where we learn from our trials and mistakes
We are easy to work with: we want our workplace to be one where everyone can share their perspective and be treated with respect and kindness

Compensation Range: $224K - $337K

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