What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability?

FL94 Inc., is a privately held, early-stage biotechnology company pioneering the new field of Protein Editing. At FL94 we create small molecules that edit protein structure and function to unlock presently undruggable targets and a broad array of therapeutic modalities.

Our platform integrates novel small molecule chemistry and chemo-proteomic discovery with Machine Learning (ML) to enable generative design. FL94 is backed by Flagship Pioneering, bringing their courage, vision, and resources to guide FL94 from platform validation to patient impact. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us! 

As a Machine Learning Engineer you will lead efforts to efficiently train massive generative models across multiple GPUs and build a world-class infrastructure that enables robust data flow between our experimental and computational platforms.

Working closely with ML scientists, biologists, and chemists you will not only lead the development of this infrastructure, you will also help identify new areas across *any* function where ML-driven automation and workflow will impact high-quality discovery.

The ideal candidate sees building robust integrated hardware/software systems for training and deploying ML models in biology as equally valuable to experimental breakthroughs and ML-focused algorithmic development.

Responsibilities include:

  • Building scalable machine learning pipelines, including efficient parallelization and use of GPUs.
  • Designing and coding data processing pipelines, ownership of company-wide data platform.
  • Working closely with Platform Development and Biology teams to automate a tight design-build-test cycle for ML generated small molecules.
  • Working in a collaborative CI/CD software development environment, including use of git, participating in code reviews, and independent development of robust code.
  • Working within an entrepreneurial, collaborative, and interdisciplinary team to actively contribute to creating, shaping, and executing the vision of the company


  • Undergraduate or Master's degree in bioinformatics, computer science, mathematics, physics or related field and 4+ years of experience is required
  • Experience with MLOps practices and tools including version control, automated testing, and CI/CD
  • Proficient in Python and experience in using deep learning libraries (i.e. PyTorch)
  • Experience with cloud computing (i.e. AWS), database scale-out (e.g. distributed postgresql), and data pipelining tools (i.e. Nextflow, Airflow)
  • Experience with Slurm or other on-site HPC cluster solutions
  • Nice-to-have, but not critical, is experience with computational chemistry or protein structure platforms and collaborative tools.

About Flagship

Flagship Pioneering is a biotechnology company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com

 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.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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 there to.*

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