Generate Biomedicines – Senior Software Engineer I, ML Ops

Official Role Description: Generate Biomedicines

About Generate:Biomedicines

Generate:Biomedicines is a new kind of therapeutics company – existing at the intersection of machine learning, biological engineering, and medicine – pioneering Generative Biology™ to create breakthrough medicines where novel therapeutics are computationally generated, instead of being discovered. The Company has built a machine learning-powered biomedicines platform with the potential to generate new drugs across a wide range of biologic modalities. This platform represents a potentially fundamental shift in what is possible in the field of biotherapeutic development.

We pursue this audacious vision because we believe in the unique and revolutionary power of generative biology to radically transform the lives of billions, with an outsized opportunity for patients in need. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Generate:Biomedicines was founded in 2018 by Flagship Pioneering and has received nearly $700 million in funding, providing the resources to rapidly scale the organization. The Company has offices in Somerville and Andover, Massachusetts with 300+ employees.

The Role:

We are seeking an experienced and pragmatic Senior Software Engineer to build and evolve the platform that powers machine learning at Generate. You will develop reliable, scalable, and observable systems that enable efficient model training, evaluation, and deployment for protein design. You will work closely with ML researchers, data scientists, and infrastructure engineers to translate research workflows into production-grade systems. This role requires 3 or more days/week onsite in our Somerville, MA location.

Here’s how you will contribute:

• Build, maintain, and scale distributed ETL pipelines to integrate proprietary and public datasets into ML model training
• Design and deliver core services for model training, evaluation, and deployment across the ML platform.
• Collaborate with scientists, engineers, and product managers to define requirements and drive system improvements.
• Ensure reproducibility, observability, and cost efficiency across ML workflows.
• Contribute to the next generation of AI driven workflow orchestration, enabling researchers to run and evaluate models autonomously.
• Implement and evolve APIs and microservices with the cloud engineering team using AWS services and infrastructure as code to automate and standardize workflows.

The Ideal Candidate will have:

• 5 or more years of experience in software engineering, ideally building infrastructure or data systems for ML workloads.
• Practical experience designing, monitoring, and optimizing data pipelines and relational databases such as PostgreSQL or Redshift.
• Strong proficiency in Python and solid understanding of software design principles and patterns.
• Experience with distributed systems and containerized deployments on AWS using Docker, ECS, or Kubernetes.
• Familiarity with CI/CD, observability, and infrastructure as code tools. 

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Generate:Biomedicines is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies: Generate:Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate:Biomedicines or its employees is strictly prohibited unless contacted directly by the Company’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate:Biomedicines and the Company will not owe any referral or other fees with respect thereto.