Machine Learning Engineer - Computational Drug Discovery

5AM Ventures•Watertown, MA

2d•Onsite

About The Position

Our team is dedicated to the development of a broad pipeline of small molecules powered by unique chemistry insights to address a wide range of highly unmet clinical needs. Our company was created within 5AM Ventures' 4:59 Initiative in 2023. The computational team has roots from D. E. Shaw Research, one of the most rigorous computational science environments in the world. You will work directly with and learn from scientists who have operated at the frontier of computational drug discovery. This role sits at the intersection of machine learning research and the experimental teams that rely on computational tools to drive scientific decisions. Your primary responsibility will be ensuring that cutting-edge models move from research into production—reliably, maintainably, and in forms that scientists can effectively use. For the right candidate, this is an unusually high-impact position. The systems you build will directly influence molecule triage, experimental prioritization, and the pace of scientific discovery. At many organizations, engineers are several layers removed from scientific decision-making. At our team, that distance is effectively zero. We value ownership, initiative, and execution. Strong performers will have opportunities to grow into areas such as machine learning research, cheminformatics, AI-driven drug discovery, or agent development. The exact trajectory is flexible and can be shaped around individual strengths and interests.

Requirements

Bachelor’s or Master’s degree in Computer Science, Chemistry, Physics, Data Science, or a related technical field
Strong software engineering fundamentals, including code quality, testing, version control, and CI/CD practices
Hands-on experience developing machine learning systems using PyTorch
Familiarity with undergraduate-level organic chemistry; you do not need to be a chemist, but should be comfortable working with molecular structures and chemical concepts
Ability to communicate effectively with scientific collaborators from non-programming backgrounds
Strong sense of ownership and the ability to independently drive ambiguous projects from concept to completion
We are particularly excited to bring in people who enjoy turning research ideas into tools that scientists actually use. The ideal candidate is comfortable operating across disciplines, takes pride in building reliable systems, and appreciates the opportunity to have a direct impact on scientific decision-making.

Nice To Haves

Experience with AWS, MLflow, SQL, Polars, pandas, Ray, or scikit-learn
Familiarity with LLM tooling, AI agents, or agent development frameworks
Background in cheminformatics, computational biology, bioinformatics, or related fields
Experience working in a startup, research, or other highly iterative technical environment

Responsibilities

Own and maintain production machine learning infrastructure, ensuring models developed by the research team are robust, maintainable, and deployable
Develop computational tools, data pipelines, and machine learning systems that support scientific workflows across chemistry and biology
Collaborate closely with chemists and biologists to understand requirements and translate them into effective software solutions
Design and build internal AI agents and automation systems, with substantial opportunity to define both the technical direction and user experience
Write clean, well-tested, version-controlled code and contribute to a strong engineering culture through code review and technical collaboration

Benefits

Competitive compensation
Meaningful equity
Comprehensive health benefits
Generous time off
Professional development opportunities
Flexibility to do your best work
Bonus target
Medical/Dental insurance with the company covering 90% of your premiums
Fully-funded HSA to cover your deductible responsibility
100% Company-paid life insurance regardless if electing benefits
Free parking on-site
Unaccrued vacation time, with the expectation for employees to take at least 3 weeks annually
401k program, employee funded
Weekly catered team lunch
On-site fitness center with free classes and amenities