Machine Learning Engineer

Who We Are

FL79 is a platform company built for the climate era. Our mission is to generate leaps in biological and material performance to unlock gigaton-scale climate solutions. We are in a moment in time when machine learning has the potential to exponentially augment the magnitude of human inventiveness to solve the most important challenges associated with protecting the planet. Our team is developing novel computational and experimental technologies to achieve unparalleled industrial speed, scale, and predictability for a more sustainable future. FL79 is looking for motivated, team-oriented problem-solvers who share our passion for accelerating our transition to a sustainable economy.

FL79 was founded by Flagship Pioneering in the Flagship Labs innovation foundry. Flagship Pioneering conceives, resources, and builds companies across both human health and sustainability. Flagship has created over 100 scientific ventures resulting in >$200 billion in aggregate value, 500+ issued patents, and >50 clinical trials, spanning Moderna TherapeuticsGenerate BiomedicinesIndigo AgTessera Therapeutics, and others. We harness science and entrepreneurialism to envision alternative futures, beginning with seemingly unreasonable propositions and navigating to transformational outcomes through an iterative, evolutionary methodology. We call this process “pioneering”.

Position Summary

We believe deep integration of data-driven machine learning with experimental approaches will be a core driver of the next generation of defining impact in sustainability, rooted in leveraging novel molecular modalities. We aim to upend the traditional approach to molecular discovery towards one characterized by intentionality, programmability, and speed by developing methods for molecular design and generation that can reliably generalize across functions and applications. We believe that immense impact potential in sustainability can come from diverse scientific and machine learning backgrounds – and are open to all backgrounds with computational excellence.

To this end, we are seeking a creative and motivated Machine Learning ML Engineer to build the machine learning platform required to drive protein engineering for sustainability and achieve our ambitious goals. You will work across the stack to develop, test, deploy, and maintain ML based software solutions. The successful candidate will work closely with ML Scientists, Computational Biologists, Materials Scientists, and Informatics/IT engineers to implement a scalable platform that rapidly advances our scientific programs.

Key responsibilities:

  • Design, develop and refine infrastructure for FL79’s ML platform, enabling rapid model development, training, evaluation at scale
  • Deploy and monitor cutting-edge ML models and algorithms
  • Implement large scale MLOps and data ETL pipelines in a distributed computing environment
  • Develop solutions for efficiently performing ML model experimentation and tuning
  • Establish data engineering processes and best-practices for data scientists utilizing our ML platform
  • Maintain awareness of commercial tools & innovations and champion new solutions internally


  • 2+ years experience working in a DevOps or data engineer role using cloud-based infrastructure such as AWS, GCP, or Microsoft Azure
  • Well versed in machine learning fundamentals.  Experience with deep learning frameworks is desired.
  • Proficiency in Python and strong object-oriented design skills coupled with a solid understanding of data structures and algorithms
  • Familiarity with workflow orchestration tools such as Airflow, Luigi, or Prefect is desired
  • Familiarity with Kubernetes or other container orchestration tools in a production setting
  • Demonstrated self-motivation and willingness to dive into complicated data engineering challenges
  • Ability to work in a fast-paced environment and strong technical communication skills

Flagship Pioneering and our ecosystem companies are 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: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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