Principal AI/Deep Learning Engineer

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.

• 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

• 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