Sr. Machine Learning Engineer - Machine Learning

The Role

Sr. Machine Learning Engineer . A research-minded machine learning engineer who thrives at the intersection of cutting-edge AI, scientific research, and rigorous engineering. This role is for someone excited to build and scale the models, infrastructure, and AI tools that accelerate the company’s work at the frontier of AI-driven genetic medicine.

Job Type: Full Time

Location: Watertown, MA; Remote

How You Will Contribute

As a Sr. Machine Learning Engineer ,  you will build and scale the ML infrastructure, tools, and workflows that power the company’s research efforts. You will partner closely with AI scientists, protein engineers, and fellow ML engineers to turn novel research into robust, reusable systems—improving model training and inference, optimizing performance, and advancing agentic AI workflows that accelerate scientific discovery.

At the company, every role is mission-driven. Whether in science, engineering, operations, or business, each AAViator contributes to solving some of the most complex challenges in genetic medicine.

Responsibilities

• Build modular, generalizable, and portable ML training systems that support the ongoing development of protein design models.

• Improve the scalability, reliability, and performance of ML training and inference infrastructure to enable rapid research experimentation.

• Optimize model performance using tools such as GPU profiling, custom kernels, and modern accelerated computing frameworks.

• Develop and standardize agentic AI workflows that increase research velocity while maintaining appropriate safety and reliability.

• Partner closely with AI scientists, protein engineers, and other ML engineers to translate research prototypes into robust, reusable tools and systems.

• Contribute across the ML engineering stack, from modeling and GPU-level optimization to distributed training and multi-node orchestration.

• Stay current on emerging ML engineering and agentic AI tools and help the team evaluate and adopt approaches that advance the company’s research.

• Support the delivery and communication of the company’s work, both internally and externally.

• Work with urgency and adaptability, balancing innovation with execution.

• Collaborate cross-functionally, leveraging the company’s high-trust, high-impact culture to drive results.

Basic qualifications

• 5+ years professional experience building software for machine learning

• Strong software engineering fundamentals (OO design, testing, version control, dependency management, API design)

• Experience containerizing code for remote environments including hands-on experience with Docker and Kubernetes.

• Experience with large-scale distributed training or inference with Ray or a similar framework

• Familiarity with ML performance engineering (identifying bottlenecks, analyzing resource usage, profiling, writing custom kernels)

• Experience designing and owning technically complex systems through requirements-setting, implementation, rollout and maintenance

• Ability to contribute to technical direction through design reviews, cross-team planning, documentation, etc.

• Alignment with the company’s core values - We seek individuals who step up when things get tough, recalibrate when priorities shift, and thrive in a high-expectation environment.

• A proactive, problem-solving mindset - you don’t just identify challenges; you find solutions.

Preferred qualifications

• Professional or academic experience in ML research / scientific computing

• Experience building internal platforms and/or developer tools

• Familiarity with common MLOps tools and practices (model monitoring, model versioning, CI/CD, model registries)

• Experience with GPU programming (CUDA, Triton, etc).

• Highly proficient in agentic and usage of modern AI tools for software development

• Exposure to biology, bioinformatics, structural biology, or protein modeling

The Company

At the company, we are a high-energy, high-impact team on a mission to build high-performance genetic technologies that transform patient lives. Our team unites world-class molecular biologists, protein engineers, software developers, data scientists, and machine learning experts—all working together at the intersection of AI and genetic medicine.

Our culture is defined by three core values that guide everything we do:

• One Mission: Everything we do is for the mission. We are a cohesive and motivated team, thinking ahead and supporting one another to overcome challenges.

• Proactive Responsibility: We take action, inject energy into our work, and hold ourselves accountable for delivering results.

• Reaching for Excellence: We constantly strive for excellence, fueled by curiosity, adaptability, and the courage to speak hard truths in pursuit of success.

These values are more than words—they drive our actions and decisions. Our greatest strength isn’t technology—it’s our work ethic. More than just technologists, we’re a team of relentlessly resourceful problem-solvers: with an unshakable drive we generate breakthroughs at the intersection of AI and genetic medicine.

🚀 What You’ll Give

• Bring an unstoppable work ethic, stepping up when things get tough and adapting as priorities shift.

• Embrace challenges as opportunities, finding solutions where none exist and driving innovation forward.

• Operate with urgency, responsibility, and resilience, because this mission demands the best from us.

🎯 What You’ll Get

• Competitive compensation & equity—your contributions drive results, and we pay accordingly.

• Mission-aligned, high-trust environment—we succeed together, supporting each other through challenges.

• A career-defining experience—work at the forefront of AI-driven genetic medicine, tackling problems that reshape healthcare.

If you’re ready to push boundaries, build the future, and thrive in a fast-moving, high-impact environment—we’d love to hear from you.

At the company, we believe in transparent and equitable compensation practices.

Base Salary Range: $178,662.29 – $213,680.10/year

This reflects the typical offer range for this role, based on experience, role scope, and internal equity. Final compensation decisions are made using a consistent leveling framework and consider the candidate’s experience, interview performance, and expected impact.

This role is eligible for

• Annual performance-based bonus

• Stock options

• Comprehensive medical, dental, and vision coverage

• 401(k) plan

• Flexible paid time off and holidays

• Perks including on-campus gym membership, onsite lunch, commuter support, and company provided laptop

Our compensation ranges are reviewed annually to ensure alignment with market trends and internal equity.

Equal Employment Opportunity (EEO) Statement

We are an equal opportunity employer and value diversity at our company. We do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status.

Fraud Alert: Please be aware of recruitment scams targeting job seekers. The company will never make an offer of employment without conducting a formal interview process, nor will we ask for personal information such as financial details over email. Official communication will only come from an [link for members] email address. If you are contacted by someone claiming to represent the company from any other domain, please report it as spam and report the communication to us at [link for members]